Biodiv Sci ›› 2022, Vol. 30 ›› Issue (10): 22441. DOI: 10.17520/biods.2022441
Special Issue: 传粉生物学; 物种形成与系统进化; 昆虫多样性与生态功能
• Reviews • Previous Articles Next Articles
Shanlin Liu, Na Qiu, Shuyi Zhang, Zhunan Zhao, Xin Zhou()
Received:
2022-08-01
Accepted:
2022-10-19
Online:
2022-10-20
Published:
2022-11-01
Contact:
Xin Zhou
Shanlin Liu, Na Qiu, Shuyi Zhang, Zhunan Zhao, Xin Zhou. Application of genomics technology in biodiversity conservation research[J]. Biodiv Sci, 2022, 30(10): 22441.
[1] |
Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
DOI URL |
[2] |
Armstrong KF, Ball SL (2005) DNA barcodes for biosecurity: Invasive species identification. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1813-1823.
DOI URL |
[3] |
Audano PA, Sulovari A, Graves-Lindsay TA, Cantsilieris S, Sorensen M, Welch AE, Dougherty ML, Nelson BJ, Shah A, Dutcher SK, Warren WC, Magrini V, McGrath SD, Li YI, Wilson RK, Eichler EE (2019) Characterizing the major structural variant alleles of the human genome. Cell, 176, 663-675.
DOI PMID |
[4] |
Baird DJ, Hajibabaei M (2012) Biomonitoring 2.0: A new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Molecular Ecology, 21, 2039-2044.
PMID |
[5] |
Berry TE, Osterrieder SK, Murray DC, Coghlan ML, Richardson AJ, Grealy AK, Stat M, Bejder L, Bunce M (2017) DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian Sea lion (Neophoca cinerea). Ecology and Evolution, 7, 5435-5453.
DOI PMID |
[6] |
Biggs J, Ewald N, Valentini A, Gaboriaud C, Dejean T, Griffiths RA, Foster J, Wilkinson JW, Arnell A, Brotherton P, Williams P, Dunn F (2015) Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus). Biological Conservation, 183, 19-28.
DOI URL |
[7] |
Bohmann K, Evans A, Gilbert MTP, Carvalho GR, Creer S, Knapp M, Yu DW,de Bruyn M (2014) Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution, 29, 358-367.
DOI URL |
[8] |
Bonasio R, Zhang G, Ye C, Mutti NS, Fang X, Qin N, Donahue G, Yang P, Li Q, Li C, Zhang P, Huang Z, Berger SL, Reinberg D, Wang J, Wang J, Liebig J (2010) Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator. Science, 329, 1068-1071.
DOI URL |
[9] |
Boyer S, Wratten SD, Holyoake A, Abdelkrim J, Cruickshank RH (2013) Using next-generation sequencing to analyse the diet of a highly endangered land snail (Powelliphanta augusta) feeding on endemic earthworms. PLoS ONE, 8, e75962.
DOI URL |
[10] |
Bruni I, Galimberti A, Caridi L, Scaccabarozzi D, de Mattia F, Casiraghi M, Labra M (2015) A DNA barcoding approach to identify plant species in multiflower honey. Food Chemistry, 170, 308-315.
DOI PMID |
[11] |
C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science, 282, 2012-2018.
DOI URL |
[12] |
Calvignac-Spencer S, Merkel K, Kutzner N, Kühl H, Boesch C, Kappeler PM, Metzger S, Schubert G, Leendertz FH (2013) Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity. Molecular Ecology, 22, 915-924.
DOI PMID |
[13] | Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences, USA, 108, 4516-4522. |
[14] |
Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, Fotakis AK, Lyon D, Moreno- Mayar JV, Bukhsianidze M, Rakownikow Jersie- Christensen R, Mackie M, Ginolhac A, Ferring R, Tappen M, Palkopoulou E, Dickinson MR, Stafford TW Jr, Chan YL, Götherström A, Nathan SKSS, Heintzman PD, Kapp JD, Kirillova I, Moodley Y, Agusti J, Kahlke RD, Kiladze G, Martínez-Navarro B, Liu SL, Sandoval Velasco M, Sinding MHS, Kelstrup CD, Allentoft ME, Orlando L, Penkman K, Shapiro B, Rook L, Dalén L, Gilbert MTP, Olsen JV, Lordkipanidze D, Willerslev E (2019) Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature, 574, 103-107.
DOI URL |
[15] |
Chang H, Guo JL, Fu XW, Liu YQ, Wyckhuys KAG, Hou YM, Wu KM (2018) Molecular-assisted pollen grain analysis reveals spatiotemporal origin of long-distance migrants of a noctuid moth. International Journal of Molecular Sciences, 19, 567.
DOI URL |
[16] |
Chiara B, Francesco C, Fulvio B, Paola M, Annalisa G, Stefania S, Luigi AP, Simone P (2021) Exploring the botanical composition of polyfloral and monofloral honeys through DNA metabarcoding. Food Control, 128, 108175.
DOI URL |
[17] |
Clare EL, Economou CK, Bennett FJ, Dyer CE, Adams K, McRobie B, Drinkwater R, Littlefair JE (2022) Measuring biodiversity from DNA in the air. Current Biology, 32, 693-700.
DOI URL |
[18] |
Cruaud P, Rasplus JY, Rodriguez LJ, Cruaud A (2017) High throughput sequencing of multiple amplicons for barcoding and integrative taxonomy. Scientific Reports, 7, 41948.
DOI URL |
[19] |
Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière- Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N, Pfrender ME, Bernatchez L (2017) Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology, 26, 5872-5895.
DOI PMID |
[20] |
Deiner K, Fronhofer EA, Mächler E, Walser JC, Altermatt F (2016) Environmental DNA reveals that rivers are conveyer belts of biodiversity information. Nature Communications, 7, 12544.
DOI PMID |
[21] |
Dejean T, Valentini A, Miquel C, Taberlet P, Bellemain E, Miaud C (2012) Improved detection of an alien invasive species through environmental DNA barcoding: The example of the American bullfrog Lithobates catesbeianus. Journal of Applied Ecology, 49, 953-959.
DOI URL |
[22] |
DeSalle R, Goldstein P (2019) Review and interpretation of trends in DNA barcoding. Frontiers in Ecology and Evolution, 7, 302.
DOI URL |
[23] | Dierckxsens N, Mardulyn P, Smits G (2016) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, 45, e18. |
[24] |
Drinkwater R, Williamson J, Clare EL, Chung AYC, Rossiter SJ, Slade E (2021) Dung beetles as samplers of mammals in Malaysian Borneo—A test of high throughput metabarcoding of iDNA. PeerJ, 9, e11897.
DOI URL |
[25] |
Driscoll CA, Menotti-Raymond M, Roca AL, Hupe K, Johnson WE, Geffen E, Harley EH, Delibes M, Pontier D, Kitchener AC, Yamaguchi N, MacDonald DW (2007) The Near Eastern origin of cat domestication. Science, 317, 519-523.
PMID |
[26] |
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong XX, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma CC, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen GE, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S (2009) Real-time DNA sequencing from single polymerase molecules. Science, 323, 133-138.
DOI PMID |
[27] |
Feng SH, Fang Q, Barnett R, Li C, Han S, Kuhlwilm M, Zhou L, Pan HL, Deng Y, Chen GJ, Gamauf A, Woog F, Prys-Jones R, Marques-Bonet T, Gilbert MTP, Zhang GJ (2019) The genomic footprints of the fall and recovery of the crested Ibis. Current Biology, 29, 340-349.
DOI URL |
[28] |
Fontsere C, Kuhlwilm M, Morcillo-Suarez C, Alvarez-Estape M, Lester JD, Gratton P, Schmidt JM, Dieguez P, Aebischer T, Álvarez-Varona P, Agbor A, Angedakin S, Assumang AK, Ayimisin EA, Bailey E, Barubiyo D, Bessone M, Carretero-Alonso A, Marques-Bonet T (2022) Population dynamics and genetic connectivity in recent chimpanzee history. Cell Genomics, 2, 100133.
DOI URL |
[29] |
Gao L, Gonda I, Sun H, Ma Q, Bao K, Tieman DM, Burzynski Chang EA, Fish TL, Stromberg KA, Sacks GL, Thannhauser TW, Foolad MR, Diez MJ, Blanca J, Canizares J, Xu Y, van der Knaap E, Huang S, Klee HJ, Giovannoni JJ, Fei Z (2019) The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics, 51, 1044-1051.
DOI PMID |
[30] |
Goldberg CS, Sepulveda A, Ray A, Baumgardt J, Waits LP (2013) Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum). Freshwater Science, 32, 792-800.
DOI URL |
[31] | González Fortes G, Paijmans JLA (2019) Ancient DNA: Methods and Protocols. Springer, New York. |
[32] | Gui FR, Lan TM, Zhao Y, Guo W, Dong Y, Fang DM, Liu H, Li HM, Wang HL, Hao RS, Cheng XF, Li YH, Yang PC, Sahu SK, Chen YP, Cheng L, He SQ, Liu P, Fan GY, Lu HR, Hu GH, Dong W, Chen B, Jiang Y, Zhang YW, Xu HH, Lin F, Slippers B, Postma A, Jackson M, Abate BA, Tesfaye K, Demie AL, Bayeleygne MD, Degefu DT, Chen F, Kuria PK, Kinyua ZM, Liu TX, Yang HM, Huang FN, Liu X, Sheng J, Kang L (2022) Genomic and transcriptomic analysis unveils population evolution and development of pesticide resistance in fall armyworm Spodoptera frugiperda. Protein & Cell, 13, 513-531. |
[33] |
Hahn C, Bachmann L, Chevreux B (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—A baiting and iterative mapping approach. Nucleic Acids Research, 41, e129.
DOI URL |
[34] |
Hajibabaei M, Baird DJ, Fahner NA, Beiko R, Golding GB (2016) A new way to contemplate Darwin’s tangled bank: How DNA barcodes are reconnecting biodiversity science and biomonitoring. Philosophical Transactions of the Royal Society B: Biological Sciences, 371, 20150330.
DOI URL |
[35] |
Hajibabaei M, Shokralla S, Zhou X, Singer GAC, Baird DJ (2011) Environmental barcoding: A next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE, 6, e17497.
DOI URL |
[36] |
Hänfling B, Lawson Handley L, Read DS, Hahn C, Li JL, Nichols P, Blackman RC, Oliver A, Winfield IJ (2016) Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Molecular Ecology, 25, 3101-3119.
DOI PMID |
[37] |
Havmøller RW, Jacobsen NS, Havmøller LW, Rovero F, Scharff N, Bohmann K (2021) DNA metabarcoding reveals that African leopard diet varies between habitats. African Journal of Ecology, 59, 37-50.
DOI URL |
[38] |
Hebert PDN, Braukmann TWA, Prosser SWJ, Ratnasingham S, DeWaard JR, Ivanova NV, Janzen DH, Hallwachs W, Naik S, Sones JE, Zakharov EV (2018) A Sequel to Sanger: Amplicon sequencing that scales. BMC Genomics, 19, 219.
DOI PMID |
[39] | Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270, 313-321. |
[40] |
Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS (2010) The genome of the Western clawed frog Xenopus tropicalis. Science, 328, 633-636.
DOI PMID |
[41] |
Hering D, Borja A, Jones JI, Pont D, Boets P, Bouchez A, Bruce K, Drakare S, Hänfling B, Kahlert M, Leese F, Meissner K, Mergen P, Reyjol Y, Segurado P, Vogler A, Kelly M (2018) Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive. Water Research, 138, 192-205.
DOI PMID |
[42] |
Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC (1984) DNA sequences from the quagga, an extinct member of the horse family. Nature, 312, 282-284.
DOI URL |
[43] |
Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MAM, Delany ME, Dodgson JB, Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang SP, Romanov MN, Rondelli CM, Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RPM, Aerts J, van der Poel JJ, Ellegren H, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MDR, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WRA, Rogers J, Buerstedde JM, Wilson SA, Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kaufman J, Salomonsen J, Skjoedt K, Wong GKS, Wang J, Liu B, Wang J, Yu J, Yang HM, Nefedov M, Koriabine M, DeJong PJ, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, Eswara P, King DC, Yang S, Tyekucheva S, Radakrishnan A, Harris RS, Chiaromonte F, Taylor J, He JB, Rijnkels M, Griffiths-Jones S, Ureta-Vidal A, Hoffman MM, Severin J, Searle SMJ, Law AS, Speed D, Waddington D, Cheng Z, Tuzun E, Eichler E, Bao ZR, Flicek P, Shteynberg DD, Brent MR, Bye JM, Huckle EJ, Chatterji S, Dewey C, Pachter L, Kouranov A, Mourelatos Z, Hatzigeorgiou AG, Paterson AH, Ivarie R, Brandstrom M, Axelsson E, Backstrom N, Berlin S, Webster MT, Pourquie O, Reymond A, Ucla C, Antonarakis SE, Long MY, Emerson JJ, Betrán E, Dupanloup I, Kaessmann H, Hinrichs AS, Bejerano G, Furey TS, Harte RA, Raney B, Siepel A, Kent WJ, Haussler D, Eyras E, Castelo R, Abril JF, Castellano S, Camara F, Parra G, Guigo R, Bourque G, Tesler G, Pevzner PA, Smit A, Fulton LA, Mardis ER, Wilson RK (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695-716.
DOI URL |
[44] | Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, van der Bank M, Chase MW, Cowan RS, Erickson DL, Fazekas AJ, Graham SW, James KE, Kim KJ, Kress WJ, Schneider H, Van Alphenstahl J, Barrett SCH, Van Den Berg C, Bogarin D, Burgess KS, Cameron KM, Carine M, Chacón J, Clarkson JJ, Conrad F, Devey DS, Ford CS, Hedderson TAJ, Hollingsworth ML, Husband BC, Kelly LJ, Kesanakurti PR, Kim JS, Kim YD, Lahaye R, Lee HL, Long DG, Madriñán S, Maurin O, Meusnier I, Newmaster SG, Park CW, Percy DM, Petersen G, Richardson JE, Salazar GA, Savolainen V, Seberg O, Wilkinson MJ, Yi DK, Little DP (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences, USA, 106, 12794-12797. |
[45] |
Hopken MW, Reyes-Torres LJ, Scavo N, Piaggio AJ, Abdo Z, Taylor D, Pierce J, Yee DA (2021) Temporal and spatial blood feeding patterns of urban mosquitoes in the San Juan metropolitan area, Puerto Rico. Insects, 12, 129.
DOI URL |
[46] | Hotaling S, Kelley JL, Frandsen PB (2021) Toward a genome sequence for every animal: Where are we now? Proceedings of the National Academy of Sciences, USA, 118, e2109019118. |
[47] |
Huhn M, Madduppa HH, Khair M, Sabrian A, Irawati Y, Anggraini NP, Wilkinson SP, Simpson T, Iwasaki K, Setiamarga DHE, Dias PJ (2020) Keeping up with introduced marine species at a remote biodiversity hotspot: Awareness, training and collaboration across different sectors is key. Biological Invasions, 22, 749-771.
DOI URL |
[48] | Hung CM, Shaner PJL, Zink RM, Liu WC, Chu TC, Huang WS, Li SH (2014) Drastic population fluctuations explain the rapid extinction of the passenger pigeon. Proceedings of the National Academy of Sciences, USA, 111, 10636-10641. |
[49] |
International Wheat Genome Sequencing Consortium IWGSC (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 361, eaar7191.
DOI URL |
[50] |
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pè ME, Valle G, Morgante M, Caboche M, Adam-Blondon AF, Weissenbach J, Quétier F, Wincker P,French-Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm Phyla. Nature, 449, 463-467.
DOI URL |
[51] |
Jakubavičiūtė E, Bergström U, Eklöf JS, Haenel Q, Bourlat SJ (2017) DNA metabarcoding reveals diverse diet of the three-spined stickleback in a coastal ecosystem. PLoS ONE, 12, e0186929.
DOI URL |
[52] |
Ji Y, Li X, Ji T, Tang J, Qiu L, Hu J, Dong J, Luo S, Liu S, Frandsen PB, Zhou X, Parey SH, Li L, Niu Q, Zhou X (2020) Gene reuse facilitates rapid radiation and independent adaptation to diverse habitats in the Asian honeybee. Science Advances, 6, eabd3590.
DOI URL |
[53] |
Ji YQ, Ashton L, Pedley SM, Edwards DP, Tang Y, Nakamura A, Kitching R, Dolman PM, Woodcock P, Edwards FA, Larsen TH, Hsu WW, Benedick S, Hamer KC, Wilcove DS, Bruce C, Wang XY, Levi T, Lott M, Emerson BC, Yu DW (2013) Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecology Letters, 16, 1245-1257.
DOI PMID |
[54] |
Ji YQ, Baker CCM, Popescu VD, Wang JX, Wu CY, Wang ZY, Li YH, Wang L, Hua CL, Yang ZX, Yang CY, Xu CCY, Diana A, Wen QZ, Pierce NE, Yu DW (2022) Measuring protected-area effectiveness using vertebrate distributions from leech iDNA. Nature Communications, 13, 1555.
DOI PMID |
[55] |
Jia N, Wang JF, Shi WQ, Du LF, Sun Y, Zhan W, Jiang JF, Wang Q, Zhang B, Ji PF, Bell-Sakyi L, Cui XM, Yuan TT, Jiang BG, Yang WF, Lam TTY, Chang QC, Ding SJ, Cao WC (2020) Large-scale comparative analyses of tick genomes elucidate their genetic diversity and vector capacities. Cell, 182, 1328-1340.
DOI PMID |
[56] |
Jiang T, Liu YZ, Jiang Y, Li JY, Gao Y, Cui Z, Liu YD, Liu B, Wang YD (2020) Long-read-based human genomic structural variation detection with cuteSV. Genome Biology, 21, 189.
DOI PMID |
[57] |
Jin JJ, Yu WB, Yang JB, Song Y, DePamphilis CW, Yi TS, Li DZ (2020) GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology, 21, 241.
DOI URL |
[58] |
Jones L, Brennan GL, Lowe A, Creer S, Ford CR,de Vere N (2021) Shifts in honeybee foraging reveal historical changes in floral resources. Communications Biology, 4, 37.
DOI PMID |
[59] |
Khansaritoreh E, Salmaki Y, Ramezani E, Akbari Azirani T, Keller A, Neumann K, Alizadeh K, Zarre S, Beckh G, Behling H (2020) Employing DNA metabarcoding to determine the geographical origin of honey. Heliyon, 6, e05596.
DOI URL |
[60] |
Kolora SRR, Owens GL, Vazquez JM, Stubbs A, Chatla K, Jainese C, Seeto K, McCrea M, Sandel MW, Vianna JA, Maslenikov K, Bachtrog D, Orr JW, Love M, Sudmant PH (2021) Origins and evolution of extreme life span in Pacific Ocean rockfishes. Science, 374, 842-847.
DOI PMID |
[61] | Kress WJ, Erickson DL (2012) DNA Barcodes: Methods and Protocols. Springer, New York. |
[62] |
Krishnamurthy P, Francis RA (2012) A critical review on the utility of DNA barcoding in biodiversity conservation. Biodiversity and Conservation, 21, 1901-1919.
DOI URL |
[63] |
Lamichhaney S, Fan GY, Widemo F, Gunnarsson U, Thalmann DS, Hoeppner MP, Kerje S, Gustafson U, Shi CC, Zhang H, Chen WB, Liang XM, Huang LH, Wang JH, Liang EJ, Wu Q, Lee SMY, Xu X, Höglund J, Liu X, Andersson L (2016) Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax). Nature Genetics, 48, 84-88.
DOI PMID |
[64] |
Lang DD, Zhang SL, Ren PP, Liang F, Sun ZY, Meng GL, Tan YT, Li XK, Lai QH, Han LL, Wang DP, Hu FY, Wang W, Liu SL (2020) Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore. GigaScience, 9, giaa123.
DOI URL |
[65] |
Li H, Feng XW, Chu C (2020) The design and construction of reference pangenome graphs with minigraph. Genome Biology, 21, 265.
DOI PMID |
[66] |
Li HB, Wang SH, Chai S, Yang ZQ, Zhang QQ, Xin HJ, Xu YC, Lin SN, Chen XX, Yao ZW, Yang QY, Fei ZJ, Huang SW, Zhang ZH (2022) Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. Nature Communications, 13, 682.
DOI PMID |
[67] |
Li JY, Yuan DJ, Wang PC, Wang QQ, Sun ML, Liu ZP, Si H, Xu ZP, Ma YZ, Zhang BY, Pei LL, Tu LL, Zhu LF, Chen LL, Lindsey K, Zhang XL, Jin SX, Wang MJ (2021) Cotton pan-genome retrieves the lost sequences and genes during domestication and selection. Genome Biology, 22, 119.
DOI PMID |
[68] |
Li RQ, Fan W, Tian G, Zhu HM, He L, Cai J, Huang QF, Cai QL, Li B, Bai YQ, Zhang ZH, Zhang YP, Wang W, Li J, Wei FW, Li H, Jian M, Li JW, Zhang ZL, Nielsen R, Li DW, Gu WJ, Yang ZT, Xuan ZL, Ryder OA, Leung FCC, Zhou Y, Cao JJ, Sun X, Fu YG, Fang XD, Guo XS, Wang B, Hou R, Shen FJ, Mu B, Ni PX, Lin RM, Qian WB, Wang GD, Yu C, Nie WH, Wang JH, Wu ZG, Liang HQ, Min JM, Wu Q, Cheng SF, Ruan J, Wang MW, Shi ZB, Wen M, Liu BH, Ren XL, Zheng HS, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie XY, Lu ZH, Zheng HC, Li YR, Steiner CC, Lam TTY, Lin SY, Zhang QH, Li GQ, Tian J, Gong TM, Liu HD, Zhang DJ, Fang L, Ye C, Zhang JB, Hu WB, Xu AL, Ren YY, Zhang GJ, Bruford MW, Li QB, Ma LJ, Guo YR, An N, Hu YJ, Zheng Y, Shi YY, Li ZQ, Liu Q, Chen YL, Zhao J, Qu N, Zhao SC, Tian F, Wang XL, Wang HY, Xu LZ, Liu X, Vinar T, Wang YJ, Lam TW, Yiu SM, Liu SP, Zhang HM, Li DS, Huang Y, Wang X, Yang GH, Jiang Z, Wang JY, Qin N, Li L, Li JX, Bolund L, Kristiansen K, Wong GKS, Olson M, Zhang XQ, Li SG, Yang HM, Wang J, Wang J (2010) The sequence and de novo assembly of the giant panda genome. Nature, 463, 311-317.
DOI URL |
[69] |
Li YH, Zhou GY, Ma JX, Jiang WK, Jin LG, Zhang ZH, Guo Y, Zhang JB, Sui Y, Zheng LT, Zhang SS, Zuo QY, Shi XH, Li YF, Zhang WK, Hu YY, Kong GY, Hong HL, Tan B, Song J, Liu ZX, Wang YS, Ruan H, Yeung CKL, Liu J, Wang HL, Zhang LJ, Guan RX, Wang KJ, Li WB, Chen SY, Chang RZ, Jiang Z, Jackson SA, Li RQ, Qiu LJ (2014) De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nature Biotechnology, 32, 1045-1052.
DOI |
[70] |
Librado P, Gamba C, Gaunitz C, der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L (2017) Ancient genomic changes associated with domestication of the horse. Science, 356, 442-445.
DOI PMID |
[71] |
Liu SL, Lang DD, Meng GL, Hu JH, Tang M, Zhou X (2022) Tracing the origin of honey products based on metagenomics and machine learning. Food Chemistry, 371, 131066.
DOI URL |
[72] |
Liu SL, Li YY, Lu JL, Su X, Tang M, Zhang R, Zhou LL, Zhou CR, Yang Q, Ji YQ, Yu DW, Zhou X (2013) SOAPBarcode: Revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons. Methods in Ecology and Evolution, 4, 1142-1150.
DOI URL |
[73] |
Liu SL, Westbury MV, Dussex N, Mitchell KJ, Sinding MHS, Heintzman PD, Duchêne DA, Kapp JD, von Seth J, Heiniger H, Sánchez-Barreiro F, Margaryan A, André-Olsen R, de Cahsan B, Meng GL, Yang CT, Chen L, van der Valk T, Gilbert MTP (2021) Ancient and modern genomes unravel the evolutionary history of the Rhinoceros family. Cell, 184, 4874-4885.
DOI PMID |
[74] | Liu SL, Yang CT, Zhou CR, Zhou X (2017) Filling reference gaps via assembling DNA barcodes using high-throughput sequencing—Moving toward barcoding the world. GigaScience, 6, gix104. |
[75] |
Liu YC, Du HL, Li PC, Shen YT, Peng H, Liu SL, Zhou GA, Zhang HK, Liu Z, Shi M, Huang XH, Li Y, Zhang M, Wang Z, Zhu BG, Han B, Liang CZ, Tian ZX (2020) Pan-genome of wild and cultivated soybeans. Cell, 182, 162-176.
DOI PMID |
[76] |
Lu Q, Hu Q, Shi XG, Jin SL, Li S, Yao M (2019) Metabarcoding diet analysis of snow leopards (Panthera uncia) in Wolong National Nature Reserve, Sichuan Province. Biodiversity Science, 27, 960-969. (in Chinese with abstract)
DOI |
[陆琪, 胡强, 施小刚, 金森龙, 李晟, 姚蒙 (2019) 基于分子宏条形码分析四川卧龙国家级自然保护区雪豹的食性. 生物多样性, 27, 960-969.]
DOI |
|
[77] |
Lynggaard C, Bertelsen MF, Jensen CV, Johnson MS, Frøslev TG, Olsen MT, Bohmann K (2022) Airborne environmental DNA for terrestrial vertebrate community monitoring. Current Biology, 32, 701-707.
DOI URL |
[78] |
Macías-Hernández N, Athey K, Tonzo V, Wangensteen OS, Arnedo M, Harwood JD (2018) Molecular gut content analysis of different spider body parts. PLoS ONE, 13, e0196589.
DOI URL |
[79] |
Mao XW, Zhang HC, Qiao SY, Liu YC, Chang FQ, Xie P, Zhang M, Wang TY, Li M, Cao P, Yang RW, Liu F, Dai QY, Feng XT, Ping WJ, Lei CZ, Olsen JW, Bennett EA, Fu QM (2021) The deep population history of northern East Asia from the Late Pleistocene to the Holocene. Cell, 184, 3256-3266.
DOI PMID |
[80] |
Meier R, Wong W, Srivathsan A, Foo M (2016) $ 1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen-rich samples. Cladistics, 32, 100-110.
DOI URL |
[81] |
Meng GL, Li YY, Yang CT, Liu SL (2019) MitoZ: A toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Research, 47, e63.
DOI URL |
[82] |
Meyer A, Schloissnig S, Franchini P, Du K, Woltering JM, Irisarri I, Wong WY, Nowoshilow S, Kneitz S, Kawaguchi A, Fabrizius A, Xiong PW, Dechaud C, Spaink HP, Volff JN, Simakov O, Burmester T, Tanaka EM, Schartl M (2021) Giant lungfish genome elucidates the conquest of land by vertebrates. Nature, 590, 284-289.
DOI URL |
[83] |
Mikheyev AS, Tin MMY, Arora J, Seeley TD (2015) Museum samples reveal rapid evolution by wild honey bees exposed to a novel parasite. Nature Communications, 6, 7991.
DOI PMID |
[84] |
Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, Niehuis O, Petersen M, Izquierdo-Carrasco F, Wappler T, Rust J, Aberer AJ, Aspöck U, Aspöck H, Bartel D, Blanke A, Berger S, Böhm A, Buckley TR, Calcott B, Chen J, Friedrich F, Fukui M, Fujita M, Greve C, Grobe P, Gu S, Huang Y, Jermiin LS, Kawahara AY, Krogmann L, Kubiak M, Lanfear R, Letsch H, Li Y, Li Z, Li J, Lu H, Machida R, Mashimo Y, Kapli P, McKenna DD, Meng G, Nakagaki Y, Navarrete-Heredia JL, Ott M, Ou Y, Pass G, Podsiadlowski L, Pohl H, von Reumont BM, Schütte K, Sekiya K, Shimizu S, Slipinski A, Stamatakis A, Song W, Su X, Szucsich NU, Tan M, Tan X, Tang M, Tang J, Timelthaler G, Tomizuka S, Trautwein M, Tong X, Uchifune T, Walzl MG, Wiegmann BM, Wilbrandt J, Wipfler B, Wong TK, Wu Q, Wu G, Xie Y, Yang S, Yang Q, Yeates DK, Yoshizawa K, Zhang Q, Zhang R, Zhang W, Zhang Y, Zhao J, Zhou C, Zhou L, Ziesmann T, Zou S, Li Y, Xu X, Zhang Y, Yang H, Wang J, Wang J, Kjer KM, Zhou X (2014) Phylogenomics resolves the timing and pattern of insect evolution. Science, 346, 763-767.
DOI PMID |
[85] |
Mitchell G, Wilson PJ, Manseau M, Redquest B, Patterson BR, Rutledge LY (2022) DNA metabarcoding of faecal pellets reveals high consumption of yew (Taxus spp.) by caribou (Rangifer tarandus) in a lichen-poor environment. FACETS, 7, 701-717.
DOI URL |
[86] |
Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of more than 230 subtropical marine species. Royal Society Open Science, 2, 150088.
DOI URL |
[87] |
Morgante M, de Paoli E, Radovic S (2007) Transposable elements and the plant pan-genomes. Current Opinion in Plant Biology, 10, 149-155.
PMID |
[88] |
Morrill A, Kaunisto KM, Mlynarek JJ, Sippola E, Vesterinen EJ, Forbes MR (2021) Metabarcoding prey DNA from fecal samples of adult dragonflies shows no predicted sex differences, and substantial inter-individual variation, in diets. PeerJ, 9, e12634.
DOI URL |
[89] | Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O’Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562. |
[90] |
Nilsson RH, Ryberg M, Abarenkov K, Sjökvist E, Kristiansson E (2009) The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiology Letters, 296, 97-101.
DOI PMID |
[91] |
Nowoshilow S, Schloissnig S, Fei JF, Dahl A, Pang AWC, Pippel M, Winkler S, Hastie AR, Young G, Roscito JG, Falcon F, Knapp D, Powell S, Cruz A, Cao H, Habermann B, Hiller M, Tanaka EM, Myers EW (2018) The axolotl genome and the evolution of key tissue formation regulators. Nature, 554, 50-55.
DOI URL |
[92] |
One Thousand Plant Transcriptomes Initiative (2019) One thousand plant transcriptomes and the phylogenomics of green plants. Nature, 574, 679-685.
DOI URL |
[93] |
Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E (2013) Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature, 499, 74-78.
DOI URL |
[94] |
Poinar HN, Schwarz C, Qi J, Shapiro B, MacPhee RDE, Buigues B, Tikhonov A, Huson DH, Tomsho LP, Auch A, Rampp M, Miller W, Schuster SC (2006) Metagenomics to paleogenomics: Large-scale sequencing of mammoth DNA. Science, 311, 392-394.
PMID |
[95] |
Pornon A, Escaravage N, Burrus M, Holota H, Khimoun A, Mariette J, Pellizzari C, Iribar A, Etienne R, Taberlet P, Vidal M, Winterton P, Zinger L, Andalo C (2016) Using metabarcoding to reveal and quantify plant-pollinator interactions. Scientific Reports, 6, 27282.
DOI PMID |
[96] |
Rytkönen S, Vesterinen EJ, Westerduin C, Leviäkangas T, Vatka E, Mutanen M, Välimäki P, Hukkanen M, Suokas M, Orell M (2019) From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web. Ecology and Evolution, 9, 631-639.
DOI URL |
[97] |
Saravanan M, Mohanapriya G, Laha R, Sathishkumar R (2019) DNA barcoding detects floral origin of Indian honey samples. Genome, 62, 341-348.
DOI PMID |
[98] | Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: Complexity, diversity, and dynamics. Science, 326, 1112-1115. |
[99] |
Schneider SS, Degrandi-Hoffman G, Smith DR (2004) The African honey bee: Factors contributing to a successful biological invasion. Annual Review of Entomology, 49, 351-376.
PMID |
[100] |
Schnell IB, Thomsen PF, Wilkinson N, Rasmussen M, Jensen LRD, Willerslev E, Bertelsen MF, Gilbert MTP (2012) Screening mammal biodiversity using DNA from leeches. Current Biology, 22, R262-R263.
DOI URL |
[101] | Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Consortium FB, List FBCA (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences, USA, 109, 6241-6246. |
[102] |
Shang L, Li X, He H, Yuan Q, Song Y, Wei Z, Lin H, Hu M, Zhao F, Zhang C, Li Y, Gao H, Wang T, Liu X, Zhang H, Zhang Y, Cao S, Yu X, Zhang B, Zhang Y, Tan Y, Qin M, Ai C, Yang Y, Zhang B, Hu Z, Wang H, Lü Y, Wang Y, Ma J, Wang Q, Lu H, Wu Z, Liu S, Sun Z, Zhang H, Guo L, Li Z, Zhou Y, Li J, Zhu Z, Xiong G, Ruan J, Qian Q (2022) A super pan-genomic landscape of rice. Cell Research, 32, 878-896.
DOI URL |
[103] |
Shao XN, Lu Q, Liu MZ, Xiong MY, Bu HL, Wang DJ, Liu SY, Zhao JD, Li S, Yao M (2021) Generalist carnivores can be effective biodiversity samplers of terrestrial vertebrates. Frontiers in Ecology and the Environment, 19, 557-563.
DOI URL |
[104] |
Shao XN, Lu Q, Xiong MY, Bu HL, Shi XY, Wang DJ, Zhao JD, Li S, Yao M (2021) Prey partitioning and livestock consumption in the world’s richest large carnivore assemblage. Current Biology, 31, 4887-4897.
DOI URL |
[105] |
Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan HL, Campbell M, Tan H, Huff CD, Hu HF, Vickrey AI, Nielsen SCA, Stringham SA, Hu H, Willerslev E, Gilbert MTP, Yandell M, Zhang GJ, Wang J (2013) Genomic diversity and evolution of the head crest in the rock pigeon. Science, 339, 1063-1067.
DOI PMID |
[106] |
Shehzad W, McCarthy TM, Pompanon F, Purevjav L, Coissac E, Riaz T, Taberlet P (2012) Prey preference of snow leopard (Panthera uncia) in South Gobi, Mongolia. PLoS ONE, 7, e32104.
DOI URL |
[107] |
Shehzad W, Riaz T, Nawaz MA, Miquel C, Poillot C, Shah SA, Pompanon F, Coissac E, Taberlet P (2012) Carnivore diet analysis based on next-generation sequencing: Application to the leopard cat (Prionailurus bengalensis) in Pakistan. Molecular Ecology, 21, 1951-1965.
DOI PMID |
[108] |
Shokralla S, Gibson JF, Nikbakht H, Janzen DH, Hallwachs W, Hajibabaei M (2014) Next-generation DNA barcoding: Using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Molecular Ecology Resources, 14, 892-901.
DOI PMID |
[109] | Shokralla S, Porter TM, Gibson JF, Dobosz R, Janzen DH, Hallwachs W, Golding GB, Hajibabaei M (2015) Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Scientific Reports, 5, 9687. |
[110] |
Sigsgaard EE, Olsen K, Hansen MDD, Hansen OLP, Høye TT, Svenning JC, Thomsen PF (2021) Environmental DNA metabarcoding of cow dung reveals taxonomic and functional diversity of invertebrate assemblages. Molecular Ecology, 30, 3374-3389.
DOI PMID |
[111] |
Šigut M, Kostovčík M, Šigutová H, Hulcr J, Drozd P, Hrček J (2017) Performance of DNA metabarcoding, standard barcoding, and morphological approach in the identification of host-parasitoid interactions. PLoS ONE, 12, e0187803.
DOI URL |
[112] |
Sollars ESA, Harper AL, Kelly LJ, Sambles CM, Ramirez- Gonzalez RH, Swarbreck D, Kaithakottil G, Cooper ED, Uauy C, Havlickova L, Worswick G, Studholme DJ, Zohren J, Salmon DL, Clavijo BJ, Li Y, He ZS, Fellgett A, McKinney LV, Nielsen LR, Douglas GC, Kjær ED, Downie JA, Boshier D, Lee S, Clark J, Grant M, Bancroft I, Caccamo M, Buggs RJA (2017) Genome sequence and genetic diversity of European ash trees. Nature, 541, 212-216.
DOI URL |
[113] |
Soria-Carrasco V, Gompert Z, Comeault AA, Farkas TE, Parchman TL, Johnston JS, Buerkle CA, Feder JL, Bast J, Schwander T, Egan SP, Crespi BJ, Nosil P (2014) Stick insect genomes reveal natural selection’s role in parallel speciation. Science, 344, 738-742.
DOI PMID |
[114] |
Sow A, Brévault T, Benoit L, Chapuis MP, Galan M, Coeur d’acier A, Delvare G, Sembène M, Haran J (2019) Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding. Scientific Reports, 9, 3646.
DOI PMID |
[115] |
Steinke D, deWaard SL, Sones JE, Ivanova NV, Prosser SWJ, Perez K, Braukmann TWA, Milton M, Zakharov EV, deWaard JR, Ratnasingham S, Hebert PDN (2022) Message in a Bottle—Metabarcoding enables biodiversity compari- sons across ecoregions. GigaScience, 11, giac040.
DOI URL |
[116] |
Suchan T, Talavera G, Sáez L, Ronikier M, Vila R (2019) Pollen metabarcoding as a tool for tracking long-distance insect migrations. Molecular Ecology Resources, 19, 149-162.
DOI PMID |
[117] |
Sun Y, Huang Y, Li XF, Baldwin CC, Zhou ZC, Yan ZX, Crandall KA, Zhang Y, Zhao XM, Wang M, Wong A, Fang C, Zhang XH, Huang H, Lopez JV, Kilfoyle K, Zhang Y, Ortí G, Venkatesh B, Shi Q (2016) Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-scale transcriptome data for fish evolution studies. GigaScience, 5, 18.
DOI PMID |
[118] |
Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH (2012) Environmental DNA. Molecular Ecology, 21, 1789-1793.
DOI PMID |
[119] |
Tang KY, Xie F, Liu HY, Pu YT, Chen D, Qin BX, Fu CK, Wang Q, Chen SD, Guo KJ (2021) DNA metabarcoding provides insights into seasonal diet variations in Chinese mole shrew (Anourosorex squamipes) with potential implications for evaluating crop impacts. Ecology and Evolution, 11, 376-389.
DOI URL |
[120] |
Tea YK, van der Wal C, Ludt WB, Gill AC, Lo N, Ho SYW (2019) Boomeranging around Australia: Historical biogeography and population genomics of the anti-equatorial fish Microcanthus strigatus (Teleostei: Microcanthidae). Molecular Ecology, 28, 3771-3785.
DOI URL |
[121] |
Toju H, Baba YG (2018) DNA metabarcoding of spiders, insects, and springtails for exploring potential linkage between above- and below-ground food webs. Zoological Letters, 4, 4.
DOI PMID |
[122] |
Troll CJ, Kapp J, Rao V, Harkins KM, Cole C, Naughton C, Morgan JM, Shapiro B, Green RE (2019) A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos. BMC Genomics, 20, 1023.
DOI PMID |
[123] |
Turvey ST, Marr MM, Barnes I, Brace S, Tapley B, Murphy RW, Zhao EM, Cunningham AA (2019) Historical museum collections clarify the evolutionary history of cryptic species radiation in the world’s largest amphibians. Ecology and Evolution, 9, 10070-10084.
DOI URL |
[124] |
Valentini A, Miquel C, Taberlet P (2010) DNA barcoding for honey biodiversity. Diversity, 2, 610-617.
DOI URL |
[125] |
van der Valk T, Pečnerová P, Díez-Del-Molino D, Bergström A, Oppenheimer J, Hartmann S, Xenikoudakis G, Thomas JA, Dehasque M, Sağlıcan E, Fidan FR, Barnes I, Liu S, Somel M, Heintzman PD, Nikolskiy P, Shapiro B, Skoglund P, Hofreiter M, Lister AM, Götherström A, Dalén L (2021) Million-year-old DNA sheds light on the genomic history of mammoths. Nature, 591, 265-269.
DOI URL |
[126] |
Vonholdt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG, Quignon P, Degenhardt JD, Boyko AR, Earl DA, Auton A, Reynolds A, Bryc K, Brisbin A, Knowles JC, Mosher DS, Spady TC, Elkahloun A, Geffen E, Pilot M, Jedrzejewski W, Greco C, Randi E, Bannasch D, Wilton A, Shearman J, Musiani M, Cargill M, Jones PG, Qian Z, Huang W, Ding ZL, Zhang YP, Bustamante CD, Ostrander EA, Novembre J, Wayne RK (2010) Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature, 464, 898-902.
DOI URL |
[127] |
Wang J, Li JG, Li ZY, Liu B, Zhang LL, Guo DL, Huang SL, Qian WQ, Guo L (2022) Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions. Horticulture Research, 9, uhac021.
DOI URL |
[128] |
Wang K, Wang J, Zhu CL, Yang LD, Ren YD, Ruan J, Fan GY, Hu J, Xu WJ, Bi XP, Zhu YA, Song Y, Chen HT, Ma TT, Zhao RP, Jiang HF, Zhang B, Feng CG, Wang W (2021) African lungfish genome sheds light on the vertebrate water-to-land transition. Cell, 184, 1362-1376.
DOI PMID |
[129] | Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison NA, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D, Human Pangenome Reference Consortium (2022) The Human Pangenome Project: A global resource to map genomic diversity. Nature, 604, 437-446. |
[130] |
Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang F, Mansueto L, Copetti D, Sanciangco M, Palis KC, Xu J, Sun C, Fu B, Zhang H, Gao Y, Zhao X, Shen F, Cui X, Yu H, Li Z, Chen M, Detras J, Zhou Y, Zhang X, Zhao Y, Kudrna D, Wang C, Li R, Jia B, Lu J, He X, Dong Z, Xu J, Li Y, Wang M, Shi J, Li J, Zhang D, Lee S, Hu W, Poliakov A, Dubchak I, Ulat VJ, Borja FN, Mendoza JR, Ali J, Li J, Gao Q, Niu Y, Yue Z, Naredo MEB, Talag J, Wang X, Li J, Fang X, Yin Y, Glaszmann JC, Zhang J, Li J, Hamilton RS, Wing RA, Ruan J, Zhang G, Wei C, Alexandrov N, McNally KL, Li Z, Leung H (2018) Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557, 43-49.
DOI URL |
[131] | Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong LS, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TAF, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AFA, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu WJ, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou SF, Mardis ER, Wilson RK (2010) The genome of a songbird. Nature, 464, 757-762. |
[132] |
Wilcox TM, McKelvey KS, Young MK, Sepulveda AJ, Shepard BB, Jane SF, Whiteley AR, Lowe WH, Schwartz MK (2016) Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis. Biological Conservation, 194, 209-216.
DOI URL |
[133] |
Wray AK, Peery MZ, Jusino MA, Kochanski JM, Banik MT, Palmer JM, Lindner DL, Gratton C (2021) Predator preferences shape the diets of arthropodivorous bats more than quantitative local prey abundance. Molecular Ecology, 30, 855-873.
DOI PMID |
[134] |
Xia Q, Zhou Z, Lu C, Cheng D, Dai F, Li B, Zhao P, Zha X, Cheng T, Chai C, Pan G, Xu J, Liu C, Lin Y, Qian J, Hou Y, Wu Z, Li G, Pan M, Li C, Shen Y, Lan X, Yuan L, Li T, Xu H, Yang G, Wan Y, Zhu Y, Yu M, Shen W, Wu D, Xiang Z, Yu J, Wang J, Li R, Shi J, Li H, Li G, Su J, Wang X, Li G, Zhang Z, Wu Q, Li J, Zhang Q, Wei N, Xu J, Sun H, Dong L, Liu D, Zhao S, Zhao X, Meng Q, Lan F, Huang X, Li Y, Fang L, Li C, Li D, Sun Y, Zhang Z, Yang Z, Huang Y, Xi Y, Qi Q, He D, Huang H, Zhang X, Wang Z, Li W, Cao Y, Yu Y, Yu H, Li J, Ye J, Chen H, Zhou Y, Liu B, Wang J, Ye J, Ji H, Li S, Ni P, Zhang J, Zhang Y, Zheng H, Mao B, Wang W, Ye C, Li S, Wang J, Wong GK, Yang H,Biology Analysis Group (2004) A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science, 306, 1937-1940.
PMID |
[135] |
Xu X, Liu X, Ge S, Jensen JD, Hu FY, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li JX, He WM, Zhang GJ, Zheng XM, Zhang FM, Li YR, Yu C, Kristiansen K, Zhang XQ, Wang J, Wright M, McCouch S, Nielsen R, Wang J, Wang W (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology, 30, 105-111.
DOI URL |
[136] |
Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q, Szpak M, Frandsen P, Chen Y, Yngvadottir B, Cooper DN, de Manuel M, Hernandez-Rodriguez J, Lobon I, Siegismund HR, Pagani L, Quail MA, Hvilsom C, Mudakikwa A, Eichler EE, Cranfield MR, Marques-Bonet T, Tyler-Smith C, Scally A (2015) Mountain Gorilla genomes reveal the impact of long-term population decline and inbreeding. Science, 348, 242-245.
DOI URL |
[137] |
Yang CT, Tan SJ, Meng GL, Bourne DG, O’Brien PA, Xu JQ, Liao S, Chen A, Chen XW, Liu SL (2018) Access COI barcode efficiently using high throughput Single-End 400 bp sequencing. bioRxiv, doi: https://doi.org/10.1101/498618.
DOI |
[138] |
Yang L, Wei FW, Zhan XJ, Fan HZ, Zhao PP, Huang GP, Chang J, Lei YH, Hu YB (2022) Evolutionary conservation genomics reveals recent speciation and local adaptation in threatened takins. Molecular Biology and Evolution, 39, msac111.
DOI URL |
[139] |
Yu DW, Ji YQ, Emerson BC, Wang XY, Ye CX, Yang CY, Ding ZL (2012) Biodiversity soup: Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution, 3, 613-623.
DOI URL |
[140] |
Yu J, Hu SN, Wang J, Wong GKS, Li SG, Liu B, Deng YJ, Dai L, Zhou Y, Zhang XQ, Cao ML, Liu J, Sun JD, Tang JB, Chen YJ, Huang XB, Lin W, Ye C, Tong W, Cong LJ, Geng JN, Han YJ, Li L, Li W, Hu GQ, Huang XG, Li WJ, Li J, Liu ZW, Li L, Liu JP, Qi QH, Liu JS, Li L, Li T, Wang XG, Lu H, Wu TT, Zhu M, Ni PX, Han H, Dong W, Ren XY, Feng XL, Cui P, Li XR, Wang H, Xu X, Zhai WX, Xu Z, Zhang JS, He SJ, Zhang JG, Xu JC, Zhang KL, Zheng XW, Dong JH, Zeng WY, Tao L, Ye J, Tan J, Ren XD, Chen XW, He J, Liu DF, Tian W, Tian CG, Xia HA, Bao QY, Li G, Gao H, Cao T, Wang J, Zhao WM, Li P, Chen W, Wang XD, Zhang Y, Hu JF, Wang J, Liu S, Yang J, Zhang GY, Xiong YQ, Li ZJ, Mao L, Zhou CS, Zhu Z, Chen RS, Hao BL, Zheng WM, Chen SY, Guo W, Li GJ, Liu SQ, Tao M, Wang J, Zhu LH, Yuan LP, Yang HM (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79-92.
DOI URL |
[141] |
Zhang F, Xue HZ, Dong XR, Li M, Zheng XM, Li ZK, Xu JL, Wang WS, Wei CC (2022) Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes. Genome Research, 32, 853-863.
DOI PMID |
[142] |
Zhang LY, Hu J, Han XL, Li JJ, Gao Y, Richards CM, Zhang CX, Tian Y, Liu GM, Gul H, Wang DJ, Tian Y, Yang CX, Meng MH, Yuan GP, Kang GD, Wu YL, Wang K, Zhang HT, Wang DP, Cong PH (2019) A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nature Communications, 10, 1494.
DOI PMID |
[143] |
Zhang S, Zheng YT, Zhan AB, Dong CX, Zhao JD, Yao M (2022) Environmental DNA captures native and non-native fish community variations across the lentic and lotic systems of a megacity. Science Advances, 8, eabk0097.
DOI URL |
[144] |
Zhang X, Yuan J, Sun Y, Li S, Gao Y, Yu Y, Liu C, Wang Q, Lü X, Zhang X, Ma KY, Wang X, Lin W, Wang L, Zhu X, Zhang C, Zhang J, Jin S, Yu K, Kong J, Xu P, Chen J, Zhang H, Sorgeloos P, Sagi A, Alcivar-Warren A, Liu Z, Wang L, Ruan J, Chu KH, Liu B, Li F, Xiang J (2019) Penaeid shrimp genome provides insights into benthic adaptation and frequent molting. Nature Communications, 10, 356.
DOI PMID |
[145] |
Zhang XM, Shi ZY, Zhang SQ, Zhang P, Wilson JJ, Shih C, Li J, Li XD, Yu GY, Zhang AB (2021) Plant-herbivorous insect networks: Who is eating what revealed by long barcodes using high-throughput sequencing and Trinity assembly. Insect Science, 28, 127-143.
DOI URL |
[146] |
Zhao SC, Zheng PP, Dong SS, Zhan XJ, Wu Q, Guo XS, Hu YB, He WM, Zhang SN, Fan W, Zhu LF, Li D, Zhang XM, Chen Q, Zhang HM, Zhang ZH, Jin XL, Zhang JG, Yang HM, Wang J, Wang J, Wei FW (2013) Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nature Genetics, 45, 67-71.
DOI PMID |
[147] |
Zhao YP, Fan GY, Yin PP, Sun S, Li N, Hong XN, Hu G, Zhang H, Zhang FM, Han JD, Hao YJ, Xu QW, Yang XW, Xia WJ, Chen WB, Lin HY, Zhang R, Chen J, Zheng XM, Lee SMY, Lee J, Uehara K, Wang J, Yang HM, Fu CX, Liu X, Xu X, Ge S (2019) Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil. Nature Communications, 10, 4201.
DOI URL |
[148] |
Zhen Y, Harrigan RJ, Ruegg KC, Anderson EC, Ng TC, Lao S, Lohmueller KE, Smith TB (2017) Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens). Molecular Ecology, 26, 4966-4977.
DOI PMID |
[149] |
Zhou X, Li YY, Liu SL, Yang Q, Su X, Zhou LL, Tang M, Fu RB, Li JG, Huang QF (2013) Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. GigaScience, 2, 4.
DOI PMID |
[150] |
Zimmermann J, Glöckner G, Jahn R, Enke N, Gemeinholzer B (2015) Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies. Molecular Ecology Resources, 15, 526-542.
DOI PMID |
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