生物多样性 ›› 2019, Vol. 27 ›› Issue (5): 475-479.doi: 10.17520/biods.2019161

• 编者按 • 上一篇    下一篇

运用基因组学方法探究生物多样性: 大数据时代的“胡克显微镜”

周欣()   

  1. 中国农业大学植物保护学院昆虫学系, 北京 100193
  • 收稿日期:2019-05-13 接受日期:2019-05-13 出版日期:2019-05-20
  • 通讯作者: 周欣 E-mail:xinzhoucaddis@icloud.com
  • 基金项目:
    科技基础资源调查专项(2018FY100403)

Understanding biodiversity using genomics: Hooke’s microscope in the era of big data

Zhou Xin()   

  1. Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193
  • Received:2019-05-13 Accepted:2019-05-13 Online:2019-05-20
  • Contact: Zhou Xin E-mail:xinzhoucaddis@icloud.com
[1] Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H ( 2018) Structure and function of the global topsoil microbiome. Nature, 560, 233-237.
doi: 10.1038/s41586-018-0386-6
[2] Bell KL, Burgess KS, Botsch JC, Dobbs EK, Read TD, Brosi BJ ( 2018) Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures. Molecular Ecology, 28, 431-455.
[3] Belles X ( 2017) MicroRNAs and the evolution of insect metamorphosis. Annual Review of Entomology, 62, 111-125.
doi: 10.1146/annurev-ento-031616-034925
[4] Calvignac-Spencer S, Leendertz FH, Gilbert MTP, Schubert G ( 2013) An invertebrate stomach’s view on vertebrate ecology. BioEssays, 35, 1004-1013.
[5] Crampton-Platt A, Yu DW, Zhou X, Vogler AP ( 2016) Mitochondrial metagenomics: Letting the genes out of the bottle. GigaScience, 5, 15.
[6] Creer S, Deiner K, Frey S, Porazinska D, Taberlet P, Thomas WK, Potter C, Bik HM ( 2016) The ecologist’s field guide to sequence-based identification of biodiversity. Methods in Ecology and Evolution, 7, 1008-1018.
[7] De Barba M, Miquel C, Boyer F, Mercier C, Rioux D, Coissac E, Taberlet P ( 2014) DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: Application to omnivorous diet. Molecular Ecology Resources, 14, 306-323.
[8] Fronhofer EA, Chler EMA, Walser JC, Deiner K, Altermatt F ( 2018) Environmental DNA reveals that rivers are conveyer belts of biodiversity information. Nature Communications, 7, 12544.
[9] 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.
[10] 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.
doi: 10.1098/rspb.2002.2218
[11] Hollingsworth PM, Li DZ, Van der Bank M, Twyford AD ( 2016) Telling plant species apart with DNA: From barcodes to genomes. Philosophical Transactions of the Royal Society B: Biological Sciences, 371, 20150338.
[12] Hooke R ( 1665) Micrographia: Or Some Physiological Descriptions of Minute Bodies Made by Magnifying Glasses, with Observations and Inquiries Thereupon. Courier Dover Publications. John Martyn and James Allestry, London.
[13] Karst SM, Dueholm MS, McIlroy SJ, Kirkegaard RH, Nielsen PH, Albertsen M ( 2018) Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias. Nature Biotechnology, 36, 190-195.
[14] Lang D, Tang M, Hu J, Zhou X ( 2018) Genome-skimming provides accurate quantification for pollen mixtures. bioRxiv, doi: https://doi.org/10.1101/408039.
[15] Lang DD, Tang M, Zhou X ( 2018) Qualitative and quantitative molecular construction of plant-pollinator network: Application and prospective. Biodiversity Science, 26, 445-456. (in Chinese with English abstract)
[ 郎丹丹, 唐敏, 周欣 ( 2018) 传粉网络构建的定性定量分子研究: 应用与展望. 生物多样性, 26, 445-456.]
[16] Li HT, Yi TS, Gao LM, Ma PF, Zhang T, Yang JB, Gitzendanner MA, Fritsch PW, Cai J, Luo Y, Wang H, Bank M, Zhang SD, Wang QF, Wang J, Zhang ZR, Fu CN, Yang J, Hollingsworth PM, Chase MW, Soltis DE, Soltis PS, Li DZ ( 2019) Origin of angiosperms and the puzzle of the Jurassic gap. Nature Plants, 5, 461-470.
doi: 10.1038/s41477-019-0421-0
[17] Li HX, Huang XN, Li SG, Zhan AB ( 2019) Environmental DNA (eDNA)-metabarcoding-based early monitoring and warning for invasive species in aquatic ecosystems. Biodiversity Science, 27, 491-504. (in Chinese with English abstract)
[ 李晗溪, 黄雪娜, 李世国, 战爱斌 ( 2019) 基于环境DNA-宏条形码技术的水生生态系统入侵生物的早期监测与预警. 生物多样性, 27, 491-504.]
[18] Li M, Wei TT, Shi BY, Hao XY, Xu HG, Sun HY ( 2019) Biodiversity monitoring of freshwater benthic macroinvertebrates using environmental DNA. Biodiversity Science, 27, 480-490. (in Chinese with English abstract)
[ 李萌, 尉婷婷, 史博洋, 郝希阳, 徐海根, 孙红英 ( 2019) 环境DNA技术在淡水底栖大型无脊椎动物多样性监测中的应用. 生物多样性, 27, 480-490.]
[19] Li YY, Molik DC, Pfrender ME ( 2019) EPPS, a metabarcoding bioinformatics pipeline using Nextflow. Biodiversity Science, 27, 567-575. (in Chinese with English abstract)
[ 李诣远 , Molik DC, Pfrender ME ( 2019) 基于Nextflow构建的宏条形码自动化分析流程EPPS. 生物多样性, 27, 567-575.]
[20] Linnaeus C ( 1758) Systema naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis (in Latin), 10th edn. Laurentius Salvius, Stockholm.
[21] Liu SL ( 2019) DNA barcoding and emerging reference construction and data analysis technologies. Biodiversity Science, 27, 526-533. (in Chinese with English abstract)
[ 刘山林 ( 2019) DNA条形码参考数据集构建和序列分析相关的新兴技术. 生物多样性, 27, 526-533.]
[22] Nie RE, Breeschoten T, Timmermans MJTN, Nadein K, Xue HJ, Bai M, Huang Y, Yang XK, Vogler AP ( 2017) The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes. Cladistics, 34, 113-130.
[23] Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Antolin M, Artiguenave F, Blottiere H, Borruel N, Bruls T, Casellas F, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Forte M, Friss C, van de Guchte M, Guedon E, Haimet F, Jamet A, Juste C, Kaci G, Kleerebezem M, Knol J, Kristensen M, Layec S, Le Roux K, Leclerc M, Maguin E, Melo Minardi R, Oozeer R, Rescigno M, Sanchez N, Tims S, Carlsen T, Varela E, de Vos W, Winogradsky Y, Zoetendal E, Bork P, Ehrlich SD, Wang J ( 2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59-65.
doi: 10.1038/nature08821
[24] Ratnasingham S, Hebert PDN ( 2007) BOLD: The Barcode of Life Data System (www.barcodinglife.org). Molecular Ecology Notes, 7, 355-364.
doi: 10.1111/j.1471-8286.2007.01678.x
[25] Shao XN, Song DZ, Huang QW, Li S, Yao M ( 2019) Fast surveys and molecular diet analysis of carnivores based on fecal DNA and metabarcoding. Biodiversity Science, 27, 543-556. (in Chinese with English abstract)
[ 邵昕宁, 宋大昭, 黄巧雯, 李晟, 姚蒙 ( 2019) 基于粪便DNA及宏条形码技术的食肉动物快速调查及食性分析. 生物多样性, 27, 543-556.]
[26] Shi M, Lin XD, Tian JH, Chen LJ, Chen X, Li CX, Qin XC, Li J, Cao JP, Eden JS, Buchmann J, Wang W, Xu JG, Holmes EC, Zhang YZ ( 2016) Redefining the invertebrate RNA virosphere. Nature, 540, 539-543.
[27] Song F, Li H, Jiang P, Zhou X, Liu J, Sun C, Vogler AP, Cai W ( 2016) Capturing the phylogeny of Holometabola with mitochondrial genome data and Bayesian site-heterogeneous mixture models. Genome Biology and Evolution, 8, 1411-1426.
[28] Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A ( 2015) Structure and function of the global ocean microbiome. Science, 348, 1261359.
doi: 10.1126/science.1261359
[29] Tang M, Zou Y, Su QZ, Zhou X ( 2019) A new perspective on landscape impact in bee populations: Considering the bee gut microbiome. Biodiversity Science, 27, 516-525. (in Chinese with English abstract)
[ 唐敏, 邹怡, 苏秦之, 周欣 ( 2019) 洞察景观环境影响蜜蜂之新视角: 肠道微生物. 生物多样性, 27, 516-525.]
[30] Tang P, Zhu JC, Zheng BY, Wei SJ, Sharkey M, Chen XX, Vogler AP ( 2019) Mitochondrial phylogenomics of the Hymenoptera. Molecular Phylogenetics and Evolution, 131, 8-18.
doi: 10.1016/j.ympev.2018.10.040
[31] Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G ( 2017) A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551, 457-463.
[32] Wang Y, Liu X, Garzón-Orduña IJ, Winterton SL, Yan Y, Aspock U, Aspock H, Yang D ( 2016) Mitochondrial phylogenomics illuminates the evolutionary history of Neuropterida. Cladistics, 33, 617-636.
[33] Woese CR, Fox GE ( 1977) Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proceedings of the National Academy of Sciences, USA, 74, 5088-5090.
doi: 10.1073/pnas.74.11.5088
[34] Xiao L, Estellé J, Kiilerich P, Ramayo-Caldas Y, Xia Z, Feng Q, Liang S, Pedersen AO, Kjeldsen NJ, Liu C, Maguin E, Doré J, Pons N, Le Chatelier E, Prifti E, Li J, Jia H, Liu X, Xu X, Ehrlich SD, Madsen L, Kristiansen K, Rogel-Gaillard C, Wang J ( 2016) A reference gene catalogue of the pig gut microbiome. Nature Microbiology, 1, 16161.
[35] Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, Liu C, Fang Z, Chou J, Glanville J, Hao Q, Kotowska D, Colding C, Licht TR, Wu D, Yu J, Sung JJY, Liang Q, Li J, Jia H, Lan Z, Tremaroli V, Dworzynski P, Nielsen HB, Bäckhed F, Doré J, Le Chatelier E, Ehrlich SD, Lin JC, Arumugam M, Wang J, Madsen L, Kristiansen K ( 2015) A catalog of the mouse gut metagenome. Nature Biotechnology, 33, 1103-1108.
[36] Xiao YQ, Liu C, Xiao L ( 2019) The role of model animals in the study of symbiotic microorganisms. Biodiversity Science, 27, 505-515. (in Chinese with English abstract)
[ 肖雅倩, 刘传, 肖亮 ( 2019) 模式动物在共生微生物研究中的作用. 生物多样性, 27, 505-515.]
[37] Xu YK, Ma Y, Hu XX, Wang J ( 2019) Analysis of prospective microbiology research using third-generation sequencing technology. Biodiversity Science, 27, 534-542. (in Chinese with English abstract)
[ 许亚昆, 马越, 胡小茜, 王军 ( 2019) 基于三代测序技术的微生物组学研究进展. 生物多样性, 27, 534-542.]
[38] Zhang X, Li XA, Su QZ, Cao QN, Li CY, Niu QS, Zheng H ( 2019) A curated 16S rRNA reference database for the classification of honeybee and bumblebee gut microbiota. Biodiversity Science, 27, 557-566. (in Chinese with English abstract)
[ 张雪, 李兴安, 苏秦之, 曹棋钠, 李晨伊, 牛庆生, 郑浩 ( 2019) 用于蜜蜂和熊蜂肠道微生物分类的细菌16S rRNA数据库优化. 生物多样性, 27, 557-566.]
[39] Zheng H, Steele MI, Leonard SP, Motta EVS, Moran NA ( 2018) Honey bees as models for gut microbiota research. Lab Animal, 47, 317-325.
doi: 10.1038/s41684-018-0173-x
[40] Zhou X, Li Y, Liu S, Yang Q, Su X, Zhou L, Tang M, Fu R, Li J, Huang Q ( 2013) Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. GigaScience, 2, 4.
No related articles found!
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed