Mitochondrial genome data of three aphid species

doi:10.17520/biods.2022204

Abstract

Abstract:

The complete mitochondrial genomes (mitogenomes) have been widely used in the studies of molecular evolution, genomics and phylogeny. Aphids are important agricultural and forestry pests. Considering the reported complete mitogenomes of aphids are still limited, it will be of great value to obtain more aphid mitogenome data for related researches. This paper reports the complete mitogenome sequences of three aphid species, Greenidea ficicola, Aphis aurantii and Mindarus keteleerifoliae. The data of their detailed annotation, their gene sequence and gene structure, and the codon usage are also presented. These data can benefit future researches such as insect phylogenetic relationships, population divergence patterns as well as insect pest control.

10.17520/biods.2022204.T0002

Database/Dataset Profile

Title	Mitochondrial genome data of three aphid species
Authors	Congcong Lu, Qian Liu, Xiaolei Huang
Corresponding author	Xiaolei Huang (huangxl@fafu.edu.cn)
Time range	2015-2017
Geographical scope	Quanzhou (Fujian), Fuzhou (Fujian)
File size	48 MB
Data format	.fasta, .xlsx, *.tif
Data link	http://www.dataopen.info/home/datafile/index/id/252 http://doi.org/10.24899/do.202204004 https://www.biodiversity-science.net/fileup/1005-0094/DATA/2022204.zip
Database/Dataset composition	The dataset consists of 7 data files in total, containing 3 sequence files, with a data volume of 50 KB; one excel data files, with a data volume of 37 KB; and 3 picture files, with a data volume of 47.4 MB.

Key words: aphids, mitochondrial genome, gene annotation, genomic data

Congcong Lu, Qian Liu, Xiaolei Huang. Mitochondrial genome data of three aphid species[J]. Biodiv Sci, 2022, 30(7): 22204.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.biodiversity-science.net/EN/10.17520/biods.2022204

https://www.biodiversity-science.net/EN/Y2022/V30/I7/22204

Figures/Tables 3

References 23

[1]	Al Arab M, Zu Siederdissen CH, Tout K, Sahyoun AH, Stadler PF, Bernt M (2017) Accurate annotation of protein-coding genes in mitochondrial genomes. Molecular Phylogenetics and Evolution, 106, 209-216. DOI URL
[2]	Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF (2013) MITOS: Improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69, 313-319. DOI URL
[3]	Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Research, 27, 1767-1780. PMID
[4]	Burger G, Gray MW, Lang BF (2003) Mitochondrial genomes: Anything goes. Trends in Genetics, 19, 709-716. DOI URL
[5]	Chen J, Wang Y, Jiang LY, Qiao GX (2017) Mitochondrial genome sequences effectively reveal deep branching events in aphids (Insecta: Hemiptera: Aphididae). Zoologica Scripta, 46, 706-717. DOI URL
[6]	Dierckxsens N, Mardulyn P, Smits G (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, 45, e18.
[7]	Favret C (2022) Aphid species file, Version 5.0/5.0. http://Aphid.SpeciesFile.org. (accessed on 2022-01-24)
[8]	Grant JR, Stothard P (2008) The CGView Server: A comparative genomics tool for circular genomes. Nucleic Acids Research, 36, W181-W184. DOI URL
[9]	Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870-1874. DOI URL
[10]	Laslett D, Canbäck B (2008) ARWEN: A program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics, 24, 172-175. PMID
[11]	Li H, Leavengood Jr JM, Chapman EG, Burkhardt D, Song F, Jiang P, Liu JP, Zhou XG, Cai WZ (2017) Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs. Proceedings of the Royal Society B: Biological Sciences, 284, 20171223.
[12]	Liu YQ, Li H, Song F, Zhao YS, Wilson JJ, Cai WZ (2019) Higher-level phylogeny and evolutionary history of Pentatomomorpha (Hemiptera: Heteroptera) inferred from mitochondrial genome sequences. Systematic Entomology, 44, 810-819. DOI URL
[13]	Lorenz R, Bernhart SH, Zu Siederdissen CH, Tafer H, Flamm C, Stadler PF, Hofacker IL (2011) ViennaRNA Package 2.0. Algorithms for Molecular Biology, 6, 26.
[14]	Ma C, Yang P, Jiang F, Chapuis MP, Shali Y, Sword GA, Kang L (2012) Mitochondrial genomes reveal the global phylogeography and dispersal routes of the migratory locust. Molecular Ecology, 21, 4344-4358. DOI URL
[15]	Mueller RL (2006) Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis. Systematic Biology, 55, 289-300. DOI URL
[16]	Nass MMK, Nass S (1963) Intramitochondrial fibers with DNA characteristics: I. Fixation and electron staining reactions. The Journal of Cell Biology, 19, 593-611. DOI URL
[17]	Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng QD, Wortman J, Young SK, Earl AM (2014) Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE, 9, e112963. DOI URL
[18]	Wang Y, Huang XL, Qiao GX (2014) The complete mitochondrial genome of Cervaphis quercus (Insecta: Hemiptera: Aphididae: Greenideinae). Insect Science, 21, 278-290. DOI URL
[19]	Wilson AC, Cann RL, Carr SM, George M, Gyllensten UB, Helm-Bychowski KM, Higuchi RG, Palumbi SR, Prager EM, Sage RD, Stoneking M (1985) Mitochondrial DNA and two perspectives on evolutionary genetics. Biological Journal of the Linnean Society, 26, 375-400. DOI URL
[20]	Wolstenholme DR (1992) Animal mitochondrial DNA: Structure and evolution. International Review of Cytology, 141, 173-216.
[21]	Zhang B, Ma C, Edwards O, Fuller S, Kang L (2014) The mitochondrial genome of the Russian wheat aphid Diuraphis noxia: Large repetitive sequences between trnE and trnF in aphids. Gene, 533, 253-260. DOI PMID
[22]	Zhang D, Gao FL, Jakovlić I, Zou H, Zhang J, Li WX, Wang GT (2020) PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources, 20, 348-355. DOI PMID
[23]	Zhang H, Liu Q, Lu CC, Deng J, Huang XL (2021) The first complete mitochondrial genome of Lachninae species and comparative genomics provide new insights into the evolution of gene rearrangement and the repeat region. Insects, 12, 55. DOI URL

亚科 Subfamily	属数 Number of genera	物种数 Number of species	线粒体基因组 Number of mitogenomes	具有线粒体基因组的物种 Number of species with mitogenome
短痣蚜亚科 Anoeciinae	4	32	-	-
蚜亚科 Aphidinae	283	3,156	59	25
波罗的毛蚜亚科 Baltichaitophorinae	2	2	-	-
长角斑蚜亚科 Calaphidinae	76	424	2	2
毛蚜亚科 Chaitophorinae	13	181	1	1
镰管蚜亚科 Drepanosiphinae	13	60	-	-
绵蚜亚科 Eriosomatinae	65	402	39	18
毛管蚜亚科 Greenideinae	18	189	11	6
扁蚜亚科 Hormaphidinae	47	236	14	6
以斑蚜亚科 Israelaphidinae	1	4	-	-
大蚜亚科 Lachninae	19	420	5	3
蜥蜴斑蚜亚科 Lizeriinae	5	44	-	-
粗腿蚜亚科 Macropodaphidinae	1	7	-	-
纩蚜亚科 Mindarinae	2	18	1	1
新叶蚜亚科 Neophyllaphidinae	3	21	-	-
平翅绵蚜亚科 Phloeomyzinae	5	5	-	-
叶蚜亚科 Phyllaphidinae	11	28	-	-
翅斑蚜亚科 Pterastheniinae	2	5	-	-
针蚜亚科 Spicaphidinae	2	16	-	-
台斑蚜亚科 Taiwanaphidinae	1	14	-	-
塔叶蚜亚科 Tamaliinae	1	6	-	-
群蚜亚科 Thelaxinae	6	21	-	-
总计 Total	580	5,291	132	62

亚科 Subfamily	属数 Number of genera	物种数 Number of species	线粒体基因组 Number of mitogenomes	具有线粒体基因组的物种 Number of species with mitogenome
短痣蚜亚科 Anoeciinae	4	32	-	-
蚜亚科 Aphidinae	283	3,156	59	25
波罗的毛蚜亚科 Baltichaitophorinae	2	2	-	-
长角斑蚜亚科 Calaphidinae	76	424	2	2
毛蚜亚科 Chaitophorinae	13	181	1	1
镰管蚜亚科 Drepanosiphinae	13	60	-	-
绵蚜亚科 Eriosomatinae	65	402	39	18
毛管蚜亚科 Greenideinae	18	189	11	6
扁蚜亚科 Hormaphidinae	47	236	14	6
以斑蚜亚科 Israelaphidinae	1	4	-	-
大蚜亚科 Lachninae	19	420	5	3
蜥蜴斑蚜亚科 Lizeriinae	5	44	-	-
粗腿蚜亚科 Macropodaphidinae	1	7	-	-
纩蚜亚科 Mindarinae	2	18	1	1
新叶蚜亚科 Neophyllaphidinae	3	21	-	-
平翅绵蚜亚科 Phloeomyzinae	5	5	-	-
叶蚜亚科 Phyllaphidinae	11	28	-	-
翅斑蚜亚科 Pterastheniinae	2	5	-	-
针蚜亚科 Spicaphidinae	2	16	-	-
台斑蚜亚科 Taiwanaphidinae	1	14	-	-
塔叶蚜亚科 Tamaliinae	1	6	-	-
群蚜亚科 Thelaxinae	6	21	-	-
总计 Total	580	5,291	132	62

物种 Species	样品编号 Sample number	亚科 Subfamily	采集时间 Date of collection	采集地点 Locality of collection	寄主植物 Host plant
榕毛管蚜 Greenidea ficicola	20150502-4	毛管蚜亚科 Greenideinae	2015/05/02	福建泉州 Quanzhou, Fujian	高山榕 Ficus altissima
橘二叉蚜 Aphis aurantii	20160327-4	蚜亚科 Aphidinae	2016/03/27	福建福州 Fuzhou, Fujian	山茶 Camellia japonica
油杉纩蚜 Mindarus keteleerifoliae	20170609-6	纩蚜亚科 Mindarinae	2017/06/09	福建福州 Fuzhou, Fujian	油杉 Keteleeria fortunei

物种 Species	样品编号 Sample number	亚科 Subfamily	采集时间 Date of collection	采集地点 Locality of collection	寄主植物 Host plant
榕毛管蚜 Greenidea ficicola	20150502-4	毛管蚜亚科 Greenideinae	2015/05/02	福建泉州 Quanzhou, Fujian	高山榕 Ficus altissima
橘二叉蚜 Aphis aurantii	20160327-4	蚜亚科 Aphidinae	2016/03/27	福建福州 Fuzhou, Fujian	山茶 Camellia japonica
油杉纩蚜 Mindarus keteleerifoliae	20170609-6	纩蚜亚科 Mindarinae	2017/06/09	福建福州 Fuzhou, Fujian	油杉 Keteleeria fortunei