[an error occurred while processing this directive] [an error occurred while processing this directive] [an error occurred while processing this directive]
[an error occurred while processing this directive]

生物多样性 >

2022 , Vol. 30 >Issue 12: 22257

DOI: https://doi.org/10.17520/biods.2022257

综述

蚯蚓基因组学的研究进展: 基于全基因组及线粒体基因组

展开
  • 1.中国农业大学资源与环境学院, 北京 100193
    2.生物多样性与有机农业北京市重点实验室, 北京 100193
    3.廊坊师范学院河北省动物多样性重点实验室, 河北廊坊 065000

收稿日期: 2022-05-11

  录用日期: 2022-10-01

  网络出版日期: 2022-12-07

基金资助

国家自然科学基金(41371305);国家自然科学基金(31172091)

收起

Advances in earthworm genomics: Based on whole genome and mitochondrial genome

Expand
  • 1. College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193
    2. Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing 100193
    3. Hebei Key Laboratory of Animal Diversity, Langfang Normal University, Langfang, Hebei 065000

Received date: 2022-05-11

  Accepted date: 2022-10-01

  Online published: 2022-12-07

Fold

摘要

蚯蚓被喻为土壤中的“生态系统工程师”, 具有高度的多样性且在全世界都有分布, 被用作土壤健康的指示生物。蚯蚓具有极强的环境适应能力, 在不断适应的过程中促进了自身基因组的进化。本文对近年来蚯蚓全基因组以及线粒体基因组的研究进展进行了综述。蚯蚓全基因组的测序、拼装和分析为研究蚯蚓生态学、污染物对蚯蚓致毒的分子机制、免疫防御的分子机制、蚯蚓再生的分子机制等奠定基础。而线粒体基因组多应用于蚯蚓分子系统发育方面的研究, 目前已有多种蚯蚓通过线粒体基因组测序完成了物种的鉴定。本文建议今后重点开展以下几方面的研究: (1)针对现有的4种蚯蚓全基因组测序结果, 进一步进行比较基因组学、进化基因组学和功能基因组学的研究。(2)完善不同种蚯蚓的基因文库和表达序列标签。(3)建立线粒体基因组、全基因组与蚯蚓物种多样性的关联分析。

关键词： 蚯蚓; 基因组学; 全基因组; 线粒体基因组; 蚯蚓多样性

本文引用格式

翟俊杰, 赵慧峰, 商光申, 孙振钧, 张玉峰, 王兴 . 蚯蚓基因组学的研究进展: 基于全基因组及线粒体基因组[J]. 生物多样性, 2022 , 30(12) : 22257 . DOI: 10.17520/biods.2022257

Abstract

Background & Aims: Earthworms, which are known as the ecosystem engineers of the soil, are highly diverse and distributed worldwide. They are used as indicators of soil health. They are highly adaptable to their environment, and their genomes have evolved through the process of adaptation. In this paper, recent research progress of the whole genome and mitochondrial genome of the earthworms are reviewed.
Progresses: The sequencing, assembly and analysis of earthworm genome lay a foundation for the study of earthworm ecology, molecular toxicity mechanism of pollutants to earthworm, molecular mechanism of immune defense, earthworm regeneration and so on. The mitochondrial genome is mostly used in the study of molecular phylogeny of earthworms. Currently, various types of earthworm species have been identified based on mitochondrial genome sequencing.
Prospects: This paper highlights the following aspects of research that should be focused in future studies: (1) Carry out the studies on comparative genomics, evolutionary genomics and functional genomics using the existing whole genome sequencing results of the four species earthworms; (2) Improve the gene libraries and expressed sequence tags of different species of earthworms; (3) Strengthen the association analysis between mitochondrial genome and whole genome with the species diversity of earthworm.

Key words： earthworm; genomics; whole genome; mitochondrial genome; earthworm diversity

参考文献

[1] Ahmed N, Al-Mutairi KA (2022) Earthworms effect on microbial population and soil fertility as well as their interaction with agriculture practices. Sustainability, 14, 7803.
[2] Anderson C, Cunha L, Sechi P, Kille P, Spurgeon D (2017) Genetic variation in populations of the earthworm, Lumbricus rubellus, across contaminated mine sites. BMC Genetics, 18, 97.
[3] Andrews KR, Good JM, Miller MR, Luikart G, Hohenlohe PA (2016) Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics, 17, 81-92.
[4] Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE, 3, e3376.
[5] Bertrand M, Barot S, Blouin M, Whalen J, Oliveira T, Roger-Estrade J (2015) Earthworm services for cropping systems. A review. Agronomy for Sustainable Development, 35, 553-567.
[6] Bhambri A, Dhaunta N, Patel SS, Hardikar M, Bhatt A, Srikakulam N, Shridhar S, Vellarikkal S, Pandey R, Jayarajan R, Verma A, Kumar V, Gautam P, Khanna Y, Khan JA, Fromm B, Peterson KJ, Scaria V, Sivasubbu S, Pillai B (2018) Large scale changes in the transcriptome of Eisenia fetida during regeneration. PLoS ONE, 13, e0204234.
[7] Bhat SA, Singh J, Vig AP (2018) Earthworms as organic waste managers and biofertilizer producers. Waste and Biomass Valorization, 9, 1073-1086.
[8] Boore JL, Brown WM (1995) Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris. Genetics, 141, 305-319.
[9] Bozorgi F, Seiedy M, Malek M, Aira M, Pérez-Losada M, Domínguez J (2019) Multigene phylogeny reveals a new Iranian earthworm genus (Lumbricidae: Philomontanus) with three new species. PLoS ONE, 14, e0208904.
[10] Conrado AC, Arruda H, Stanton DWG, James SW, Kille P, Brown G, Silva E, Dupont L, Taheri S, Morgan AJ, Sim?es N, Rodrigues A, Montiel R, Cunha L (2017) The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning. ZooKeys, 688, 1-13.
[11] Csuzdi CS (2012) Earthworm species, a searchable database. Opuscula Zoologica Budapest, 43(41), 97-99.
[12] Darwin C (1892) The Formation of Vegetable Mould, through the Action of Worms: With Observations on Their Habits. John Murray, London.
[13] Ding SY, Lin XT, He SE (2019) Earthworms: A source of protein. Journal of Food Science and Engineering, 9, 159-170.
[14] Giska I, Sechi P, Babik W (2015) Deeply divergent sympatric mitochondrial lineages of the earthworm Lumbricus rubellus are not reproductively isolated. BMC Evolutionary Biology, 15, 217.
[15] Gong P, Perkins EJ (2016) Earthworm toxicogenomics: A renewed genome-wide quest for novel biomarkers and mechanistic insights. Applied Soil Ecology, 104, 12-24.
[16] Hong Y, Kim MJ, Wang AR, Kim I (2017) Complete mitochondrial genome of the earthworm, Amynthas jiriensis (Clitellata: Megascolecidae). Mitochondrial DNA Part A, 28, 163-164.
[17] Jiang JB, Qiu JP (2018) Origin and evolution of earthworms belonging to the family Megascolecidae in China. Biodiversity Science, 26, 1074-1082. (in Chinese with English abstract)
[17] [ 蒋际宝, 邱江平 (2018) 中国巨蚓科蚯蚓的起源与演化. 生物多样性, 26, 1074-1082.]
[18] Jin F, Zhou ZL, Guo Q, Liang ZW, Yang RY, Jiang JB, He YL, Zhao Q, Zhao Q (2020) High-quality genome assembly of Metaphire vulgaris. PeerJ, 8, e10313.
[19] Li Y, Tang H, Hu Y, Wang X, Ai X, Tang L, Matthew C, Cavanagh J, Qiu J (2016) Enrofloxacin at environmentally relevant concentrations enhances uptake and toxicity of cadmium in the earthworm Eisenia fetida in farm soils. Journal of Hazardous Materials, 308, 312-320.
[20] Li Y, Wang X, Sun Z (2020) Ecotoxicological effects of petroleum-contaminated soil on the earthworm Eisenia fetida. Journal of Hazardous Materials, 393, 122384.
[21] Liu C, Wang X, Tian JB, Ma PY, Meng FX, Zhang Q, Yu BF, Guo R, Liu ZZ, Wang HL, Xie J, Cheng NL, Wang JH, Niu B, Sun GQ (2019) Construction of a cDNA library and preliminary analysis of the expressed sequence tags of the earthworm Eisenia fetida (Savigny, 1826). Molecular Medicine Reports, 19, 2537-2550.
[22] Liu CQ, Liu D, Guo Y, Lu TF, Li XC, Zhang MH, Ma JZ, Ma YH, Guan WJ (2013) Construction of a full-length enriched cDNA library and preliminary analysis of expressed sequence tags from Bengal tiger Panthera Tigris Tigris. International Journal of Molecular Sciences, 14, 11072-11083.
[23] Liu HY, Xu N, Zhang QZ, Wang GB, Xu HM, Ruan HH (2020) Characterization of the complete mitochondrial genome of Drawida gisti (Metagynophora, Moniligastridae) and comparison with other Metagynophora species. Genomics, 112, 3056-3064.
[24] Liu HY, Zhang YF, Xu W, Fang Y, Ruan HH (2021) Characterization of five new earthworm mitogenomes (Oligochaeta: Lumbricidae): Mitochondrial phylogeny of Lumbricidae. Diversity, 13, 580.
[25] Liu T, Chen XY, Gong X, Lubbers IM, Jiang YY, Feng W, Li XP, Whalen JK, Bonkowski M, Griffiths BS, Hu F, Liu MQ (2019) Earthworms coordinate soil biota to improve multiple ecosystem functions. Current Biology, 29, 3420-3429.
[26] Marchán DF, Deca?ns T, Domínguez J, Novo M (2022) Perspectives in earthworm molecular phylogeny: Recent advances in Lumbricoidea and standing questions. Diversity, 14, 30.
[27] Marchán DF, Fernandez R, de Sosa I, Díaz Cosín DJ, Novo M (2017) Pinpointing cryptic borders: Fine-scale phylogeography and genetic landscape analysis of the Hormogaster elisae complex (Oligochaeta, Hormogastridae). Molecular Phylogenetics and Evolution, 112, 185-193.
[28] Marchán DF, Fernández R, Domínguez J, Díaz Cosín DJ, Novo M (2020a) Genome-informed integrative taxonomic description of three cryptic species in the earthworm genus Carpetania (Oligochaeta, Hormogastridae). Systematics and Biodiversity, 18, 203-215.
[29] Marchán DF, Novo M, Sánchez N, Domínguez J, Díaz Cosín DJ, Fernández R (2020b) Local adaptation fuels cryptic speciation in terrestrial annelids. Molecular Phylogenetics and Evolution, 146, 106767.
[30] Medina-Sauza RM, álvarez-Jiménez M, Delhal A, Reverchon F, Blouin M, Guerrero-Analco JA, Cerdán CR, Guevara R, Villain L, Barois I (2019) Earthworms building up soil microbiota, a review. Frontiers in Environmental Science, 7, 81.
[31] Parolini M, Ganzaroli A, Bacenetti J (2020) Earthworm as an alternative protein source in poultry and fish farming: Current applications and future perspectives. Science of the Total Environment, 734, 139460.
[32] Paul S, Arumugaperumal A, Rathy R, Ponesakki V, Arunachalam P, Sivasubramaniam S (2018) Data on genome annotation and analysis of earthworm Eisenia fetida. Data in Brief, 20, 525-534.
[33] Pérez-Losada M, Ricoy M, Marshall JC, Domínguez J (2009) Phylogenetic assessment of the earthworm Aporrectodea caliginosa species complex (Oligochaeta: Lumbricidae) based on mitochondrial and nuclear DNA sequences. Molecular Phylogenetics and Evolution, 52, 293-302.
[34] Phillips HRP, Guerra CA, Bartz MLC, Briones MJI, Brown G, Crowther TW, Ferlian O, Gongalsky KB, van den Hoogen J, Krebs J, Orgiazzi A, Routh D, Schwarz B, Bach EM, Bennett JM, Brose U, Deca?ns T, K?nig-Ries B, Loreau M, Mathieu J, Mulder C, van der Putten WH, Ramirez KS, Rillig MC, Russell D, Rutgers M, Thakur MP, de Vries FT, Wall DH, Wardle DA, Arai M, Ayuke FO, Baker GH, Beauséjour R, Bedano JC, Birkhofer K, Blanchart E, Blossey B, Bolger T, Bradley RL, Callaham MA, Capowiez Y, Caulfield ME, Choi A, Crotty FV, Crumsey JM, Dávalos A, Diaz Cosin DJ, Dominguez A, Duhour AE, van Eekeren N, Emmerling C, Falco LB, Fernández R, Fonte SJ, Fragoso C, Franco ALC, Fugère M, Fusilero AT, Gholami S, Gundale MJ, López MG, Hackenberger DK, Hernández LM, Hishi T, Holdsworth AR, Holmstrup M, Hopfensperger KN, Lwanga EH, Huhta V, Hurisso TT, Iannone BV III, Iordache M, Joschko M, Kaneko N, Kanianska R, Keith AM, Kelly CA, Kernecker ML, Klaminder J, Koné AW, Kooch Y, Kukkonen ST, Lalthanzara H, Lammel DR, Lebedev IM, Li YQ, Jesus Lidon JB, Lincoln NK, Loss SR, Marichal R, Matula R, Moos JH, Moreno G, Morón-Ríos A, Muys B, Neirynck J, Norgrove L, Novo M, Nuutinen V, Nuzzo V, Pansu J, Paudel S, Pérès G, Pérez-Camacho L, Pi?eiro R, Ponge JF, Rashid MI, Rebollo S, Rodeiro-Iglesias J, Rodríguez Má, Roth AM, Rousseau GX, Rozen A, Sayad E, van Schaik L, Scharenbroch BC, Schirrmann M, Schmidt O, Schr?der B, Seeber J, Shashkov MP, Singh J, Smith SM, Steinwandter M, Talavera JA, Trigo D, Tsukamoto J, Vanek SJ, Virto I, Wackett AA, Warren MW, Wehr NH, Whalen JK, Wironen MB, Wolters V, Zenkova IV, Zhang WX, Cameron EK, Eisenhauer N,Mujeeb Rahman P (2019) Global distribution of earthworm diversity. Science, 366, 480-485.
[35] Pirooznia M, Gong P, Guan X, Inouye LS, Yang K, Perkins EJ, Deng YP (2007) Cloning, analysis and functional annotation of expressed sequence tags from the earthworm Eisenia fetida. BMC Bioinformatics, 8, S7.
[36] Rajesh D, Anant S (2020) Eisenia fetida and Eisenia andrei delimitation by automated barcode gap discovery and neighbor-joining analyses: A review. Journal of Applied Biology & Biotechnology, 8, 93-100.
[37] Seto A, Endo H, Minamiya Y, Matsuda M (2021) The complete mitochondrial genome sequences of Japanese earthworms Metaphire hilgendorfi and Amynthas yunoshimensis (Clitellata: Megascolecidae). Mitochondrial DNA Part B, Resources, 6, 965-967.
[38] Shao Y, Wang XB, Zhang JJ, Li ML, Wu SS, Ma XY, Wang X, Zhao HF, Li Y, Zhu HH, Irwin DM, Wang DP, Zhang GJ, Ruan J, Wu DD (2020) Genome and single-cell RNA-sequencing of the earthworm Eisenia andrei identifies cellular mechanisms underlying regeneration. Nature Communications, 11, 2656.
[39] Shekhovtsov SV, Efremov YR, Poluboyarova TV, Peltek SE (2021) Variation in nuclear genome size within the Eisenia nordenskioldi complex (Lumbricidae, Annelida). Vavilov Journal of Genetics and Breeding, 25, 647-651.
[40] Shekhovtsov SV, Golovanova EV, Ershov NI, Poluboyarova TV, Berman DI, Bulakhova NA, Szederjesi T, Peltek SE (2020) Phylogeny of the Eisenia nordenskioldi complex based on mit Eisenia nordenskioldi complex based on mitochondrial genomes. European Journal of Soil Biology, 96, 103137.
[41] Shekhovtsov SV, Golovanova EV, Peltek SE (2016) Mitochondrial DNA variation in Eisenia n. nordenskioldi (Lumbricidae) in Europe and Southern Urals. Mitochondrial DNA Part A, 27, 4643-4645.
[42] Shekhovtsov SV, Peltek SE (2019) The complete mitochondrial genome of Aporrectodea rosea (Annelida: Lumbricidae). Mitochondrial DNA Part B, 4, 1752-1753.
[43] Shi ZM, Tang ZW, Wang CY (2017) A brief review and evaluation of earthworm biomarkers in soil pollution assessment. Environmental Science and Pollution Research, 24, 13284-13294.
[44] Sinha RK, Chauhan K, Valani D, Chandran V, Soni BK, Patel V (2010) Earthworms: Charles Darwin’s ‘unheralded soldiers of mankind’: Protective & productive for man & environment. Journal of Environmental Protection, 1, 251-260.
[45] Velki M, E?imovi? S (2017) Important issues in ecotoxicological investigations using earthworms. Reviews of Environmental Contamination and Toxicology, 239, 157-184.
[46] Wang AR, Hong Y, Win TM, Kim I (2015) Complete mitochondrial genome of the Burmese giant earthworm, Tonoscolex birmanicus (Clitellata: Megascolecidae). Mitochondrial DNA, 26, 467-468.
[47] Wang X, Zhang Y, Zhang YF, Kang MM, Li YB, James SW, Yang Y, Bi YM, Jiang H, Zhao Y, Sun ZJ (2021) Amynthas corticis genome reveals molecular mechanisms behind global distribution. Communications Biology, 4, 135.
[48] Yuan Z, Jiang J, Dong Y, Zhao Q, Sun J, Qiu J (2020) Unearthing the genetic divergence and gene flow of the earthworm Amynthas_YN 2017 sp. (Oligochaeta: Megascolecidae) populations based on restriction site-associated DNA sequencing. European Journal of Soil Biology, 99, 103210.
[49] Zhang LL, Jiang JB, Dong Y, Qiu JP (2015) Complete mitochondrial genome of four pheretimoid earthworms (Clitellata: Oligochaeta) and their phylogenetic reconstruction. Gene, 574, 308-316.
[50] Zhang LL, Jiang JB, Dong Y, Qiu JP (2016a) Complete mitochondrial genome of a pheretimoid earthworm Metaphire vulgaris (Oligochaeta: Megascolecidae). Mitochondrial DNA Part A, DNA Mapping, Sequencing, and Analysis, 27, 297-298.
[51] Zhang LL, Jiang JB, Dong Y, Qiu JP (2016b) Complete mitochondrial genome of an Amynthas earthworm, Amynthas aspergillus (Oligochaeta: Megascolecidae). Mitochondrial DNA Part A, DNA Mapping, Sequencing, and Analysis, 27, 1876-1877.
[52] Zhang LL, Sechi P, Yuan ML, Jiang JB, Dong Y, Qiu JP (2016c) Fifteen new earthworm mitogenomes shed new light on phylogeny within the Pheretima complex. Scientific Reports, 6, 20096.
[53] Zhang QZ, Liu HY, Zhang YF, Ruan HH (2019) The complete mitochondrial genome of Lumbricus rubellus (Oligochaeta, Lumbricidae) and its phylogenetic analysis. Mitochondrial DNA Part B, Resources, 4, 2677-2678.
[54] Zhang YF, Ganin GN, Atopkin DM, Wu DH (2020) Earthworm Drawida (Moniligastridae) molecular phylogeny and diversity in Far East Russia and Northeast China. The European Zoological Journal, 87, 180-191.
[55] Zhang YF, Zhang YM, Wu H, Li CS, Aspe NM, Wu DH (2022) Patterns of genetic variation in the Eisenia nordenskioldi complex (Oligochaeta: Lumbricidae) along an elevation gradient in Northern China. Diversity, 14, 35.
[56] Zhao HF, Fan SH, Aspe NM, Feng LC, Zhang YF (2022) Characterization of 15 earthworm mitogenomes from Northeast China and its phylogenetic implication (Oligochaeta: Lumbricidae, Moniligastridae). Diversity, 14, 714.
[57] Zwarycz AS, Nossa CW, Putnam NH, Ryan JF (2015) Timing and scope of genomic expansion within Annelida: Evidence from homeoboxes in the genome of the earthworm Eisenia fetida. Genome Biology and Evolution, 8, 271-281.
Options
文章导航

/

〈 〉

[an error occurred while processing this directive]