蚯蚓基因组学的研究进展: 基于全基因组及线粒体基因组

doi:10.17520/biods.2022257

生物多样性 ›› 2022, Vol. 30 ›› Issue (12): 22257. DOI: 10.17520/biods.2022257

所属专题：土壤生物与土壤健康

蚯蚓基因组学的研究进展: 基于全基因组及线粒体基因组

翟俊杰¹^,², 赵慧峰³, 商光申¹^,², 孙振钧¹, 张玉峰³^,^*(), 王兴¹^,²^,^*()

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 接受日期:2022-10-01 出版日期:2022-12-20 发布日期:2022-12-07
通讯作者: *E-mail: qqzyf123@126.com; swwangxing@cau.edu.cn
基金资助:
国家自然科学基金(41371305);国家自然科学基金(31172091)

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

Junjie Zhai¹^,², Huifeng Zhao³, Guangshen Shang¹^,², Zhenjun Sun¹, Yufeng Zhang³^,^*(), Xing Wang¹^,²^,^*()

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:2022-05-11 Accepted:2022-10-01 Online:2022-12-20 Published:2022-12-07
Contact: *E-mail: qqzyf123@126.com; swwangxing@cau.edu.cn

摘要/Abstract

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

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

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

Junjie Zhai, Huifeng Zhao, Guangshen Shang, Zhenjun Sun, Yufeng Zhang, Xing Wang (2022) Advances in earthworm genomics: Based on whole genome and mitochondrial genome. Biodiversity Science, 30, 22257. DOI: 10.17520/biods.2022257.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2022257

https://www.biodiversity-science.net/CN/Y2022/V30/I12/22257

图/表 5

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蚯蚓 Earthworm	基因组大小 Genome length	染色体数量 Number of chromosomes	染色体倍体 Chromosome ploidy	GC含量 GC content (%)	蛋白编码基因数 Number of protein-coding gene	测序组装技术 Sequencing assembly technology	参考文献 References
赤子爱胜蚓 Eisenia foetida	1.05 Gb	22	2	28.6	?	Illumina HiSeq 2000 2 × 100PE	2015
赤子爱胜蚓 E. foetida	1.47 Gb	22	2	40	?	Illumina HiSeq 2500	2018
通俗腔蚓 Metaphire vulgaris	728.6 Mb	41	2	40	?	PromethION Single Molecule Platform, Illumina NovaSeq Sequencing Platform, Hi-C	2020
安德爱胜蚓 Eisenia andrei	1.3 Gb	22	2	35?45	31,817	PacBio三代测序 PacBio RS Platform, Hi-C	2020
皮质远盲蚓 Amynthas corticis	1.2 Gb	42	3	40.34	29,256	PacBio三代测序 PacBio SMRT Sequencing, Hi-C	2021

蚯蚓 Earthworm	基因组大小 Genome length	染色体数量 Number of chromosomes	染色体倍体 Chromosome ploidy	GC含量 GC content (%)	蛋白编码基因数 Number of protein-coding gene	测序组装技术 Sequencing assembly technology	参考文献 References
赤子爱胜蚓 Eisenia foetida	1.05 Gb	22	2	28.6	?	Illumina HiSeq 2000 2 × 100PE	2015
赤子爱胜蚓 E. foetida	1.47 Gb	22	2	40	?	Illumina HiSeq 2500	2018
通俗腔蚓 Metaphire vulgaris	728.6 Mb	41	2	40	?	PromethION Single Molecule Platform, Illumina NovaSeq Sequencing Platform, Hi-C	2020
安德爱胜蚓 Eisenia andrei	1.3 Gb	22	2	35?45	31,817	PacBio三代测序 PacBio RS Platform, Hi-C	2020
皮质远盲蚓 Amynthas corticis	1.2 Gb	42	3	40.34	29,256	PacBio三代测序 PacBio SMRT Sequencing, Hi-C	2021

分类单元 Taxa	GenBank登录号 GenBank accession no.	参考文献 References
正蚓科 Lumbricidae
Aporrectodea caliginosa	CM035405.1	未发表 Unpublished
A. rosea	NC_046733.1	2019
A. tuberculata	OL840316?OL840317, OM687883?OM687886	2022
A. trapezoides	OM687887	2022
Bimastos parvus	MZ857199.1	2021
Dendrobaena octaedra	MZ857197.1	2021
Eisenia andrei	MZ857198.1	2021
E. nordenskioldi	MZ857200.1 OL840314?OL840315 OM687887?OM687890	2021 2022 2022
Lumbricus rubellus	MN102127.1	2019
L. terrestris	NC_001673.1	1995
Octolasion tyrtaeum	MZ857201.1	2021
Pontoscolex corethrurus	NC_034783.1	未发表 Unpublished
巨蚓科 Megascolecidae
Amynthas aspergillus	NC_025292.1	2016b
A. carnosus	KT429008.1	2016c
A. corticis	KM199290.1	2015
A. cucullatus	KT429012.1	2016c
A. gracilis	KP688582.1	2015
A. hupeiensis	KT429009.1	2016c
A. instabilis	KT429007.1	2016c
A. jiriensis	NC_029879.1	2017
A. longisiphonus	KM199289.1	2015
A. moniliatus	KT429020.1	2016c
A. morrisi	KT429011.1	2016c
A. pectiniferus	KT429018.1	2016c
A. redactus	KT429010.1	2016c
A. robustus	KT429019.1	2016c
A. rongshuiensis	KT429014.1	2016c
A. seungpanensis	OL321943.1	未发表 Unpublished
A. spatiosus	KT429013.1	2016c
A. triastriatus	KT429016.1	2016c
A. yunoshimensis	LC573969.1	2021
Duplodicodrilus schmardae	KT429015.1	2016c
Metaphire californica	KP688581.1	2015
M. guillelmi	KT429017.1	2016c
M. hilgendorfi	LC573968.1	2021
M. vulgaris	NC_023836.1	2016a
Perionyx excavatus	NC_009631.1	未发表 Unpublished
Tonoscolex birmanicus	KF425518.1	2015
链胃蚓科 Moniligastridae
Drawida gisti	NC_058285.1	2020
D. japonica	KM199288.1	2016c
D. ghilarovi	OL840312?OL840313	2022

分类单元 Taxa	GenBank登录号 GenBank accession no.	参考文献 References
正蚓科 Lumbricidae
Aporrectodea caliginosa	CM035405.1	未发表 Unpublished
A. rosea	NC_046733.1	2019
A. tuberculata	OL840316?OL840317, OM687883?OM687886	2022
A. trapezoides	OM687887	2022
Bimastos parvus	MZ857199.1	2021
Dendrobaena octaedra	MZ857197.1	2021
Eisenia andrei	MZ857198.1	2021
E. nordenskioldi	MZ857200.1 OL840314?OL840315 OM687887?OM687890	2021 2022 2022
Lumbricus rubellus	MN102127.1	2019
L. terrestris	NC_001673.1	1995
Octolasion tyrtaeum	MZ857201.1	2021
Pontoscolex corethrurus	NC_034783.1	未发表 Unpublished
巨蚓科 Megascolecidae
Amynthas aspergillus	NC_025292.1	2016b
A. carnosus	KT429008.1	2016c
A. corticis	KM199290.1	2015
A. cucullatus	KT429012.1	2016c
A. gracilis	KP688582.1	2015
A. hupeiensis	KT429009.1	2016c
A. instabilis	KT429007.1	2016c
A. jiriensis	NC_029879.1	2017
A. longisiphonus	KM199289.1	2015
A. moniliatus	KT429020.1	2016c
A. morrisi	KT429011.1	2016c
A. pectiniferus	KT429018.1	2016c
A. redactus	KT429010.1	2016c
A. robustus	KT429019.1	2016c
A. rongshuiensis	KT429014.1	2016c
A. seungpanensis	OL321943.1	未发表 Unpublished
A. spatiosus	KT429013.1	2016c
A. triastriatus	KT429016.1	2016c
A. yunoshimensis	LC573969.1	2021
Duplodicodrilus schmardae	KT429015.1	2016c
Metaphire californica	KP688581.1	2015
M. guillelmi	KT429017.1	2016c
M. hilgendorfi	LC573968.1	2021
M. vulgaris	NC_023836.1	2016a
Perionyx excavatus	NC_009631.1	未发表 Unpublished
Tonoscolex birmanicus	KF425518.1	2015
链胃蚓科 Moniligastridae
Drawida gisti	NC_058285.1	2020
D. japonica	KM199288.1	2016c
D. ghilarovi	OL840312?OL840313	2022

蚯蚓基因组学的研究进展: 基于全基因组及线粒体基因组

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

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