Biodiv Sci ›› 2022, Vol. 30 ›› Issue (12): 22257. DOI: 10.17520/biods.2022257
Special Issue: 土壤生物与土壤健康
• Reviews • Previous Articles Next Articles
Junjie Zhai1,2, Huifeng Zhao3, Guangshen Shang1,2, Zhenjun Sun1, Yufeng Zhang3,*(), Xing Wang1,2,*()
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
Junjie Zhai, Huifeng Zhao, Guangshen Shang, Zhenjun Sun, Yufeng Zhang, Xing Wang. Advances in earthworm genomics: Based on whole genome and mitochondrial genome[J]. Biodiv Sci, 2022, 30(12): 22257.
Fig. 1 Number of published papers on earthworm genomics. Literature source: Web of Science Core Collection; Publication years: 1995?2022; Search keywords: Earthworm, Genome.
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 |
Table 1 Basic information of whole genome sequencing in earthworm
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 |
Table 2 Taxonomic distribution of earthworm species based on mitochondriai genomes
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 |
Fig. 3 The mitochondrial genome of Eisenia nordenskioldi. Cyan color represents protein-coding genes, red color represents transporter RNA, orange color represents ribosomal RNA, and blue color represents the control region.
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