High-quality genome assembly of <i>Metaphire vulgaris</i>

Jin, Feng; Zhou, Zhaoli; Guo, Qi; Liang, Zhenwen; Yang, Ruoyu; Jiang, Jibao; He, Yanlin; Zhao, Qi; Zhao, Qiang

doi:10.7717/peerj.10313

Cited by 11 publications

(9 citation statements)

References 46 publications

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“…Of these, 38 are members of the ANTP/HOXL class, which is involved in embryonic development. This number is comparable to that found in the recently assembled high-quality genome of Metaphire vulgaris 53 , another annelid. Supplementary Fig.…”

Section: Resultssupporting

confidence: 82%

Annelid genomes: Enchytraeus crypticus, a soil model for the innate (and primed) immune system

et al. 2021

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Enchytraeids (Annelida) are soil invertebrates with worldwide distribution that have served as ecotoxicology models for over 20 years. We present the first high-quality reference genome of Enchytraeus crypticus, assembled from a combination of Pacific Bioscience single-molecule real-time and Illumina sequencing platforms as a 525.2 Mbp genome (910 gapless scaffolds and 18,452 genes). We highlight isopenicillin, acquired by horizontal gene transfer and conferring antibiotic function. Significant gene family expansions associated with regeneration (long interspersed nuclear elements), the innate immune system (tripartite motif-containing protein) and response to stress (cytochrome P450) were identified. The ACE (Angiotensin-converting enzyme) — a homolog of ACE2, which is involved in the coronavirus SARS-CoV-2 cell entry — is also present in E. crypticus. There is an obvious potential of using E. crypticus as a model to study interactions between regeneration, the innate immune system and aging-dependent decline.

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Section: Resultssupporting

confidence: 82%

Annelid genomes: Enchytraeus crypticus, a soil model for the innate (and primed) immune system

et al. 2021

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“…On top of the enhanced inter-chromosomal translocation rate, our analysis also detected whole genome duplications, confirming the already reported duplication in Metaphire (Jin et al 2020). We observed the same duplicated karyotype in Amynthas, but not in Perionyx, which narrows the likely timing of this duplication event.…”

Section: Widespread Loss Of Chromosomal Synteny Among Clitellate Anne...supporting

confidence: 90%

“…The following chromosome-scale and scaffold-level annelid and mollusk genomes, as well as their genome annotations and protein sequences, were downloaded for this project: Helobdella robusta (GCF_000326865.2) (Simakov et al 2013), Hirudinaria manillensis (GCA_034509925.1) (Guan et al 2019), Metaphire vulgaris (GCA_018105865.1) (Jin et al 2020), Amynthas corticis (GCA_900184025.1) (Wang et al 2021), Eisenia andrei (GWHACBE00000000) (Shao et al 2020) The genomes were prepared for use with the odp software package (Schultz et al 2023) by extracting the protein coordinate information to rbh files.…”

Section: Genome Database Preparationmentioning

confidence: 99%

Acceleration of genome rearrangement in clitellate annelids

Schultz,

Heath-Heckman,

Winchell

et al. 2024

Preprint

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Comparisons of multiple metazoan genomes have revealed the existence of ancestral linkage groups (ALGs), genomic scaffolds sharing sets of orthologous genes that have been inherited from ancestral animals for hundreds of millions of years (Simakov et al. 2022; Schultz et al. 2023) These ALGs have persisted across major animal taxa including Cnidaria, Deuterostomia, Ecdysozoa and Spiralia. Notwithstanding this general trend of chromosome-scale conservation, ALGs have been obliterated by extensive genome rearrangements in certain groups, most notably including Clitellata (oligochaetes and leeches), a group of easily overlooked invertebrates that is of tremendous ecological, agricultural and economic importance (Charles 2019; Barrett 2016). To further investigate these rearrangements, we have undertaken a comparison of 12 clitellate genomes (including four newly sequenced species) and 11 outgroup representatives. We show that these rearrangements began at the base of the Clitellata (rather than progressing gradually throughout polychaete annelids), that the inter-chromosomal rearrangements continue in several clitellate lineages and that these events have substantially shaped the evolution of the otherwise highly conserved Hox cluster.

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“…The protein models underlying this article are individually available at a variety of repositories Zenodo (Copley et al 2018;Kvist et al 2019;schultz and Francis 2020), National Center for Biotechnology Information (NCBI), Ensembl, SIMRBASE (Data), OIST Marine Genome Projects (Data), Github (Ryan), Harvard Dataverse(Qingxiang), Plos One (Delroisse et al 2016), Google Drive (Data), Neurobase (Data), Bitbucket, Dryad (Data), Ephybase (Data), Reefgenomics (Liew et al 2016), GigaDB (Data), National Genomics Data Center (NGDC) (Chen et al 2021), Figshare (Data), PeerJ (Jin et al 2020), Planmine (Rozanski et al 2019), NHGRI (Data), and the Ryan Lab website (Ryan). All protein models have their assembly information listed in Supplementary Table 1.…”

Section: Data Availabilitymentioning

confidence: 99%

Highly Dynamic Gene Family Evolution Suggests Changing Roles for PON Genes Within Metazoa

Lucas

Graham

Presnell

et al. 2022

Preprint

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Change in gene family size has been shown to facilitate adaptation to different selective pressures. This includes gene duplication to increase dosage or diversification of enzymatic substrates and gene deletion due to relaxed selection. We recently found that the PON1 gene, an enzyme with arylesterase and lactonase activity, was lost repeatedly in different aquatic mammalian lineages, suggesting that the PON gene family is responsive to environmental change. We further investigated if these fluctuations in gene family size were restricted to mammals and approximately when this gene family was expanded within mammals. Using 112 metazoan protein models, we explored the evolutionary history of the PON family to characterize the dynamic evolution of this gene family. We found that there have been multiple, independent expansion events in tardigrades, cephalochordates, and echinoderms. In addition, there have been partial gene loss events in monotremes and sea cucumbers and what appears to be complete loss in arthropods, urochordates, platyhelminths, ctenophores, and placozoans. In addition, we show the mammalian expansion to three PON paralogs occurred in the ancestor of all mammals after the divergence of sauropsida but before the divergence of monotremes from therians. We also provide evidence of a novel PON expansion within the brushtail possum. In the face of repeated expansions and deletions in the context of changing environments, we suggest a range of selective pressures, including pathogen infection and mitigation of oxidative damage, are likely influencing the diversification of this dynamic gene family across metazoa.

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High-quality genome assembly of Metaphire vulgaris

Cited by 11 publications

References 46 publications

Annelid genomes: Enchytraeus crypticus, a soil model for the innate (and primed) immune system

Annelid genomes: Enchytraeus crypticus, a soil model for the innate (and primed) immune system

Acceleration of genome rearrangement in clitellate annelids

Highly Dynamic Gene Family Evolution Suggests Changing Roles for PON Genes Within Metazoa

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