The Draft Genome of Chinese Endemic Species Phascolosoma esculenta (Sipuncula, Phascolosomatidae) Reveals the Phylogenetic Position of Sipuncula

Zhong, Shaobin; Ma, Xiaowan; Jiang, Yan; Qiao, Ying; Zhao, Longyan; Huang, Lianghua; Huang, Guoqiang; Zhao, Yang; Liu, Yonghong; Chen, Xiuli

doi:10.3389/fgene.2022.910344

Cited by 3 publications

(1 citation statement)

References 50 publications

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“…Within this dataset of 23 annelids, we describe unique chromosome rearrangements that can be used as rare genomic changes to define seven different taxonomic groups at levels varying from class to family. For example, genome structure definitively supports Sipuncula (in the past considered a separate phylum) as an annelid and Oweniidae as a basal annelid lineage due to the presence of the C2⊗(J2⊗L) fusion in the former and absence in the latter, confirming data from sequence-based phylogenetics (Weigert et al 2014;Struck et al 2015;Zhong et al 2022;Zheng et al 2023). Importantly, the observed stepwise manner of ALG rearrangements suggests that changes to genome structure as clade-defining characters need not be restricted to a specific taxonomic level but can be applied at any level from metazoan-wide to genus and species.…”

Section: Algssupporting

confidence: 54%

Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians

Lewin,

Liao,

Luo

2024

Preprint

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The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while most annelids have maintained the conserved bilaterian genome structure, a group containing leeches and earthworms possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show leeches and earthworms to have the most highly rearranged genomes of any currently sampled bilaterian. We further show that bilaterian genomes can be classified into two distinct categories—high and low rearrangement—largely influenced by the presence or absence, respectively, of chromosome fission events. Our findings demonstrate that animal genome structure can be highly variable within a phylum and reveal that genome rearrangement can occur both in a gradual, stepwise fashion or as rapid, all-encompassing changes over short evolutionary timescales.

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Section: Algssupporting

confidence: 54%

Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians

Lewin,

Liao,

Luo

2024

Preprint

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The first high-quality chromosome-level genome of the Sipuncula Sipunculus nudus using HiFi and Hi-C data

Zheng

Lai

et al. 2023

Sci Data

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Sipuncula is a class of exocoelomic unsegmented animals whose evolutionary relationships are unresolved. The peanut worm Sipunculus nudus is a globally distributed, economically important species belonging to the class Sipuncula. Herein, we present the first high-quality chromosome-level assembly of S. nudus based on HiFi reads and high-resolution chromosome conformation capture (Hi-C) data. The assembled genome was 1,427 Mb, with a contig N50 length of 29.46 Mb and scaffold N50 length of 80.87 Mb. Approximately 97.91% of the genome sequence was anchored to 17 chromosomes. A BUSCO assessment showed that 97.7% of the expectedly conserved genes were present in the genome assembly. The genome was composed of 47.91% repetitive sequences, and 28,749 protein-coding genes were predicted. A phylogenetic tree demonstrated that Sipuncula belongs to Annelida and diverged from the common ancestor of Polychaeta. The high-quality chromosome-level genome of S. nudus will serve as a valuable reference for studies of the genetic diversity and evolution of Lophotrochozoa.

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Annelid Comparative Genomics and the Evolution of Massive Lineage-Specific Genome Rearrangement in Bilaterians

Lewin,

Liao,

Luo

2024

Molecular Biology and Evolution

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The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while many annelid lineages have maintained the conserved bilaterian genome structure, the Clitellata, a group containing leeches and earthworms, possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show that, compared to the last common ancestor of bilaterians, leeches and earthworms have among the most highly rearranged genomes of any currently sampled species. We further show that bilaterian genomes can be classified into two distinct categories—high and low rearrangement—largely influenced by the presence or absence, respectively, of chromosome fission events. Our findings demonstrate that animal genome structure can be highly variable within a phylum and reveal that genome rearrangement can occur both in a gradual, stepwise fashion or as rapid, all-encompassing changes over short evolutionary timescales.

show abstract

The Draft Genome of Chinese Endemic Species Phascolosoma esculenta (Sipuncula, Phascolosomatidae) Reveals the Phylogenetic Position of Sipuncula

Cited by 3 publications

References 50 publications

Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians

Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians

The first high-quality chromosome-level genome of the Sipuncula Sipunculus nudus using HiFi and Hi-C data

Annelid Comparative Genomics and the Evolution of Massive Lineage-Specific Genome Rearrangement in Bilaterians

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