Long-read genome assemblies reveals acis-regulatory landscape associated with phenotypic divergence in two sisterSinipercafishes DOI Creative Commons

Guangxian Tu,

Qi Chen, Xinshuang Zhang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Nov. 10, 2022

Abstract Background Dissecting the genetic basis of variation in regulation gene expression is essential for understanding phenotypic evolution. Structural variants intersecting cis -regulatory elements are found to cause several developmental genes, resulting morphological divergence between species. Due difficulty identifying structural accurately across genome, a comprehensive study impacts closely related species, especially fish still scarce. Recently identified broad H3K4me3 domains genes involved biological processes. However, role remain poorly understood. Siniperca chuatsi and S. scherzeri two species diverge traits, making them an ideal model evolution Results We generated chromosome-level genomes . The evolutionary histories were studied by inferring dynamic changes ancestral population sizes. adaptation was dissected performing family expansion contraction analysis positively selected (PSGs). To investigate SVs we high-quality , as well H3K27ac domains. Integrated revealed that caused played differentiation metabolism, skin pigmentation, immunity Additionally, divergent mostly associate with cancer-related contribute their divergence. Conclusions Our reveals play sister which turn contributes association has ancient origin.

Language: Английский

A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation DOI Creative Commons
Yujin Pu, Yang Zhou, Jun Liu

et al.

GigaScience, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 1, 2024

Chiridota heheva is a cosmopolitan holothurian well adapted to diverse deep-sea ecosystems, especially chemosynthetic environments. Besides high hydrostatic pressure and limited light, concentrations of metal ions also represent harsh conditions in hydrothermal Few species can live such extreme conditions. Therefore, it valuable elucidate the adaptive genetic mechanisms C. Herein, we report high-quality reference genome assembly from Kairei vent, which first chromosome-level Apodida. The size was 1.43 Gb, with scaffold N50 53.24 Mb BUSCO completeness score 94.5%. Contig sequences were clustered, ordered, assembled into 19 natural chromosomes. Comparative analysis found that expanded gene families positively selected genes involved DNA damage repair process. unique contributed maintaining iron homeostasis an iron-enriched environment. RFC2 10 sites played essential role under This reveals adaptation holothurians. As order Apodida, this will provide resource for investigating evolution class Holothuroidea.

Language: Английский

Citations

4
Comprehensive analysis of Metacrinus rotundus full length transcriptome DOI Creative Commons
Zhong Li, Yue Dong,

Xuebao He

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Feb. 25, 2025

Modern stalked crinoids, an important group of echinoderms, represent the ancestral mode and studying their evolution is key to understanding echinoderms. In this study, we selected Metacrinus rotundus, a species modern for investigation. We generated M. rotundus transcripts using Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology. A total 160,849 full-length (FL) were captured by Iso-Seq, with mean length 2,470 bp. Of these FL transcripts, 110,859 well-annotated based on public database. portion remained unannotated, representing potential novel genes rotundus. Additionally, identified 71,740 long-noncoding RNA (LncRNAs), 57,548 simple sequence repeats (SSRs), 3,486 hypothetical transcript factors (TFs). By comparing Holothuroid Echinoid, have higher proportion zf-CCCH TF_Otx within TFs, as well trinucleotide SSRs SSRs. Notably, transposable elements (TEs) make up large transcriptome transposons being largest class annotated TEs. Our study enhances characteristics provides valuable genetic resource further studies adaptive in species, other crinoids.

Language: Английский

Citations

0
Vitellogenin receptor mediates heat adaptability of oocyte development in mud crabs and zebrafish DOI Creative Commons
Long Zhang, Kun Wu, Haoyang Li

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: April 19, 2025

Language: Английский

Citations

0
Sea cucumbers: an emerging system in evo-devo DOI Creative Commons
Margherita Perillo, Rosa Maria Sepe, Periklis Paganos

et al.

EvoDevo, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 17, 2024

A challenge for evolutionary developmental (evo-devo) biology is to expand the breadth of research organisms used investigate how animal diversity has evolved through changes in embryonic development. New experimental systems should couple a relevant phylogenetic position with available molecular tools and genomic resources. As phylum sister group chordates, echinoderms extensively contributed our knowledge patterning, organ development cell-type evolution. Echinoderms display variety larval forms diverse shapes, making them suitable compare evolution strategies. However, because laboratory accessibility already techniques, most studies focus on sea urchins stars mainly. comparative approach, field would benefit from including information other members this group, like cucumbers (holothuroids), which little known basis their Here, we review spawning culture methods, morphological information, current state transcriptomic resources cucumbers. With goal system accessible broader community, discuss cucumber embryos larvae can be powerful address open questions evo-devo, understanding origins bilaterian structures.

Language: Английский

Citations

2
A Chromosome-level genome assembly of giant river prawn (Macrobrachium rosenbergii) DOI Creative Commons

Yang Zheng,

Guangyu Guo,

Yanrong Lv

et al.

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: Aug. 28, 2024

The giant river prawn (Macrobrachium rosenbergii) is one of the most widely cultured crustacean species. In recent years, its aquaculture has faced challenges, including degradation germplasm resources and emergence viral diseases. Genomic information can be a valuable resource for developing molecular breeding programs this important Here we constructed high-quality reference genome M. rosenbergii by integrating Nanopore, Illumina, high-throughput chromosome conformation capture (Hi-C) technologies. final assembly 3.18 Gb in size, with scaffold N50 contig 62.73 Mb 8.92 Mb, respectively. Approximately 98.6% assembled sequences were anchored into 59 pseudo-chromosomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark reached 94.5%. Repetitive comprise 43.77% genome, 17,436 protein-coding genes annotated. will empower efforts provide invaluable comparative genomic analysis decapod

Language: Английский

Citations

2
The draft genome of the tropical sea cucumber Stichopus monotuberculatus (Echinodermata, Stichopodidae) reveals critical genes in fucosylated chondroitin sulfates biosynthetic pathway DOI Creative Commons
Shengping Zhong, Xiaowan Ma, Yan Jiang

et al.

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 14

Published: May 12, 2023

DATA REPORT article Front. Genet., 12 May 2023Sec. Livestock Genomics Volume 14 - 2023 | https://doi.org/10.3389/fgene.2023.1182002

Language: Английский

Citations

6
Admixture of Holothurian Species in the Hellenic Seas (Eastern Mediterranean) as Revealed by RADseq DOI Open Access
Georgios A. Gkafas, Joanne Sarantopoulou, Chrysoula Apostologamvrou

et al.

Sustainability, Journal Year: 2023, Volume and Issue: 15(15), P. 11493 - 11493

Published: July 25, 2023

Admixture and hybridization may play a key role in population dynamics speciation with respect to habitat, demographic history, adaptive selection. The present study examines the genetic diversity of two congeneric—but different subgenera—holothurians that live sympatry mixed populations. Strong evidence admixture was provided by analyzing RAD sequencing data from 90 67 individuals Holothuria (Holothuria) tubulosa (Roweothuria) poli, respectively, various areas Hellenic Seas (eastern Mediterranean). Coalescent analysis revealed recent directional gene flow H. poli tubulosa. species populations diverged around 13.5 thousand years ago, just after Last Glacial Maximum. According pairwise sequential Markovian coalescent approach, historical effective sizes for both declined during last Pleistocene glaciations, probably due decline, followed relative rapid recovery as it is calculated using LD methods. presented results imply upon secondary contact are consistent suggestion genomic underpinning ecological often has an older, allopatric origin.

Language: Английский

Citations

6
Genetic adaptations of marine invertebrates to hydrothermal vent habitats DOI
Haibin Zhang, Yang Zhou,

Zhuo Yang

et al.

Trends in Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Language: Английский

Citations

1
Induciblein vivogenome editing in the sea starPatiria miniata DOI Creative Commons

Olga Zueva,

Veronica F. Hinman

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 10, 2023

Abstract For centuries, echinoderms, a marine-invertebrate phylum, have fascinated scientists for their developmental and postembryonic phenomen. Experimentation on eggs embryos in particular contributed foundation scientific advances. However, powerful molecular genetic studies are restricted to embryonic stages which amenable perturbation by microinjection of reagents into the zygotes. This represents significant bottleneck study processes where earliest function gene must remain intact. We therefore sought establish spatio-temporal turnable editing tool these species. Here, using sea star Patiria miniata as model we introduce chemically inducible, Tet-ON, expression system. Pairing this Tet-ON system with CRISPR-mediated alteration technology show proof-of-principle demonstration an inducible transgenic cell populations first time echinoderm biology. The approach here can be adapted use other species echinoderms will also extend experimental possibilities tremendously.

Language: Английский

Citations

3
Long-read genome assemblies reveal a <i>cis</i>-regulatory landscape associated with phenotypic divergence in two sister <i>Siniperca</i> fish species DOI Open Access

Guangxian Tu,

Xinshuang Zhang,

Ruirun Jiang

et al.

动物学研究, Journal Year: 2023, Volume and Issue: 44(2), P. 287 - 302

Published: Jan. 1, 2023

Due to the difficulty in accurately identifying structural variants (SVs) across genomes, their impact on cis-regulatory divergence of closely related species, especially fish, remains be explored. Recently identified broad H3K4me3 domains are essential for regulation genes involved several biological processes. However, role phenotypic poorly understood. Siniperca chuatsi and S. scherzeri but divergent traits, making them an ideal model study evolution sister species. Here, we generated chromosome-level genomes scherzeri, with assembled genome sizes 716.35 740.54 Mb, respectively. The evolutionary histories were studied by inferring dynamic changes ancestral population sizes. To explore genetic basis adaptation performed gene family expansion contraction analysis positively selected (PSGs). investigate SVs fish high-quality as well H3K27ac scherzeri. Integrated revealed that caused played between Additionally, mostly associated cancer-related contributed divergence.由于难以在基因组中全面地鉴定结构变异，我们仍然缺乏对结构变异在近缘物种，特别是鱼类近缘物种顺式调控趋异中作用的认知。近期的研究发现，宽H3K4me3峰在多个生物学过程的基因调控中起关键作用。然而，宽H3K4me3峰在物种表型趋异中的作用仍然未知。翘嘴鳜（ chuatsi）和斑鳜（ scherzeri）是一对姐妹种，但是它们在多个性状上有很大差异。这使得它们成为研究顺式调控演化的良好模型。我们构建了染色体级别的翘嘴鳜和斑鳜基因组，组装大小分别为716.35 Mb和740.54 Mb。通过推断历史种群大小，我们分析了翘嘴鳜和斑鳜的演化历史。通过基因家族扩张和收缩分析，以及鉴定正选择基因，我们解析了翘嘴鳜和斑鳜适应环境的遗传学基础。为了阐明结构变异在近缘鱼类物种顺式调控趋异中的作用，我们在翘嘴鳜和斑鳜基因组中鉴定了高质量的结构变异，以及差异H3K27ac和H3K4me3峰。联合分析发现，由结构变异引起的顺式调控趋异在翘嘴鳜和斑鳜表型趋异中起关键作用。此外，在翘嘴鳜和斑鳜中，差异宽H3K4me3峰主要与癌症相关基因相关联，并导致这两个物种的表型趋异。.

Language: Английский

Citations

2