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

Guangxian Tu,

Qi Chen, Xinshuang Zhang

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Ноя. 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.

Язык: Английский

Mesozoic stem-group zoroasterid sea stars imply a delayed radiation of the crown group and adaptation to the deep seas DOI
Marine Fau, Loïc Villier

Journal of Systematic Palaeontology, Год журнала: 2023, Номер 21(1)

Опубликована: Янв. 1, 2023

AbstractThe family Zoroasteridae is a clade of extant sea stars found exclusively in deep marine environments (i.e. bathyal deeper than 200 m). In the fossil record, seven species have been compared and/or assigned to Zoroasteridae, on time span ranging from Middle Jurassic Miocene. This study describes new taxon, Viridisaster guerangeri gen. et sp. nov., Cenomanian Le Mans (Sarthe, France) and reappraises two Mesozoic species, Terminaster cancriformis Early Cretaceous Protothyraster priscus. To test relationships putative zoroasterids with modern taxa, phylogenetic analysis was performed combining six best-known 29 forcipulatacean including four Zoroasteridae. Many characters that define do not appear record before Cenozoic. The name maintained for crown group only. Terminasteridae, accounted genera Alkaidia, paraphyletic rejected here. order Zorocallida, initially erected only, redefined as sister Forcipulatida includes crown-group its stem relatives. Zorocallida are small size Cenozoic they express morphological typical juvenile Zoroasteridae; thus, emergence forms likely associated peramorphic evolution. palaeoecology their restriction deep-sea after Eocene discussed.http://zoobank.org/urn:lsid:zoobank.org:pub:1755AFC6-198F-45F2-A2F6-011EAC6BE10FKeywords: CretaceousAsteroideaEchinodermataphylogenynew taxon AcknowledgementsThe authors grateful collection managers who facilitated access specimens: Nicolas Morel (MHNLM); Walter Etter Sergio Kühni (NMB Basel); Timothy A. M. Ewin (NHMUK); Christian Meister (MHNG); Marc Eléaume Pierre Lozouet (MNHN); Eric Lazo-Wasem Lourdes Rojas (YPM). We thank anonymous reviewers comments helped improve manuscript. Marine Fau received financial support Department Geosciences Fribourg University during period 2016–2020, grant program Synthesys (GB-TAF-6581) visit Natural History Museum, London, June 2017.Disclosure statementNo potential conflict interest reported by author(s).Supplemental materialSupplemental material this article can be accessed here: https://doi.org/10.1080/14772019.2023.2243268.Associate Editor: Erin Maxwell

Язык: Английский

Процитировано

2
The genome of the deep-sea anemone Actinernus sp. contains a mega-array of ANTP-class homeobox genes DOI
Sean T.S. Law, Yifei Yu, Wenyan Nong

и другие.

Proceedings of the Royal Society B Biological Sciences, Год журнала: 2023, Номер 290(2009)

Опубликована: Окт. 25, 2023

Members of the phylum Cnidaria include sea anemones, corals and jellyfish, have successfully colonized both marine freshwater habitats throughout world. The understanding how cnidarians adapt to extreme environments such as dark, high-pressure deep-sea habitat has been hindered by lack genomic information. Here, we report first chromosome-level cnidarian genome, anemone Actinernus sp., which was 1.39 Gbp in length contained 44 970 gene models including 14 806 tRNA genes 30 164 protein-coding genes. Analyses homeobox revealed longest chromosome hosts a mega-array Hox cluster, HoxL, NK cluster NKL genes; until now, an array only hypothesized existed ancient ancestral genomes. In addition this striking arrangement genes, analyses microRNAs cnidarian-specific complements that are distinctive for nested clades these animals, presumably reflecting progressive evolution regulatory networks they embedded. Also, compared with other circadian rhythm were lost likely reflects adaptation living dark. This high-quality genome thus reveals some molecular adaptations ecologically important group metazoans environment. It also deepens our content organization animals general particular, specifically from viewpoint key developmental control like homeobox-encoding where find now ancestor pre-dated bilaterians.

Язык: Английский

Процитировано

2
New evidence for a cosmopolitan holothurian species at deep-sea reducing environments DOI Creative Commons
Elin A. Thomas, Julia D. Sigwart, Sarah Helyar

и другие.

Marine Biodiversity, Год журнала: 2022, Номер 52(6)

Опубликована: Ноя. 18, 2022

Abstract The deep-sea holothurian Chiridota heheva Pawson & Vance, 2004 was recently recognised as a cosmopolitan species which exploits the organic enrichment at three types of reducing environments: hydrothermal vents, cold seeps, and falls. Here, we apply phylogenetic reconstruction delimitation approaches using new COI 12S sequence data to show that C. is genetically congruent with only other vent holothurian, hydrothermica Smirnov Gebruk, 2000, strong supporting morphological, ecological, biogeographical parallels between two. As such, propose junior synonym , subsequent chiridotid holothurians discovered environments likely also belong this single globally distributed species. endemic yet known sites across Atlantic, Indian, Pacific Oceans, unique provides an interesting case study for connectivity, biogeography, speciation in deep sea, has important implications conservation planning.

Язык: Английский

Процитировано

4
Genome variations in sea cucumbers: Insights from genome survey sequencing and comparative analysis of mitochondrial genomes DOI

Chunxi Jiang,

Hongsheng Yang,

Bohong Liu

и другие.

Comparative Biochemistry and Physiology Part D Genomics and Proteomics, Год журнала: 2024, Номер 52, С. 101328 - 101328

Опубликована: Сен. 15, 2024

Язык: Английский

Процитировано

0
A modified CTAB method for high-molecular-weight DNA preparation from deep-sea holothurians DOI
Yujin Pu, Jun Liu, Nannan Zhang

и другие.

Marine and Freshwater Behaviour and Physiology, Год журнала: 2023, Номер 56(5-6), С. 137 - 150

Опубликована: Авг. 1, 2023

ABSTRACTWith the features as global distribution and all depths dwelling, holothurians function an ideal model for study of deep-sea adaptation. Acquisition high-molecular-weight DNA is basic requirement molecular biology analyses. However, extraction from difficult by degradation contamination. Here, we presented a modified CTAB (lysis buffer with cetyl trimethyl ammonium bromide) method compared its efficiency other five common methods, i.e. Tiangen Biotech kit, Qiagen Omega Bio-tek Sangon SDS sodium dodecyl sulfate). Based on results yield, integrity, purity, found that more suitable to extract high-quality holothurians, large amount minimized degradation, higher purity. This provides genome sequencing further studies.KEYWORDS: extractiondeep-sea holothurianshigh-molecular-weight DNACTAB AcknowledgmentsWe thank captains, crews, scientific staff R/V Tansuo 1, pilots HOV Shenhaiyongshi. Special thanks Dr. El-Hadji Malick Cisse (Hainan University) improving English writing in this manuscript.Disclosure statementNo potential conflict interest was reported author(s).Supplementary materialSupplemental data article can be accessed online at https://doi.org/10.1080/10236244.2023.2241977.Additional informationFundingThis supported major technological projects Hainan Province [ZDKJ2021036, ZDKJ2019011], National Natural Science Foundation China [42106121], Strategic Priority Research Program Chinese Academy Sciences [XDA22050303].

Язык: Английский

Процитировано

1
The First Genome Survey of the Snail Provanna glabra Inhabiting Deep-Sea Hydrothermal Vents DOI Creative Commons
Min Hui, Yu Zhang,

Aiyang Wang

и другие.

Animals, Год журнала: 2023, Номер 13(21), С. 3313 - 3313

Опубликована: Окт. 25, 2023

The snail P. glabra is an endemic species in deep-sea chemosynthetic ecosystems of the Northwest Pacific Ocean. To obtain more genetic information on this and provide basis for subsequent whole-genome map construction, a genome survey was performed from hydrothermal vent Okinawa Trough. genomic size estimated to be 1.44 Gb, with heterozygosity 1.91% repeated sequence content 69.80%. Based sequencing data, draft 1.32 Gb assembled. Transposal elements (TEs) accounted 40.17% entire genome, DNA transposons taking highest proportion. It found that most TEs were inserted recently. In simple repeats, dinucleotide motif enriched microsatellite type, accounting 53% microsatellites. A complete mitochondrial total length 16,268 bp assembled data. After comparison published Provanna sp. methane seep, 331 potential single nucleotide polymorphism (SNP) sites identified protein-coding genes (PCGs). Except cox1 gene, nad2, nad4, nad5, cob are expected candidate markers population phylogenetic studies other snails. Compared shallow-water species, three gastropods exhibited higher evolutionary rate, indicating strong selection operating mitochondria species. This study provides insights into characteristics supplies resources further adaptive evolution extreme environments.

Язык: Английский

Процитировано

1
Comparative Analysis of Bivalve and Sea Urchin Genetics and Development: Investigating the Dichotomy in Bilateria DOI Open Access

А. Л. Дроздов,

Egor Lebedev, Leonid Adonin

и другие.

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(24), С. 17163 - 17163

Опубликована: Дек. 5, 2023

This comprehensive review presents a comparative analysis of early embryogenesis in Protostomia and Deuterostomia, the first which exhibit mosaic pattern development, where cells are fated deterministically, while Deuterostomia display regulatory fate is indeterminate. Despite these fundamental differences, there common transcriptional mechanisms that underline their evolutionary linkages, particularly field functional genomics. By elucidating both conserved unique strategies, this provides essential insights into embryology developmental dynamics groups. The objective to clarify shared distinctive characteristics mechanisms. will contribute extensive areas genomics, biology biology, possibly lay foundation for future research discussion on seminal topic.

Язык: Английский

Процитировано

1
A high-quality chromosome-level genome assembly of Pelteobagrus vachelli provides insights into its environmental adaptation and population history DOI Creative Commons
Jie Li, Tao Wang, Wei Liu

и другие.

Frontiers in Genetics, Год журнала: 2022, Номер 13

Опубликована: Ноя. 14, 2022

Pelteobagrus vachelli is a freshwater fish with high economic value, but the lack of genome resources has severely restricted its industrial development and population conservation. Here, we constructed first chromosome-level assembly P. total length approximately 662.13 Mb contig N50 was 14.02 Mb, scaffolds covering 99.79% were anchored to 26 chromosomes. Combining comparative results transcriptome data under environmental stress (high temperature, hypoxia Edwardsiella. ictaluri infection), MAPK signaling pathway, PI3K-Akt pathway apelin play an important role in adaptation vachelli, these pathways interconnected by ErbB family involved cell proliferation, differentiation apoptosis. Population evolution analysis showed that artificial interventions have affected wild populations vachelli. This study provides useful genomic information for genetic breeding as well references further studies on biology evolution.

Язык: Английский

Процитировано

2
Novel biomaterials and biotechnological applications derived from North Atlantic sea cucumbers: A systematic review DOI
Miroslava Atanassova,

Lisa Kolden Midtbø,

Jennifer Mildenberger

и другие.

Elsevier eBooks, Год журнала: 2023, Номер unknown, С. 585 - 609

Опубликована: Ноя. 3, 2023

Язык: Английский

Процитировано

0
Long-read genome assemblies reveals acis-regulatory landscape associated with phenotypic divergence in two sisterSinipercafishes DOI Creative Commons

Guangxian Tu,

Qi Chen, Xinshuang Zhang

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Ноя. 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.

Язык: Английский

Процитировано

0