Identification of sex determination locus in sea cucumber Apostichopus japonicus using genome-wide association study

Wang, Yixin; Yang, Yujia; Li, Yulong; Chen, Muyan

doi:10.1186/s12864-022-08632-3

Cited by 14 publications

(5 citation statements)

References 88 publications

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“…Another study reported the first high-quality, chromosome-level genome assembly of Holothuria leucospilota , an ecologically significant sea cucumber species with a prototypical Cuvierian organ (CO), that is a defensive organ with bioadhesive properties [ 35 ] The H. leucospilota genome reveals characteristic long-repeat signatures in CO-specific proteins, analogous to fibrous proteins of disparate organisms, including spider spidroin and silkworm fibroin, offering new insights into the molecular features and evolution of this unique defensive organ. Likewise, integrated genome-wide association study (GWAS) and the analysis of the distribution of characteristic sex-specific SNPs have clarified sex determination mechanisms and identified sex-linked markers, showing that multiple sex-associated loci are located on several chromosomes in A. japonicus [ 158 ].…”

Section: Genomic-transcriptomic Information and Cellular And Molecula...mentioning

confidence: 99%

Sea cucumbers: an emerging system in evo-devo

Perillo,

Sepe,

Paganos

et al. 2024

EvoDevo

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

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Section: Genomic-transcriptomic Information and Cellular And Molecula...mentioning

confidence: 99%

Sea cucumbers: an emerging system in evo-devo

Perillo,

Sepe,

Paganos

et al. 2024

EvoDevo

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“…Compared with other echinoderms ( Supplemental Table S3 ), the repetitive gene percentage of C. heheva (Kairei vent) in this study is more than that in the Haima cold seep (56.64%) [ 21 ] and only less than that of Paelopatides sp. Yap (73.93%) [ 23 ], and the percentage of shallow water A. japonicus is only 27.20% [ 55 , 64 ]. After repeat masking, protein-coding genes annotated used a combination of ab initio , homology-based, and transcript evidence–predicted approaches, and a total of 32,434 were successfully identified (Table 3 ).…”

Section: Resultsmentioning

confidence: 99%

“…Chromosome-level genome in our study of C. heheva (CHEH_vent1.0) and A. japonicus (AJH1.0) [ 55 ] was selected as comparisons for syntenic analysis. BLAST version 2.9.0 (BLAST Similarity Search, RRID:SCR_008419 ) with parameter “-evalue 1e-10” was used to identify similar gene pairs [ 56 ].…”

Section: Methodsmentioning

confidence: 99%

A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation

Pu,

Zhou,

Liu

et al. 2024

GigaScience

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

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“…The positions of TRP genes on the chromosomes were determined by annotations based on the genome database (China National GeneBank DataBase (CNGBdb) under BioProject Accession No. CNP0002776) and mapped by TBtools software (Chen et al, 2020;Wang et al, 2022b). To further investigate the relationship of AjTRPs with those from other representative species, ClustalW was used to make multiple sequence alignments of full-length proteins and the phylogenetic analysis based on the Maximum Likelihood method were performed using MEGA 11 with WAG+G+I+F model and then edited with EvolView (https://evolgenius.info// evolview-v2/).…”

Section: Sequence Analysis and Number Comparisons Of Trp Genes And Ph...mentioning

confidence: 99%

Characterization and expression profile of transient receptor potential channels in sea cucumber Apostichopus japonicus

Wang

et al. 2023

Front. Mar. Sci.

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BackgroundIn the past few decades, heat waves and seasonal variation linked with global warming are causing frequent fluctuations of water temperature in aquatic environments, resulting in further challenges for marine organisms. As a poikilothermic marine animal and a temperate species, sea cucumber A. japonicus is also very sensitive to temperature variation and shows a limited ability to adapt to environmental temperature changes. However, the molecular mechanisms by which A. japonicus perceives signals from such a diverse environment including the trigger of aestivation still remain unclear. TRP (transient receptor potential) superfamily, as the great potential “sentinel” of the organism in response to the changes of the external environment signals, perceived little attention and will be the future great candidates for sensory function research in echinoderm.MethodsBLAST program was applied to identify the AjTRPs based on A. japonicus transcriptome database. Gene structure analysis of AjTRPs and phylogenetic analysis of TRPs were performed. The expression profiles of AjTRPs in different tissues and in response to different heat stress treatments (chronic/ acute) were measured using qRT-PCR.ResultsA total of 54 TRPs were identified in A. japonicus. Gene structure analysis showed that the exon numbers and the domains of AjTRPs varied greatly. Phylogenetic analysis indicated that AjTPRs were mainly grouped into six subfamilies: TRPA, TRPM, TRPC, TRPV, TRPML, and TRPP. Copy numbers of each TRP member in marine invertebrates including A. japonicus were more than those in vertebrates, however some TRP channel members were lost in invertebrates. Expression profile detection suggested that the representative 15 AjTRP genes belonging to 6 subfamilies were expressed in all tissues examined.ConclusionOur findings indicate that the plastic evolutionary history of TRP channel genes and suggest that TRPM2-1, TRPM2-2, TRPM3, and TRPC3-1 are potential thermo-TRP proteins involved in thermal regulation in A. japonicus. This work facilitates the knowledge of TRP-mediated sensory systems in echinoderms, provides new insights into the mechanisms of aestivation and global warming adaptation in marine invertebrates.

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Identification of sex determination locus in sea cucumber Apostichopus japonicus using genome-wide association study

Cited by 14 publications

References 88 publications

Sea cucumbers: an emerging system in evo-devo

Sea cucumbers: an emerging system in evo-devo

A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation

Characterization and expression profile of transient receptor potential channels in sea cucumber Apostichopus japonicus

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