Chromosome number and telomere sequence mapping of the Japanese sea cucumber Apostichopus japonicus

Okumura, Seiichi; Kimura, Kazuma; Sakai, Mizuho; Waragaya, Takashi; Furukawa, Suehiro; Takahashi, Akiyoshi; Yamamori, Kunio

doi:10.1007/s12562-008-0025-5

Cited by 13 publications

(5 citation statements)

References 12 publications

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“…Furthermore, genomic scaffolds have been mapped to twenty-two linkage groups in A . japonicus 5,6 , consistent with the haploid chromosome number in this species 77,127 . By analysing data from Li et al .…”

Section: Resultssupporting

confidence: 81%

Neuropeptide precursors and neuropeptides in the sea cucumber Apostichopus japonicus: a genomic, transcriptomic and proteomic analysis

Chen

Talarovičová

Zheng

et al. 2019

Sci Rep

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The sea cucumber Apostichopus japonicus is a foodstuff with very high economic value in China, Japan and other countries in south-east Asia. It is at the heart of a multibillion-dollar industry and to meet demand for this product, aquaculture methods and facilities have been established. However, there are challenges associated with optimization of reproduction, feeding and growth in non-natural environments. Therefore, we need to learn more about the biology of A . japonicus , including processes such as aestivation, evisceration, regeneration and albinism. One of the major classes of molecules that regulate physiology and behaviour in animals are neuropeptides, and a few bioactive peptides have already been identified in A . japonicus . To facilitate more comprehensive investigations of neuropeptide function in A . japonicus , here we have analysed genomic and transcriptomic sequence data and proteomic data to identify neuropeptide precursors and neuropeptides in this species. We identified 44 transcripts encoding neuropeptide precursors or putative neuropeptide precursors, and in some instances neuropeptides derived from these precursors were confirmed by mass spectrometry. Furthermore, analysis of genomic sequence data enabled identification of the location of neuropeptide precursor genes on genomic scaffolds and linkage groups (chromosomes) and determination of gene structure. Many of the precursors identified contain homologs of neuropeptides that have been identified in other bilaterian animals. Precursors of neuropeptides that have thus far only been identified in echinoderms were identified, including L- and F-type SALMFamides, AN peptides and others. Precursors of several peptides that act as modulators of neuromuscular activity in A . japonicus were also identified. The discovery of a large repertoire of neuropeptide precursors and neuropeptides provides a basis for experimental studies that investigate the physiological roles of neuropeptide signaling systems in A . japonicus . Looking ahead, some of these neuropeptides may have effects that could be harnessed to enable improvements in the aquaculture of this economically important species.

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Section: Resultssupporting

confidence: 81%

Neuropeptide precursors and neuropeptides in the sea cucumber Apostichopus japonicus: a genomic, transcriptomic and proteomic analysis

Chen

Talarovičová

Zheng

et al. 2019

Sci Rep

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“…In total 6311 and 5517 markers were used to construct female and male map separately, after linkage mapping, 2302 and 1525 markers were eliminated. For both sex-specific maps, 22 linkage groups (LGs) were obtained ( Supplementary Figure F2 and F3 ), which were consistent with the haploid chromosome number of A. japonicus 32 . The female genetic map consisted of 4009 markers mapped on 2908 distinct positions spanned 3728.9 cM, with an average marker interval of 0.93 cM, ranging from 0.72 in LG5 to 1.31 in LG14, while the male genetic map contained 3992 markers on 2138 distinct positions, with a much shorter genetic length (1824.3 cM) and shorter average marker interval (0.46 cM) ( Table 3 ).…”

Section: Resultssupporting

confidence: 65%

Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus

Tian

Jing

et al. 2015

Sci Rep

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Genetic linkage maps are critical and indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density and high-resolution linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as echinoderms. In this study, high-density, high-resolution genetic map was constructed for a sea cucumber species, Apostichopus japonicus, utilizing the 2b-restriction site-associated DNA (2b-RAD) method. A total of 7839 markers were anchored to the linkage map with the map coverage of 99.57%, to our knowledge, this is the highest marker density among echinoderm species. QTL mapping and association analysis consistently captured one growth-related QTL located in a 5 cM region of linkage group (LG) 5. An annotated candidate gene, retinoblastoma-binding protein 5 (RbBP5), which has been reported to be an important regulator of cell proliferation, was recognized in the QTL region. This linkage map represents a powerful tool for research involving both fine-scale QTL mapping and marker assisted selection (MAS), and will facilitate chromosome assignment and improve the whole-genome assembly of sea cucumber in the future.

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“…In this study, we analyzed 130 F 1 offspring and their parents using GBS technology to construct the first high-density, SNP-based genetic linkage map of sea cucumber ( A. japonicus ). The map was divided into 22 LGs, which is consistent with the results of an earlier investigation regarding A. japonicus chromosomes [ 1 ]. The established genetic linkage map provides a foundation for the mapping QTL associated with important quantitative and economically valuable traits as well as for inferring the genes responsible for these traits in A. japonicus .…”

Section: Discussionsupporting

confidence: 78%

“…Significant progress has been made in the development of sea cucumber genetic and genomic resources, which has laid a solid foundation for the promotion of MAS. For example, previous studies on sea cucumber have resulted in information regarding its diploid genome (2n = 44) [ 1 ]; two low-density genetic maps based on amplified fragment length polymorphisms (AFLPs), microsatellites, and single nucleotide polymorphisms (SNPs) [ 2 , 3 ]; a high-density map constructed according to a 2b-restriction site-associated DNA (2b-RAD) method [ 4 ]; and the release of a sequenced genome [ 5 ]. The transition from traditional breeding methods to MAS-based breeding has become an irreversible trend.…”

Section: Introductionmentioning

confidence: 99%

Construction of a High-Density Genetic Linkage Map for the Mapping of QTL Associated with Growth-Related Traits in Sea Cucumber (Apostichopus japonicus)

Cui

Huo

Liu

et al. 2021

Biology

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Genetic linkage maps have become an indispensable tool for genetics and genomics research. Sea cucumber (Apostichopus japonicus), which is an economically important mariculture species in Asia, is an edible echinoderm with medicinal properties. In this study, the first SNP-based high-density genetic linkage map was constructed by sequencing 132 A. japonicus individuals (2 parents and 130 offspring) according to a genotyping-by-sequencing (GBS) method. The consensus map was 3181.54 cM long, with an average genetic distance of 0.52 cM. A total of 6144 SNPs were assigned to 22 linkage groups (LGs). A Pearson analysis and QTL mapping revealed the correlations among body weight, body length, and papillae number. An important growth-related candidate gene, protein still life, isoforms C/SIF type 2 (sif), was identified in LG18. The gene was significantly highly expressed during the larval developmental stages. Its encoded protein reportedly functions as a guanine nucleotide exchange factor. These results would facilitate the genetic analysis of growth traits and provide valuable genomic resources for the selection and breeding of new varieties of sea cucumbers with excellent production traits.

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Chromosome number and telomere sequence mapping of the Japanese sea cucumber Apostichopus japonicus

Cited by 13 publications

References 12 publications

Neuropeptide precursors and neuropeptides in the sea cucumber Apostichopus japonicus: a genomic, transcriptomic and proteomic analysis

Neuropeptide precursors and neuropeptides in the sea cucumber Apostichopus japonicus: a genomic, transcriptomic and proteomic analysis

Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus

Construction of a High-Density Genetic Linkage Map for the Mapping of QTL Associated with Growth-Related Traits in Sea Cucumber (Apostichopus japonicus)

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