De novo transcriptome sequencing and comparative analysis to discover genes involved in ovarian maturity in Strongylocentrotus nudus

Jia, Zhiying; Wang, Qiai; Wu, Kuan; Wei, Zhenlin; Zhou, Zunchun; Liu, Xiaolin

doi:10.1016/j.cbd.2017.05.002

Cited by 17 publications

(17 citation statements)

References 60 publications

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“…Sampling locality is shown for newly sequenced taxa, citations for data obtained from the literature. For deep-sea specimens, sampling depth is also reportedCladeSpeciesData type a Sampling locality (depth)/SourceVoucher numberSRA/Genome numbersArbacioida Gregory, 1900 Arbacia punctulata (Lamarck, 1816)T[43]SIO-BIC E6740SRR2843235Camarodonta Jackson, 1912 Colobocentrotus atratus (Linnaeus, 1758)TKailua Kona, Hawaii IslandSIO-BIC E7012SRR7513588 Echinometra mathaei (Blainville, 1825)TAl-Fahal Reef, Red Sea, Makkah, Saudi ArabiaSIO-BIC E6896SRR7513581 Evechinus chloroticus (Valenciennes, 1846)T[131]–SRR1014619 Heliocidaris erythrogramma (Valenciennes, 1846)T[132]–SRR1211283 Lytechinus variegatus (Lamarck, 1816)T[5]–SRR1139214 Mesocentrotus nudus (A. Agassiz, 1864)T[133]–SRR5017175 Paracentrotus lividus (Lamarck, 1816)T[134]–SRR1735501 Sphaerechinus granularis (Lamarck, 1816)T[5]–SRR1139199 Strongylocentrotus purpuratus (Stimpson, 1857)G[45]; Spur_4.2–GCF 000002235.4Cidaroida Claus, 1880 Eucidaris tribuloides (Lamarck, 1816)T[43]SIO-BIC E6742SRR2844625 Prionocidaris baculosa (Lamarck, 1816)TAl-Fahal Reef, Red Sea, Makkah, Saudi ArabiaSIO-BIC E6897SRR7513584Clypeasteroida sensu A. Agassiz, 1872-1874 Clypeaster rosaceus (Linnaeus, 1758)TBocas del Toro, Panama–SRR7513591 Clypeaster subdepressus (Gray, 1825)TBocas del Toro, Panama–SRR7513586 Dendraster excentricus (Eschscholtz, 1831)T[43]SIO-BIC E5640…”

Section: Resultsmentioning

confidence: 99%

A phylogenomic resolution of the sea urchin tree of life

Koch¹,

Coppard²,

Lessios³

et al. 2018

BMC Evol Biol

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BackgroundEchinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a variety of morphological data, molecular attempts have relied on only a handful of genes. Both of these approaches have had limited success at resolving the deepest nodes of the tree, and their disagreement over the positions of a number of clades remains unresolved.ResultsWe performed de novo sequencing and assembly of 17 transcriptomes to complement available genomic resources of sea urchins and produce the first phylogenomic analysis of the clade. Multiple methods of probabilistic inference recovered identical topologies, with virtually all nodes showing maximum support. In contrast, the coalescent-based method ASTRAL-II resolved one node differently, a result apparently driven by gene tree error induced by evolutionary rate heterogeneity. Regardless of the method employed, our phylogenetic structure deviates from the currently accepted classification of echinoids, with neither Acroechinoidea (all euechinoids except echinothurioids), nor Clypeasteroida (sand dollars and sea biscuits) being monophyletic as currently defined. We show that phylogenetic signal for novel resolutions of these lineages is strong and distributed throughout the genome, and fail to recover systematic biases as drivers of our results.ConclusionsOur investigation substantially augments the molecular resources available for sea urchins, providing the first transcriptomes for many of its main lineages. Using this expanded genomic dataset, we resolve the position of several clades in agreement with early molecular analyses but in disagreement with morphological data. Our efforts settle multiple phylogenetic uncertainties, including the position of the enigmatic deep-sea echinothurioids and the identity of the sister clade to sand dollars. We offer a detailed assessment of evolutionary scenarios that could reconcile our findings with morphological evidence, opening up new lines of research into the development and evolutionary history of this ancient clade.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1300-4) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

A phylogenomic resolution of the sea urchin tree of life

Koch¹,

Coppard²,

Lessios³

et al. 2018

BMC Evol Biol

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“…For instance, the testis tastes sweet and creamy, whereas the ovaries are bitter and sour [18]. The regulatory mechanisms of gonad development in sea urchins have thus attracted increasing attention in recent years [19,20]. However, sea urchins breeding has to suffer long reproductive cycle and low survival rate (range from less than 0.1 to 1%) that usually cause intractability.…”

Section: Introductionmentioning

confidence: 99%

Molecular Cloning and Sexually Dimorphic Expression Analysis of nanos2 in the Sea Urchin, Mesocentrotus nudus

Zhang

Han

Wang

et al. 2019

IJMS

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Sea urchin (Mesocentrotus nudus) is an economically important mariculture species in China and the gonads are the solely edible parts to human. The molecular mechanisms of gonad development have attracted increasing attention in recent years. Although the nanos2 gene has been identified as a germ cell marker in several invertebrates, little is known about nanos2 in adult sea urchins. Hereinto, we report the characterization of Mnnano2, an M. nudus nanos2 homology gene. Mnnanos2 is a maternal factor and can be detected continuously during embryogenesis and early ontogeny. Real-time quantitative PCR (RT-qPCR) and section in situ hybridization (ISH) analysis revealed a dynamic and sexually dimorphic expression pattern of Mnnano2 in the gonads. Its expression reached the maximal level at Stage 2 along with the gonad development in both ovary and testis. In the ovary, Mnnanos2 is specifically expressed in germ cells. In contrast, Mnnanos2 is expressed in both nutritive phagocytes (NP) cells and male germ cells in testis. Moreover, knocking down of Mnnanos2 by means of RNA interference (RNAi) reduced nanos2 and boule expression but conversely increased the expression of foxl2. Therefore, our data suggest that Mnnanos2 may serve as a female germ cell marker during gametogenesis and provide chances to uncover its function in adult sea urchin.

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“…Recently, large arrays of RNA sequence data have been generated and stored in public repositories such as the Short Read Archive sequence database (). Many full sea urchin mt genomes (see Table S1) and transcriptomes are there available [108,109,110,111,112,113,114,115,116]. To assess directly the alternative hypotheses outlined above, we compared the ND6 genomic sequences with the corresponding ND6 transcripts using the BLAST algorithm [35].…”

Section: Resultsmentioning

confidence: 99%

Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins

Balakirev

2019

Genes

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Mitochondrial (mt) genomes of the sea urchins Strongylocentrotus intermedius and Mesocentrotus nudus demonstrate the identical patterns of intraspecific length variability of the ND6 gene, consisting of 489 bp (S variant) and 498 bp (L variant), respectively. For both species, the ND6 length difference is due to the 488A>G substitution, which changes the stop codon TAG in S variant for a tryptophan codon TGG in L variant and elongates the corresponding ND6 protein by three additional amino acids, Trp-Leu-Trp. The phylogenetic analysis based on mt genomes of sea urchins and related echinoderm groups from GenBank has shown the S and L ND6 variants as shared among the camarodont sea urchins; the rest of the echinoderms demonstrate the S variant only. The data suggest that the ND6 488A>G substitution can be the first example of the trans-species polymorphism in sea urchins, persisting at least since the time of the Odontophora diversification at the Eocene/Oligocene boundary (approximately 34 million years ago), which was characterized by an abrupt climate change and significant global ocean cooling. Alternative hypotheses, including the convergent RNA editing and/or codon reassignment, are not supported by direct comparisons of the ND6 gene sequences with the corresponding transcripts using the basic local alignment search tool (BLAST) of full sea urchin transcriptomes.

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De novo transcriptome sequencing and comparative analysis to discover genes involved in ovarian maturity in Strongylocentrotus nudus

Cited by 17 publications

References 60 publications

A phylogenomic resolution of the sea urchin tree of life

A phylogenomic resolution of the sea urchin tree of life

Molecular Cloning and Sexually Dimorphic Expression Analysis of nanos2 in the Sea Urchin, Mesocentrotus nudus

Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins

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