Complete mitochondrial genome of <i>Holothuria leucospilata</i> (Holothuroidea, Holothuriidae) and phylogenetic analysis

Yang, Qiuhua; Lin, Qiang; Wu, Jianshao; Tran, Ngoc Tuan; Huang, Ruifang; Sun, Zaiqiao; Zhu, Zhihuang; Lu, Zhen; Li, Shengkang; Zhou, Changyong

doi:10.1080/23802359.2019.1644226

Cited by 8 publications

(10 citation statements)

References 10 publications

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“…The H. glaberrima mitochondrial genome is 15,617 bp, a similar size to that of previously reported holothuroids (H. scabra=15,779 bp, H. leucospilata=15,904 bp) [40]. Likewise, mitochondrial genome features of H. glaberrima showed the same gene order reported for H. scabra and similar characteristics to those of H. scabra and H. leucospilata [41,42]. Differences included the length of the putative control region (PC region) which was significantly smaller in H. glaberrima with 272 base pairs compared to 456 bp and 551 bp for H. scabra and H. leucospilata, respectively.…”

Section: Mitochondrial Genomesupporting

confidence: 84%

Draft Genome of the Sea Cucumber Holothuria glaberrima, a model for the study of regeneration

Medina-Feliciano

Pirro

García‐Arrarás

et al. 2020

Preprint

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Regeneration is one of the most fascinating and yet least understood processes of animals. Echinoderms, one of the closest related invertebrate groups to humans, can contribute to our understanding of the genetic basis of regenerative processes. Amongst echinoderms, sea cucumbers have the ability to grow back most of their body parts following injury, including the intestine and nervous tissue. The cellular and molecular events underlying these abilities in sea cucumbers have been most extensively studied in the species Holothuria glaberrima. However, research into the regenerative abilities of this species have been impeded due to the lack of adequate genomic resources. Here, we report the first draft genome assembly of H. glaberrima and demonstrate its value for future genetic studies. Using only short sequencing reads, we assembled the genome into 2,960,762 scaffolds totaling 1.5 gigabases with an N50 of 15 kilobases. Our BUSCO assessment of the genome resulted in 882 (90.2%) complete and partial genes from 978 genes queried. We incorporated transcriptomic data from several different life history stages to annotate 41,076 genes in our final assembly. To demonstrate the usefulness of the genome, we fully annotated the melanotransferrin (Mtf) gene family, which have a potential role in regeneration of the sea cucumber intestine. Using these same data, we extracted the mitochondrial genome, which showed high conservation to that of other holothuroids. Thus, these data will be a critical resource for ongoing studies of regeneration and other studies in sea cucumbers.

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Section: Mitochondrial Genomesupporting

confidence: 84%

Draft Genome of the Sea Cucumber Holothuria glaberrima, a model for the study of regeneration

Medina-Feliciano

Pirro

García‐Arrarás

et al. 2020

Preprint

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“…The complete S. variegatus mitogenome is a circular DNA molecule with the length of 16,315 bp. The genomic organization is identical to that of the typical Holothuroidea ground pattern (Scouras et al 2004;Uthicke et al 2009;Perseke et al 2010;Yang et al 2019), including 13 proteincoding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. The overall base composition was calculated by MEGA 6 (MEGA Inc., Tampa, FL) (Tamura et al 2011): 31.58% (A), 29.16% (T), 23.48% (C) and 15.78% (G) showing a bias toward A þ T (60.74%), similar to other Echinodermata mitochondrial genomes (Fan et al 2011).…”

mentioning

confidence: 89%

“… 2010 ; Yang et al. 2019 ), including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. The overall base composition was calculated by MEGA 6 (MEGA Inc., Tampa, FL) (Tamura et al.…”

mentioning

confidence: 99%

The complete mitochondrial genome sequence of Stichopus variegatus (Echinodermata: Holothuroidea) and phylogenetic studies of Echinodermata

Yang

Lin

et al. 2019

Mitochondrial DNA Part B

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At present, there exist some confusing issues on the species classification and phylogeny in Echinodermata. In this study, we first determined and described the complete mitochondrial genome of Stichopus variegatus. The complete mitogenome sequence had a circular mapping molecular with the total length of 16,315 bp and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. To further validate the newly determined sequences, phylogenetic trees involving all the Holothuroidea and other Echinodermata species available in GenBank Database were constructed. These results would be used for the species identification and further phylogenetic studies of Echinodermata.

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“… 2004 ; Holothuria leucospilata , MK940237, Yang et al. 2019 ; Parastichopus parvimensis , KU168761 # ; Peniagone sp. YYH-2013, KF915304 # ; Phyllophorella liuwutiensis , MN198190, Yang et al.…”

unclassified

Complete mitochondrial genome of a sea cucumber, Euapta godeffroyi (Echinodermata, Holothuroidea, Apodida, Synaptidae)

Ogawa

Hiruta

Aung

et al. 2022

Mitochondrial DNA Part B

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We determined the complete mitochondrial genome sequence of a holothurian Euapta godeffroyi belonging to the order Apodida. The complete mitogenome of E. godeffroyi was 16,410 bp in length and consisted of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. The orders of PCGs and rRNAs did not match those of any recorded holothurian mitogenomes. The maximum likelihood (ML) phylogenetic tree placed E. godeffroyi as the sister group to chiridotid species and supported the monophyly of the order Apodida.

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Complete mitochondrial genome of Holothuria leucospilata (Holothuroidea, Holothuriidae) and phylogenetic analysis

Cited by 8 publications

References 10 publications

Draft Genome of the Sea Cucumber Holothuria glaberrima, a model for the study of regeneration

Draft Genome of the Sea Cucumber Holothuria glaberrima, a model for the study of regeneration

The complete mitochondrial genome sequence of Stichopus variegatus (Echinodermata: Holothuroidea) and phylogenetic studies of Echinodermata

Complete mitochondrial genome of a sea cucumber, Euapta godeffroyi (Echinodermata, Holothuroidea, Apodida, Synaptidae)

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