Microscopic ossicle analyses and the complete mitochondrial genome sequence of Holothuria (Roweothuria) polii (Echinodermata; Holothuroidea) provide new information to support the phylogenetic positioning of this sea cucumber species

Utzeri, Valerio Joe; Ribani, Anisa; Bovo, Samuele; Taurisano, Valeria; Calassanzio, Matteo; Baldo, David

doi:10.1016/j.margen.2019.100735

Cited by 9 publications

(6 citation statements)

References 54 publications

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“…In contrast to the AT skew (0.09), the GC skew (−0.14) was negative, which indicated that in the mitochondrial genome of B. argus , the A bases occur more frequently than the T bases, and the C bases occur more frequently than the G bases ( Table 2 ). In sea cucumbers, the AT content of the mitochondrial genome varies, but most of the sea cucumbers in the family Cucurbitaceae have a higher AT content than GC content, e.g., Holothuria polii , Holothuria fuscocinerea , Holothuria leucospilota and Holothuria spinifera [ 36 , 37 , 38 , 39 ]. In bacteria, GC skew is considered a footprint of genome evolution driven by DNA replication [ 40 ].…”

Section: Resultsmentioning

confidence: 99%

Analysis of Complete Mitochondrial Genome of Bohadschia argus (Jaeger, 1833) (Aspidochirotida, Holothuriidae)

et al. 2022

Animals

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Bohadschia argu is a kind of sea cucumber with high economic value; it is the only undisputed species in the genus Bohadschia. In this study, the complete mitochondrial genome (mitogenome) of B. argus was acquired through high-throughput sequencing. The mitochondrial genome of B. argus was 15,656 bp in total length and contained a putative control region (CR) and 37 typical genes of animal mitochondrial genomes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes (tRNA). The sizes of the PCGs ranged from 168 bp to 1833 bp, and all PCGs except nad6 were encoded on the heavy chain (H). Both rrnS and rrnL were also encoded on the H chain. Twenty-two tRNA genes had positive AT skew and GC skew. All tRNAs had a typical cloverleaf secondary structure except for trnI, in which an arm of dihydrouridine was missing. B. argus shared the same gene arrangement order (the echinoderm ground pattern) as other species in Aspidochirotida. Phylogenetic analysis clearly revealed that B. argus belongs as a member of the Holothuriidae, and it is closely related to members of Actinopyga and Holothuria.

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Section: Resultsmentioning

confidence: 99%

Analysis of Complete Mitochondrial Genome of Bohadschia argus (Jaeger, 1833) (Aspidochirotida, Holothuriidae)

et al. 2022

Animals

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“…However, when dried or preserved, their identification is rather difficult based on macroscopic morphological characters, as both species manifest increased phenotypic plasticity in relation to habitat features [58]. Accordingly, most authors argue that calcareous structures (i.e., ossicles) are the most prominent method for the precise taxonomy of holothurians [59][60][61]. However, a complete typology of ossicles is missing for most Holothuria species, and their skeletal elements are highly variable with respect to body region [62].…”

Section: Discussionmentioning

confidence: 99%

Admixture of Holothurian Species in the Hellenic Seas (Eastern Mediterranean) as Revealed by RADseq

Gkafas,

Sarantopoulou,

Apostologamvrou

et al. 2023

Sustainability

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Admixture and hybridization may play a key role in population dynamics and speciation with respect to habitat, demographic history, and adaptive selection. The present study examines the genetic diversity of two congeneric—but in different subgenera—holothurians that live in sympatry in mixed populations. Strong evidence of admixture was provided by analyzing RAD sequencing data from 90 and 67 individuals of Holothuria (Holothuria) tubulosa and Holothuria (Roweothuria) poli, respectively, from various areas of the Hellenic Seas (eastern Mediterranean). Coalescent demographic analysis revealed a recent directional gene flow from H. poli to H. tubulosa. The two species populations diverged around 13.5 thousand years ago, just after the Last Glacial Maximum. According to the pairwise sequential Markovian coalescent approach, the historical population effective sizes for both species declined during the last Pleistocene glaciations, probably due to population decline, followed by a relative rapid recovery as it is calculated using LD methods. The presented results imply a role for admixture upon secondary contact and are consistent with the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin.

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“…The back muscle of sea cucumber was clipped, fixed by anhydrous ethanol and stored at À20°C [11]. The back wall bone fragment was used to identify the species using a scanning electron microscope [13]. The body wall of the sea cucumber was treated with a 10% NaClO solution for 1-2 min.…”

Section: Sample Collection and Identificationmentioning

confidence: 99%

Comparison of the complete mitochondrial genome of Phyllophorus liuwutiensis (Echinodermata: Holothuroidea: Phyllophoridae) to that of other sea cucumbers

et al. 2020

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Sea cucumber species are abundant (>1400 species) and widely distributed globally. mtDNA sequencing is frequently used to identify the phylogenetic and evolutionary relationships among species. However, there are no reports on the mitochondrial genome of Phyllophorus liuwutiensis. Here, we performed mtDNA sequencing of P. liuwutiensis to examine its phylogenetic relationships with other echinoderms. Its mitochondrial genome (15 969 bp) contains 37 coding genes, including 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes. Except for one protein-coding gene (nad6) and five tRNA genes encoded on the negative strand, all other genes were encoded on the positive strand. The mitochondrial bases of P. liuwutiensis were composed of 29.55% T, 22.16% C, 35.64% A and 12.64% G. The putative control region was 703 bp in length. Seven overlapping regions (1-10 bp) were found. The noncoding region between the genes ranged from 1 to 130 bp in length. One putative control region has been found in the P. liuwutiensis mitogenome. All of the tRNA genes were predicted to fold into a cloverleaf structure. In addition, we compared the gene arrangements of six echinoderms, revealing that the gene order of P. liuwutiensis was a new arrangement.

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Microscopic ossicle analyses and the complete mitochondrial genome sequence of Holothuria (Roweothuria) polii (Echinodermata; Holothuroidea) provide new information to support the phylogenetic positioning of this sea cucumber species

Cited by 9 publications

References 54 publications

Analysis of Complete Mitochondrial Genome of Bohadschia argus (Jaeger, 1833) (Aspidochirotida, Holothuriidae)

Analysis of Complete Mitochondrial Genome of Bohadschia argus (Jaeger, 1833) (Aspidochirotida, Holothuriidae)

Admixture of Holothurian Species in the Hellenic Seas (Eastern Mediterranean) as Revealed by RADseq

Comparison of the complete mitochondrial genome of Phyllophorus liuwutiensis (Echinodermata: Holothuroidea: Phyllophoridae) to that of other sea cucumbers

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