Genomic organization of <scp>H</scp>ox and <scp>P</scp>ara<scp>H</scp>ox clusters in the echinoderm, <scp><i>A</i></scp><i>canthaster planci</i>

Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs.

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“…purpuratus , 588 Kb) [32], and sea star ( A . planci , 1,195Kb) [33]. However, the gene order of Hox clusters in A .…”

Section: Resultsmentioning

confidence: 99%

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

et al. 2017

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“…Therefore, it has been suggested that the Hox genes showing inverted transcriptional orientation are involved in the patterning of the pentaradial body plan instead of the anterior/posterior patterning in sea urchins (Tsuchimoto and Yamaguchi 2014). However, a recent study showed that the Hox cluster of a starfish Acanthaster planci generally resembles the chordate and hemichordate clusters exhibiting numerical order of Hox genes in the cluster (Baughman et al 2014). This finding suggests that translocation and/or inverted transcriptional orientation of Hox1, Hox2, Hox3, and Hox5 is not responsible for the patterning of the pentaradial body plan.…”

Section: Pentameral Expression Of Hox Genesmentioning

confidence: 96%

“…As we have already identified AjHox5, AjHox7 and AjHox8 in this study, the two sequences might represent Hox4 and Hox6 in A. japonicus. In echinoderms, complete Hox cluster organizations were reported from the sea urchin (S. purpuratus) and sea star (Acanthaster planci) showing that they have four medial Hox genes (Hox4/6, Hox5, Hox7 and Hox8) Baughman et al 2014). Thus it is of great interest whether sea cucumbers have five medial Hox genes.…”

Section: Isolation and Identification Of Ajhox Genesmentioning

confidence: 98%

Patterning of anteroposterior body axis displayed in the expression of Hox genes in sea cucumber Apostichopus japonicus

et al. 2015

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The presence of an anteroposterior body axis is a fundamental feature of bilateria. Within this group, echinoderms have secondarily evolved pentameral symmetric body plans. Although all echinoderms present bilaterally symmetric larval stages, they dramatically rearrange their body axis and develop a pentaradial body plan during metamorphosis. Therefore, the location of their anteroposterior body axis in adult forms remains a contentious issue. Unlike other echinoderms, sea cucumbers present an obvious anteroposterior axis not rearranged during metamorphosis, thus representing an interesting group to study their anteroposterior axis patterning. Hox genes are known to play a broadly conserved role in anteroposterior axis patterning in deuterostomes. Here, we report the expression patterns of Hox genes from early development to pentactula stage in sea cucumber. In early larval stages, five Hox genes (AjHox1, AjHox7, AjHox8, AjHox11/13a, and AjHox11/13b) were expressed sequentially along the archenteron, suggesting that the role of anteroposterior patterning of the Hox genes is conserved in bilateral larvae of echinoderms. In doliolaria and pentactula stages, eight Hox genes (AjHox1, AjHox5, AjHox7, AjHox8, AjHox9/10, AjHox11/13a, AjHox11/13b, and AjHox11/13c) were expressed sequentially along the digestive tract, following a similar expression pattern to that found in the visceral mesoderm of other bilateria. Unlike other echinoderms, pentameral expression patterns of AjHox genes were not observed in sea cucumber. Altogether, we concluded that AjHox genes are involved in the patterning of the digestive tract in both larvae and metamorphosis of sea cucumbers. In addition, the anteroposterior axis in sea cucumbers might be patterned like that of other bilateria.

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“…In the recent paper by Baughman et al 2014 the authors show that the sea star Acanthaster planci has an almost complete HOX cluster, without any major reorganization as it is seen in the genome of the echinoid Strongylocentrotus purpuratus . This would suggest that the HOX cluster was reorganized specifi cally in the echinoid lineage and that the other echinoderm classes do not share the structure described for S. purpuratus.…”

Section: Note Added In Proofsmentioning

confidence: 96%

Echinodermata

Arnone

Byrne

Martinez

2015

Evolutionary Developmental Biology of Invertebrates 6

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Genomic organization of Hox and ParaHox clusters in the echinoderm, Acanthaster planci

Cited by 44 publications

References 32 publications

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

Patterning of anteroposterior body axis displayed in the expression of Hox genes in sea cucumber Apostichopus japonicus

Echinodermata

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