Weighted gene co-expression network analysis reveals potential genes involved in early metamorphosis process in sea cucumber Apostichopus japonicus

Li, Yongxin; Kikuchi, Mani; Li, Xueyan; Gao, Qionghua; Xiong, Zijun; Ren, Yandong; Zhao, Ruoping; Mao, Bingyu; Kondo, Mariko; Irie, Naoki; Wang, Wen

doi:10.1016/j.bbrc.2017.11.154

Cited by 16 publications

(22 citation statements)

References 29 publications

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“…1b, Supplementary Fig. 7, and Supplementary Table [23][24] robustly corroborated recent reports 4,5 that Echinodermata consists of the early diverged Crinoidea (including feather star), Asterozoa (including brittle star and sea star), and Echinozoa (including sea urchin and sea cucumber). This is consistent with paleontological evidence that suggests echinoderms first evolved with a stemmed, or imperforate extra-axial morphology 3 .…”

Section: Resultssupporting

confidence: 89%

“…Apostichopus japonicus: Embryos of fertilized eggs, 4 cell (2 h post fertilization (hpf)), morula (6 hpf), blastula (14 hpf), gastrula (29 hpf), late gastrula (34 hpf), early auricularia larva (48 hpf), mid-auricularia larva (69 hpf), late auricularia larva (15 days post fertilization (dpf)), metamorphosis 1-4 (17-19 dpf), doliolaria larva (19 dpf), pentactula larva (27 dpf), and juvenile (51 dpf) stage were collected and used for this study, as previously described 23 . Three independent biological samples were prepared for all the sampled stages.…”

Section: Methodsmentioning

confidence: 99%

“…Recent studies reported that the transcriptomic conservation is instead around blastula to gastrula in sea urchins 19,20 , however, these studies only examined embryonic sea urchins. We thus analyzed gene expression profiles by covering early-to-late embryos of four diverse echinoderm species, including the publicly available data of purple sea urchins 21,22 and a sea cucumber 23 ( Supplementary Figs. 15 and 16).…”

Section: Echinoderm Embryogenesis Show Hourglass-like Conservationmentioning

confidence: 99%

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Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms

Omori

Flores

et al. 2020

Commun Biol

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Echinoderms are an exceptional group of bilaterians that develop pentameral adult symmetry from a bilaterally symmetric larva. However, the genetic basis in evolution and development of this unique transformation remains to be clarified. Here we report newly sequenced genomes, developmental transcriptomes, and proteomes of diverse echinoderms including the green sea urchin (L. variegatus), a sea cucumber (A. japonicus), and with particular emphasis on a sister group of the earliest-diverged echinoderms, the feather star (A. japonica). We learned that the last common ancestor of echinoderms retained a well-organized Hox cluster reminiscent of the hemichordate, and had gene sets involved in endoskeleton development. Further, unlike in other animal groups, the most conserved developmental stages were not at the body plan establishing phase, and genes normally involved in bilaterality appear to function in pentameric axis development. These results enhance our understanding of the divergence of protostomes and deuterostomes almost 500 Mya.

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Section: Resultssupporting

confidence: 89%

Section: Methodsmentioning

confidence: 99%

Section: Echinoderm Embryogenesis Show Hourglass-like Conservationmentioning

confidence: 99%

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Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms

Omori

Flores

et al. 2020

Commun Biol

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“…RNA-seq has been applied independently to analyze the DEGs between normal and regenerating radial nerve cord in Holothuria glaberrima, and revealed the key roles of extracellular matrix (ECM) remodeling and ECM-cell interactions in regeneration [20]. In addition, the applications of transcriptomic analyses in sea cucumber include identification of long noncoding RNA species [21], illustration of the mechanisms of aestivation [22], abnormal development [23], and body wall pigmentation [24]. Moreover, immune-related genes in the A. japonicus coelomocytes under Vibrio splendidus challenge have been identified, which are clustered into the immune pathways of endocytosis, lysosome, chemokine, and MAPK and ERBB signaling [25].…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis of sea cucumber (Holothuria leucospilota) coelomocytes revealed the echinoderm cytokine response during immune challenge

Chen

Huo

et al. 2020

BMC Genomics

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Background: The sea cucumber Holothuria leucospilota belongs to echinoderm, which is evolutionally the most primitive group of deuterostomes. Sea cucumber has a cavity between its digestive tract and the body wall that is filled with fluid and suspended coelomic cells similar to blood cells. The humoral immune response of the sea cucumber is based on the secretion of various immune factors from coelomocytes into the coelomic cavity. The aim of this study is to lay out a foundation for the immune mechanisms in echinoderms and their origins in chordates by using RNA-seq. Results: Sea cucumber primary coelomocytes were isolated from healthy H. leucospilota and incubated with lipopolysaccharide (LPS, 10 μg/ml), polyinosinic-polycytidylic acid [Poly (I:C), 10 μg/ml] and heat-inactived Vibrio harveyi (10 7 cell/ml) for 24 h, respectively. After high-throughput mRNA sequencing on an Illumina HiSeq2500, a de novo transcriptome was assembled and the Unigenes were annotated. Thirteen differentially expressed genes (DEGs) were selected randomly from our data and subsequently verified by using RT-qPCR. The results of RT-qPCR were consistent with those of the RNA-seq (R 2 = 0.61). The top 10 significantly enriched signaling pathways and immune-related pathways of the common and unique DEGs were screened from the transcriptome data. Twentyone cytokine candidate DEGs were identified, which belong to 4 cytokine families, namely, BCL/CLL, EPRF1, IL-17 and TSP/TPO. Gene expression in response to LPS dose-increased treatment (0, 10, 20 and 50 μg/ml) showed that IL-17 family cytokines were significantly upregulated after 10 μg/ml LPS challenge for 24 h.

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“…However, this network analysis is quite rare and needs a more elaborate method to represent as much as information regarding the strength of the connections. Subsequently, various network-based analyses have been applied to the gene co-expression network [9,10,11,12,13,14,15,16,17]. Some of the simple and widely used local network measurements are the degree centrality (or hub centrality) [13,14,17,18,19] and clustering coefficient [17,20,21,22,23,24,25].…”

Section: Introductionmentioning

confidence: 99%

Two-State Co-Expression Network Analysis to Identify Genes Related to Salt Tolerance in Thai Rice

Suratanee

Chokrathok

Chutimanukul

et al. 2018

Genes

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Khao Dawk Mali 105 (KDML105) rice is one of the most important crops of Thailand. It is a challenging task to identify the genes responding to salinity in KDML105 rice. The analysis of the gene co-expression network has been widely performed to prioritize significant genes, in order to select the key genes in a specific condition. In this work, we analyzed the two-state co-expression networks of KDML105 rice under salt-stress and normal grown conditions. The clustering coefficient was applied to both networks and exhibited significantly different structures between the salt-stress state network and the original (normal-grown) network. With higher clustering coefficients, the genes that responded to the salt stress formed a dense cluster. To prioritize and select the genes responding to the salinity, we investigated genes with small partners under normal conditions that were highly expressed and were co-working with many more partners under salt-stress conditions. The results showed that the genes responding to the abiotic stimulus and relating to the generation of the precursor metabolites and energy were the great candidates, as salt tolerant marker genes. In conclusion, in the case of the complexity of the environmental conditions, gaining more information in order to deal with the co-expression network provides better candidates for further analysis.

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Weighted gene co-expression network analysis reveals potential genes involved in early metamorphosis process in sea cucumber Apostichopus japonicus

Cited by 16 publications

References 29 publications

Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms

Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms

Transcriptomic analysis of sea cucumber (Holothuria leucospilota) coelomocytes revealed the echinoderm cytokine response during immune challenge

Two-State Co-Expression Network Analysis to Identify Genes Related to Salt Tolerance in Thai Rice

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