Transcriptome analysis reveals the pigmentation related genes in four different shell color strains of the Manila clam Ruditapes philippinarum

Nie, Hongtao; Jiang, Kunyin; Jiang, Liwen; Huo, Zhongming; Ding, Jianfeng; Yan, Xiwu

doi:10.1016/j.ygeno.2019.11.013

Cited by 36 publications

(10 citation statements)

References 41 publications

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“…Among 15 DEGs selected from the transcriptome for validation, one DEG showed inconsistencies between qPCR and RNE-Seq data. This situation also happens in other species [31], and it is likely caused by false-positivity [9].…”

Section: Discussionmentioning

confidence: 94%

Transcriptomic Analysis of Mating Responses in Bemisia tabaci MED Females

Huo

Liu

Yang

et al. 2020

Insects

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Mating triggers substantial changes in gene expression and leads to subsequent physiological and behavioral modifications. However, postmating transcriptomic changes responding to mating have not yet been fully understood. Here, we carried out RNA sequencing (RNAseq) analysis in the sweet potato whitefly, Bemisia tabaci MED, to identify genes in females in response to mating. We compared mRNA expression in virgin and mated females at 24 h. As a result, 434 differentially expressed gene transcripts (DEGs) were identified between the mated and unmated groups, including 331 up- and 103 down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that many of these DEGs encode binding-related proteins and genes associated with longevity. An RT-qPCR validation study was consistent with our transcriptomic analysis (14/15). Specifically, expression of P450s (Cyp18a1 and Cyp4g68), ubiquitin-protein ligases (UBR5 and RNF123), Hsps (Hsp68 and Hsf), carboxylase (ACC-2), facilitated trehalose transporters (Tret1-2), transcription factor (phtf), and serine-protein kinase (TLK2) were significantly elevated in mated females throughout seven assay days. These combined results offer a glimpe of postmating molecular modifications to facilitate reproduction in B. tabaci females.

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Section: Discussionmentioning

confidence: 94%

Transcriptomic Analysis of Mating Responses in Bemisia tabaci MED Females

Huo

Liu

Yang

et al. 2020

Insects

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“…The pathway has also been identified in some molluscan species, such as marine snails Clanculus margaritarius and C. pharaonius , and has been shown to be related to shell colouration [ 18 ]. Transcriptome analyses in the Manila clam ( Ruditapes philippinarum ) [ 20 ], hard clam ( Mercenaria mercenaria ) [ 21 ] and Yesso scallop [ 15 , 19 ] have identified that the ‘porphyrin and chlorophyll metabolism’ (KO00860) pathway, which is a large pathway containing the heme biosynthesis pathway, is involved in shell colour formation. In the present study, GO functions, including porphyrin and heme biosynthetic processes, and the porphyrin and chlorophyll metabolism pathway were also significantly enriched in the DMRs between the two shell colour scallops, indicating that the biosynthesis process of porphyrins may be regulated by DNA methylation.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide DNA methylation profile changes associated with shell colouration in the Yesso scallop (Patinopecten yessoensis) as measured by whole-genome bisulfite sequencing

et al. 2021

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Background Mollusca, a phylum of highly rich species, possess vivid shell colours, but the underlying molecular mechanism remains to be elucidated. DNA methylation, one of the most common epigenetic modifications in eukaryotes, is believed to play a vital role in various biological processes. However, analysis of the effects of DNA methylation on shell colouration has rarely been performed in molluscs, limiting the current knowledge of the molecular mechanism of shell colour formation. Results In the present study, to reveal the role of epigenetic regulation in shell colouration, WGBS, the “gold standard” of DNA methylation analysis, was first performed on the mantle tissues of Yesso scallops (Patinopecten yessoensis) with different shell colours (brown and white), and DNA methylomes at single-base resolution were generated. About 3% of cytosines were methylated in the genome of the Yesso scallop. A slight increase in mCG percentage and methylation level was found in brown scallops. Sequence preference of nearby methylated cytosines differed between high and low methylation level sites and between the brown- and white-shelled scallops. DNA methylation levels varied among the different genomic regions; all the detected regions in the brown group exhibited higher methylation levels than the white group. A total of 41,175 DMRs (differentially methylated regions) were detected between brown and white scallops. GO functions and pathways associated with the biosynthesis of melanin and porphyrins were significantly enriched for DMRs, among which several key shell colour-related genes were identified. Further, different correlations between mRNA expression levels and DNA methylation status were found in these genes, suggesting that DNA methylation regulates shell colouration in the Yesso scallop. Conclusions This study provides genome-wide DNA methylation landscapes of Yesso scallops with different shell colours, offering new insights into the epigenetic regulatory mechanism underlying shell colour.

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“…Genetic maps have been used to study the genetic architecture of traits of interest in various bivalve species, such as growth in Zhikong scallop (Chlamys farreri; Zhan et al, 2009), bay scallop (Argopecten irradians; Li et al, 2012) or Crassostrea gigas (Li et al, 2018), various pearl-quality traits in triangle sail mussel (Hyriopsis cumingii; Bai et al, 2016) and resistance to pathologies (Harrang et al, 2015). Previous studies have also identified QTL for shell colouration in several bivalves including Manila clam (Ruditapes philippinarum; Nie et al, 2017Nie et al, , 2020Nie et al, , 2021, hard clam (Mercenaria mercenaria; Hu et al, 2019), Pacific oyster (Crassostrea gigas; Feng et al, 2018;Song et al, 2018;Wang et al, 2018;Han et al, 2021), blacklip pearl oyster (Pinctada margaritifera; Lemer et al, 2015), Akoya pearl oyster (Pinctada fucata martensii; Xu et al, 2019) and Yesso scallop (Patinopecten yessoensis; Ding et al, 2015;Zhao et al, 2017), and therefore, similar strategies might be employed to ascertain the genetic component underlying differences in shell colouration in common cockle.…”

Section: Introductionmentioning

confidence: 99%

The broad shell colour variation in common cockle (Cerastoderma edule) from Northeast Atlantic relies on a major QTL revealed by GWAS using a new high-density genetic map

Hermida

Robledo

Díaz

et al. 2022

Preprint

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Shell colour pattern shows broad diversity in molluscs, and both genetic and environmental factors seem to interact to some extent on the final phenotype. Despite information on the genetic component and pathways involved in shell construction and colour has increased in the last decade, more data are needed particularly to understand colour variation and its putative role on adaptation. The European common cockle (Cerastoderma edule) is a valuable species from ecological and commercial perspectives with important variation in colour pattern, but this diversity has never been characterized and the underlying genetic architecture is unknown. In this study, we constructed a high-density genetic map, as an essential tool for genomic screening in common cockle, that was applied to ascertain the genetic basis of colour pattern variation in the species. The consensus map, including 13,874 2b-RAD SNPs, was constituted by the 19 linkage groups (LGs) corresponding to the n = 19 chromosomes of its karyotype and spanned 1,073 cM (730 markers per LG; inter-marker distance of 0.13 cM). Five full-sib families showing segregation for several colour-associated traits were used to perform a GWAS analysis. A major QTL on chromosome 13 explained most of the variation for shell colour patterns. Mining on this genomic region revealed the presence of several candidate genes enriched on Gene Ontology terms such as anatomical structure development, ion transport, membrane transport and cell periphery, closely related to shell architecture, including six chitin-related, one ependymin, several ion binding and transporters, and others related to transit across the cell membrane. Interestingly, this major QTL overlaps with a genomic region previously reported associated with divergent selection in the distribution range of the species, suggesting a putative role on local adaptation.

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Transcriptome analysis reveals the pigmentation related genes in four different shell color strains of the Manila clam Ruditapes philippinarum

Cited by 36 publications

References 41 publications

Transcriptomic Analysis of Mating Responses in Bemisia tabaci MED Females

Transcriptomic Analysis of Mating Responses in Bemisia tabaci MED Females

Genome-wide DNA methylation profile changes associated with shell colouration in the Yesso scallop (Patinopecten yessoensis) as measured by whole-genome bisulfite sequencing

The broad shell colour variation in common cockle (Cerastoderma edule) from Northeast Atlantic relies on a major QTL revealed by GWAS using a new high-density genetic map

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