Transcriptome analysis reveals the pigmentation-related genes in two shell color strains of the Manila clam<i>Ruditapes philippinarum</i>

Nie, Hongtao; Jiang, Kunyin; Li, Ning; Jahan, Kifat; Jiang, Liwen; Huo, Zhongming; Yan, Xiwu

doi:10.1080/10495398.2020.1714635

Cited by 15 publications

(4 citation statements)

References 46 publications

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“…This study combined the PacBio Iso-Seq and Illumina RNA-Seq technologies to generate a full-length transcriptome for M. lateralis. After correction, the average length of full-length consensus transcripts was 3,267 bp with an N50 of 3,879 bp (Table S2), which were much longer than that of the de novo assembled transcripts (Hu et al, 2019;Nie et al, 2021;Núñez-Acuña et al, 2022) and comparative with the full-length transcriptome of bivalve species recently reported (Liao et al, 2022;Zeng et al, 2022). The average mapping rate of Illumina sequences was greater than 75%, indicating that a good reference dataset was established.…”

Section: Resultsmentioning

confidence: 99%

Full-length transcriptome analysis provides insights into larval shell formation in Mulinia lateralis

Guo

Zhao

et al. 2023

Front. Mar. Sci.

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Mollusca is the second largest animal phylum and represents one of the most evolutionarily successful animal groups. Mulinia lateralis, a small bivalve, is a promising model organism to facilitate studies of mollusc development. However, because of the lack of published genomic and transcriptomic resources, integrated research on the formation of larval shells in this species, which is a representative developmental process of molluscs and of great importance for larva survival, is hindered. In this study, the blastula, gastrula, trochophore larva, and D-shaped larva of M. lateralis were utilized for generating a comprehensive full-length transcriptome through Pacific BioSciences (PacBio) isoform sequencing (Iso-seq) and Illumina RNA-Seq. A total of 238,919 full-length transcripts with an average length of 3,267 bp and 121,424 annotated genes were obtained. Illumina RNA-Seq data analysis showed that 4,512, 10,637, and 17,829 differentially expressed genes (DEGs) were obtained between the two adjacent developmental stages. Functional annotation and enrichment analysis revealed the specific function of genes in shell biomineralization during different developmental stages. Twelve genes that may be involved in the formation of the larval shell of M. lateralis were identified, including insoluble shell matrix protein-encoding gene 1 (ISMP1), ISMP2, ISMP5, chitin synthase, tyrosinase, chitin-binding protein, collagen and pu14 involved in shell matrix deposition, and carbonic anhydrase, solute carrier family 4 member 8 (slc4a8), EF-hand, and a calmodulin coding gene C-2442 participated in ion transportation. In addition, calcium ion binding function, calcium signaling pathway, and endocrine and other factor-regulated calcium reabsorption pathways were significantly enriched. Weighted gene correlation network analysis (WGCNA) identified two modules related to biomineralization and larval shell formation, and slc4a8 and ring finger protein 41 (rnf41) were key hub genes that may be involved in this process. Moreover, it could be implied that the process of ion transport occurs earlier than the deposition of the shell matrix. This work provided a clear view of the transcriptome for M. lateralis and will be valuable in elucidating the mechanisms of larval shell formation as well as other developmental processes in molluscs.

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Section: Resultsmentioning

confidence: 99%

Full-length transcriptome analysis provides insights into larval shell formation in Mulinia lateralis

Guo

Zhao

et al. 2023

Front. Mar. Sci.

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“…Melanization is sometimes accompanied with biomineralization that melanized invaders will be embedded in a new-formed calcified shell layer, as found in brown ring disease (BRD) of clams and Roseovarius oyster disease (ROD) of oysters [ 13 – 16 ]. Though many studies have been conducted to identify genes or pathways involved in shell biomineralization and pigmentation [ 12 , 17 – 21 ], the molecular mechanisms of which have still not been thoroughly elucidated due to their high complexity.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis reveals core lncRNA-mRNA networks regulating melanization and biomineralization in Patinopecten yessoensis shell-infested by Polydora

Wang,

Mao,

Fan

et al. 2023

BMC Genomics

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Background Patinopecten yessoensis, a large and old molluscan group, has been one of the most important aquaculture shellfish in Asian countries because of its high economic value. However, the aquaculture of the species has recently been seriously affected by the frequent outbreaks of Polydora disease, causing great economic losses. Long non-coding RNAs (lncRNAs) exhibit exhibit crucial effects on diverse biological processes, but still remain poorly studied in scallops, limiting our understanding of the molecular regulatory mechanism of P. yessoensis in response to Polydora infestation. Results In this study, a high-throughput transcriptome analysis was conducted in the mantles of healthy and Polydora-infected P. yessoensis by RNA sequencing. A total of 19,133 lncRNAs with 2,203 known and 16,930 novel were identified. The genomic characterizations of lncRNAs showed shorter sequence and open reading frame (ORF) length, fewer number of exons and lower expression levels in comparison with mRNAs. There were separately 2280 and 1636 differentially expressed mRNAs and lncRNAs (DEGs and DELs) detected in diseased individuals. The target genes of DELs were determined by both co-location and co-expression analyses. Functional enrichment analysis revealed that DEGs involved in melanization and biomineralization were significantly upregulated; further, obviously increased melanin granules were observed in epithelial cells of the edge mantle in diseased scallops by histological and TEM study, indicating the crucial role of melanizaiton and biomineralization in P. yessoensis to resist against Polydora infestation. Moreover, many key genes, such as Tyrs, Frizzled, Wnts, calmodulins, Pifs, perlucin, laccase, shell matrix protein, mucins and chitins, were targeted by DELs. Finally, a core lncRNA-mRNA interactive network involved in melanization and biomineralization was constructed and validated by qRT-PCR. Conclusions This work provides valuable resources for studies of lncRNAs in scallops, and adds a new insight into the molecular regulatory mechanisms of P. yessoensis defending against Polydora infestation, which will contribute to Polydora disease control and breeding of disease-resistant varieties in molluscs.

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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 ( Azumapecten farreri ; 27 ), bay scallop ( Argopecten irradians ; 28 ) or Pacific oyster ( Crassostrea gigas 29 ; ), various pearl-quality traits in triangle sail mussel ( Hyriopsis cumingii ; 30 ) and resistance to pathologies in European flat oyster ( Ostrea edulis ; 31 ). Previous studies have also identified QTL for shell coloration in several bivalves including Manila clam ( Ruditapes philippinarum ; 32 – 34 ), hard clam ( Mercenaria mercenaria ; 35 ), Pacific oyster ( Crassostrea gigas ; 36 – 39 ), black-lip pearl oyster ( Pinctada margaritifera ; 40 ), Akoya pearl oyster ( Pinctada fucata ; 41 ) and Yesso scallop ( Mizuhopecten yessoensis ; 42 , 43 ), and therefore, similar strategies might be employed to ascertain the genetic component underlying differences in shell coloration in common cockle.…”

Section: Introductionmentioning

confidence: 99%

The first high-density genetic map of common cockle (Cerastoderma edule) reveals a major QTL controlling shell color variation

Hermida

Robledo

Díaz

et al. 2022

Sci Rep

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Shell color shows broad variation within mollusc species and despite information on the genetic pathways involved in shell construction and color has recently increased, more studies are needed to understand its genetic architecture. The common cockle (Cerastoderma edule) is a valuable species from ecological and commercial perspectives which shows important variation in shell color across Northeast Atlantic. In this study, we constructed a high-density genetic map, as a tool for screening common cockle genome, which was applied to ascertain the genetic basis of color variation in the species. The consensus genetic map comprised 19 linkage groups (LGs) in accordance with the cockle karyotype (2n = 38) and spanned 1073 cM, including 730 markers per LG and an inter-marker distance of 0.13 cM. Five full-sib families showing segregation for several color-associated traits were used for a genome-wide association study and a major QTL on chromosome 13 associated to different color-traits was detected. Mining on this genomic region revealed several candidate genes related to shell construction and color. A genomic region previously reported associated with divergent selection in cockle distribution overlapped with this QTL suggesting its putative role on adaptation.

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Transcriptome analysis reveals the pigmentation-related genes in two shell color strains of the Manila clamRuditapes philippinarum

Cited by 15 publications

References 46 publications

Full-length transcriptome analysis provides insights into larval shell formation in Mulinia lateralis

Full-length transcriptome analysis provides insights into larval shell formation in Mulinia lateralis

Transcriptome analysis reveals core lncRNA-mRNA networks regulating melanization and biomineralization in Patinopecten yessoensis shell-infested by Polydora

The first high-density genetic map of common cockle (Cerastoderma edule) reveals a major QTL controlling shell color variation

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