The Chromosome-Level Genome Assembly and Comprehensive Transcriptomes of the Razor Clam (Sinonovacula constricta)

Dong, Yan; Zeng, Qifan; Ren, Jianfeng; Yao, Hanhan; Lv, Liyuan; He, Lin; Ruan, Wenbin; Xue, Qinggang; Bao, Zhenmin; Wang, Shi; Zhang, Lin

doi:10.3389/fgene.2020.00664

Cited by 23 publications

(15 citation statements)

References 45 publications

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“…Coding sequences from the 41,065 predicted genes had a mean length of 375.84 amino acids and 22,568 were annotated by available protein databases. The number of annotated genes aligns with other bivalve genomes (e.g., Bai et al 2019 ; Dong et al 2020 ), but suggests some hypothetical proteins may be lineage specific.…”

Section: Resultsmentioning

confidence: 69%

A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida)

Smith

2021

Genome Biology and Evolution

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From a genomics perspective, bivalves (Mollusca: Bivalvia) have been poorly explored with the exception for those of high economic value. The bivalve order Unionida, or freshwater mussels, has been of interest in recent genomic studies due to their unique mitochondrial biology and peculiar life cycle. However, genomic studies have been hindered by the lack of a high-quality reference genome. Here, I present a genome assembly of Potamilus streckersoni using Pacific Bioscience single-molecule real-time long reads and 10X Genomics linked read sequencing. Further, I use RNA sequencing from multiple tissue types and life stages to annotate the reference genome. The final assembly was far superior to any previously published freshwater mussel genome and was represented by 2,368 scaffolds (2,472 contigs) and 1,776,755,624 bp, with a scaffold N50 of 2,051,244 bp. A high proportion of the assembly was comprised of repetitive elements (51.03%), aligning with genomic characteristics of other bivalves. The functional annotation returned 52,407 gene models (41,065 protein, 11,342 tRNAs), which was concordant with the estimated number of genes in other freshwater mussel species. This genetic resource, along with future studies developing high-quality genome assemblies and annotations, will be integral toward unraveling the genomic bases of ecologically and evolutionarily important traits in this hyper-diverse group.

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Section: Resultsmentioning

confidence: 69%

A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida)

Smith

2021

Genome Biology and Evolution

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“…Recently, the genomic sequence and a large number of transcriptomic data of S. constricta have been available (Niu et al, 2013;Ran et al, 2019;Dong et al, 2020), however, the genes related with sex determination/differentiation or gametogenesis were still not identified. In this study, we analyzed the female and male gonadal transcriptomes of S. constricta using Illumina sequencing technology, compared expression patterns of differentially expressed genes between female and male gonads, and identified potential sex-related genes.…”

Section: Introductionmentioning

confidence: 99%

Gonad Transcriptome Analysis of the Razor Clam (Sinonovacula constricta) Revealed Potential Sex-Related Genes

et al. 2021

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The razor clam, Sinonovacula constricta is a commercially important bivalve in the western Pacific Ocean, yet little is known about the mechanisms of sex determination/differentiation and gametogenesis. In the present study, the comparative transcriptome analysis of adult gonads (female gonads and male gonads) was conducted to identify potential sex-related genes in S. constricta. The number of reads generated for each target library (three females and three males) ranged from 31,853,422 to 37,750,848, and 20,489,472 to 26,152,448 could be mapped to the reference genome of S. constricta (the map percentage ranging from 63.71 to 71.48%). A total of 8,497 genes were identified to be differentially expressed between the female and male gonads, of which 4,253 were female-biased (upregulated in females), and 4,244 were male-biased. Forty-five genes were identified as potential sex-related genes, including DmrtA2, Sox9, Fem-1b, and Fem-1c involved in sex determination/differentiation and Vg, CYP17A1, SOHLH2, and TSSK involved in gametogenesis. The expression profiles of 12 genes were validated by qRT-PCR, which further confirmed the reliability and accuracy of the RNA-Seq results. Our results provide basic information about the genes involved in sex determination/differentiation and gametogenesis, and pave the way for further studies on reproduction and breeding in S. constricta and other marine bivalves.

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“…Due to their wide distribution and characteristics in eukaryotes, the histones are deemed to represent a model system for studying multigene families with their organization, structure, and expression, which are of interest in phylogenetic and evolutionary studies [29]. Recently, completion of the razor clam genome sequencing project [30] offers a reliable genome. Furthermore, abundant transcriptome datasets for razor clam enable systematic characterization of the crucial histone gene family.…”

Section: Introductionmentioning

confidence: 99%

“…The razor clam (Sinonovacula constricta) is a mariculture bivalve mollusc in China with economic importance because of its delicious taste and high nutritional value [30,31]. This species is widely distributed in the intertidal region and can be vulnerable to bacterial stresses during its lifetime, especially from the pathogenic Vibrios.…”

Section: Introductionmentioning

confidence: 99%

“…This species is widely distributed in the intertidal region and can be vulnerable to bacterial stresses during its lifetime, especially from the pathogenic Vibrios. V. parahaemolyticus is a curved, rod-shaped, and Gram-negative bacterium found in the sea, which has been reported to cause adverse effects such as decreasing growth, weakened immunity, and even outbreaks of mass mortality of shellfish [30,32]. Notably, bivalve species have no adaptive immune defense mechanism and rely on innate immunity [33].…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Characterization and Analysis of Expression of the Histone Gene Family in Razor Clam, Sinonovacula constricta

Lian

Yao

et al. 2021

Fishes

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The Chinese razor clam (Sinonovacula constricta), a bivalve species widely distributed in estuaries and mudflats, is often exposed to extreme environmental and microbial stresses. Histones are fundamental components of chromatin and play an important role in innate immunity, as demonstrated by its antimicrobial activities in clams. However, little attention has been paid to histones in bivalves. To fill this gap, we investigated the genomic distribution, structural characteristics, conserved motifs, and phylogenetic relationships of histones in S. constricta. A total of 114 histone genes were detected in the S. constricta genome, which were divided into 25 types in phylogenetic analysis. Among them, partial histones exhibited a tissue-dependent expression pattern, indicating that they may be involved in sustaining the homeostasis of organs/tissues in adult S. constricta. Furthermore, mRNA expression of certain histones changed significantly in S. constricta when infected with Vibrio parahaemolyticus, suggesting that histones play a role in the immune defense of S. constricta. All together, this study on histone genes in S. constricta not only greatly expands our knowledge of histone function in the clam, but also histone evolution in molluscs.

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The Chromosome-Level Genome Assembly and Comprehensive Transcriptomes of the Razor Clam (Sinonovacula constricta)

Abstract: This manuscript has been released as a pre-print at bioRxiv (Dong et al., 2019).

Cited by 23 publications

References 45 publications

A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida)

A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida)

Gonad Transcriptome Analysis of the Razor Clam (Sinonovacula constricta) Revealed Potential Sex-Related Genes

Genome-Wide Characterization and Analysis of Expression of the Histone Gene Family in Razor Clam, Sinonovacula constricta

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