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Transcriptomic analysis provides insights into candidate genes and molecular pathways involved in growth of Manila clam Ruditapes philippinarum

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Abstract

Growth is one of the most important traits of aquaculture breeding programs. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Ruditapes philippinarum is an economically important marine bivalve. In order to gain insights into the molecular mechanisms to growth variability in marine shellfish, we conducted the transcriptome sequencing and examined the expression differences in growth-related gene and molecular pathways involved in growth trait of R. philippinarum. In this study, we investigated the molecular and gene expression differences in fast-growing and slow-growing Manila clam and focused on the analysis of the differential expression patterns of specific genes associated with growth by RNA-seq and qPCR analysis. A total of 61 differentially expressed genes (DEGs) were captured significantly differentially expressed, and were categorized into Ras signaling pathway, hedgehog signaling pathway, AMPK signaling pathway, p53 signaling pathway, regulation of actin cytoskeleton, focal adhesion, mTOR signaling pathway, VEGF signaling pathway, and TGF-beta signaling pathway. A total of 34 growth-related genes were validated significantly and up/downregulated at fast growing and slow growing of R. philippinarum. Functional enrichment analysis revealed the insulin signaling pathway, PI3K-Akt signaling pathway, and mTOR signaling pathway play pivotal roles in molecular function and regulation of growth trait in R. philippinarum. The growth-related genes and pathways obtained here provide important insights into the molecular basis of physiological acclimation, metabolic activity, and growth variability in marine bivalves.

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Data Availability

The raw sequences for R. philippinarum have been deposited in the NCBI PRJNA478927 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA478927). The RNA-seq datasets are available in the NCBI Sequence Read Archive (SRA) with the accession numbers SRP151797.

Abbreviations

DEGs:

differentially expressed genes

GO:

Gene Ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes pathways

KOG:

eukaryotic orthologous groups

qPCR:

quantitative real-time PCR

ATP:

adenosine-5′-triphosphate

COG:

Clusters of Orthologous Groups

pp1c:

serine/threonine-protein phosphatase PP1 catalytic subunit

megf:

multiple epidermal growth factor

igf:

insulin-like growth factor

en:

homeobox protein engrailed

tuba:

tubulin alpha

mitf:

microphthalmia-associated transcription factor

tagln3:

transgelin-like protein-3

fbn2:

fibrillin-2-like

degs:

sphingolipid 4-desaturase/C4-monooxygenase

mstn:

myostatin

Eps15l1:

epidermal growth factor receptor substrate 15-like 1

aoc1\abp1:

diamine oxidase

myosin:

myosin II heavy chain

tst\mpst\ssea:

thiosulfate/3-mercaptopyruvate sulfurtransferase

ppif:

peptidyl-prolyl isomerase F

alpha-amylase:

alpha-amylase

eef2k:

elongation factor 2 kinase

hspb1:

heat shock protein beta-1

hspa1s:

heat shock 70kDa protein 1

ltbp1:

latent-transforming growth factor beta-binding protein 1

tgfb1:

transforming growth factor beta-1

notch1:

notch 1

thbs1:

thrombospondin 1

erk\mapk1\3:

mitogen-activated protein kinase 1/3

flna:

filamin

smad2:

mothers against decapentaplegic homolog 2

smad-binding:

SMAD binding

madhip\sara:

MAD, mothers against decapentaplegic interacting protein

5hspa5\bip:

heat shock 70kDa protein

pla1a:

phospholipase A1 member A

gas1:

growth arrest-specific 1

wnt1:

WNT inhibitory factor 1

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Funding

This work was supported by the Chinese Ministry of Science and Technology through the National Key Research and Development Program of China (2018YFD0901400), the Modern Agro-industry Technology Research System (CARS-49), the Scientific Research Project of Liaoning Education Department (QL201703), and the Dalian high-level talent innovation support program (Dalian Youth Science and Technology Star Project Support Program) (2016RQ065). The project is sponsored by “Liaoning BaiQianWan Talents Program”.

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Authors and Affiliations

  1. College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China

    Hongtao Nie, Mengge Zheng, Zhengxing Wang, Qiaoyue Xu, Zhihui Yin, Yanming Zhang & Xiwu Yan

  2. Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, China

    Hongtao Nie, Mengge Zheng, Zhengxing Wang, Qiaoyue Xu, Zhihui Yin, Yanming Zhang & Xiwu Yan

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  1. Hongtao Nie
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  2. Mengge Zheng
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  3. Zhengxing Wang
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  5. Zhihui Yin
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  6. Yanming Zhang
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Correspondence to Hongtao Nie.

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Supplementary information

Fig. S1

Sequence length distribution of transcripts and unigenes assembled from Illumina reads of the transcriptome of Ruditapes philippinarum. The x-axis indicates the lengths of the transcripts and unigenes, and the y-axis indicates the number of transcripts and unigenes in each size category. (PDF 4 kb)

Fig. S2

The BUSCO assessment result. (PNG 90 kb)

Fig. S3

The unigenes annotated in different database. (PNG 17 kb)

Fig. S4

Species distribution of sequences matched to the Nr database. (PNG 26 kb)

Fig. S5

GO (Gene Ontology) categorization (biological process, cellular component, and molecular function) of the unigenes in the gill transcriptome of R. philippinarum. Each annotated sequence is assigned at least one GO term. (PNG 356 kb)

Fig. S6

KOG (euKaryotic Ortholog Groups) classifications of putative proteins in the gill transcriptome of R. philippinarum. (PNG 54 kb)

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Nie, H., Zheng, M., Wang, Z. et al. Transcriptomic analysis provides insights into candidate genes and molecular pathways involved in growth of Manila clam Ruditapes philippinarum. Funct Integr Genomics 21, 341–353 (2021). https://doi.org/10.1007/s10142-021-00780-1

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