For the six samples, 79.3–82.2% of the total clean reads were aligned to the genome, of which 71.0–73.1% had a unique alignment and 8.1–9.1% had multiple alignment positions on the genome (A total of 1,303 differentially expressed genes (DEGs) were identified between the “breed” and “wild” Pacific oysters, of which 888 genes were expressed at higher levels in “breed” oysters while 415 genes were expressed at higher levels in the unselected “wild” oysters (Twelve DEGs were selected for qRT-PCR validation, and the results were compared with those from RNA-Seq data analysis. It is most easily identified by its blue-gray shell with highly fluted edges (Fig. The total bases of clean reads generated from each sample ranged from 7.0 to 8.2 Gb, which is about 15× of the oyster genome size. All authors have read and approved the final version of the manuscript.This study was supported by the grants from National Natural Science Foundation of China (31741122 and 31802293), Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology (2017-2A04), China Postdoctoral Science Foundation (2017M622283), and the Fundamental Research Funds for the Central Universities (201812013).The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.We are grateful to Chengxun Xu, Ziqiang Han, and the oyster breeding team of our research group for their assistance in maintaining and collecting the samples used in this work.The Supplementary Material for this article can be found online at:
Transcriptome-wide analysis of positively selected genes revealed the important roles of ribosomal protein genes, which further suggested that the process of protein biosynthesis may be a key biological process related to the growth difference between selectively bred oysters and unselected wild oysters. The Pacific oyster, Growth is one of the most important traits related to fitness and production for any organism. 1). The Pacific oyster, Crassostrea gigas, naturally distributing along the coast of northwest Pacific, is one of the most important bivalve species due to its high economic value and fecundity. QL provided reagents and materials and supervised the study. Nucleotides carry packets of chemical energy in the form of the nucleoside triphosphates (ATP, GTP, CTP, and UTP) and plays an important role in metabolism at the cellular level, such as synthesis of amino acids and proteins, movement of the cell and cell parts, and division of the cell (Gene functional annotation analysis showed that both differentially expressed genes and alternatively spliced genes were significantly enriched in long-term potentiation, phosphatidylinositol signaling system, ABC transporters, and salivary secretion pathways. PRJNA524442 (sequence accessions: SRR9089186-SRR9089191).SL conceived and designed the study. Therefore, genetic breeding of fast-growing varieties or strains have been extensively conducted in aquaculture species.Growth is a complex trait in marine mollusks, which is genetically controlled but affected by environmental variables such as temperature and food availability (The fast-growing oyster variety provides us a good research model for studies of growth trait. Ribosomal proteins are crucial for the growth and development of the organisms (To unravel the molecular basis for fast growth of the selectively bred Pacific oyster, we performed comparative transcriptome analysis of the fast-growing “breed” with the unselected “wild” Pacific oysters in terms of gene expression, alternative splicing, and molecular evolution. These ribosomal protein-related genes include Growth trait is implicated in a variety of cellular processes and is subject to regulation by multiple complex biological processes.
Currently, triploid oysters are commercially cultured primarily in two species: the Pacific oyster Crassostrea gigas, a species cultured worldwide, and the eastern oyster Crassostrea virginica, a species cultured along the East Coast of the United States and in the Gulf of Mexico.
The Pacific oyster, Crassostrea gigas, is a common oyster species that grows individually or in dense mats on rocks and soft substrates in temperate tidal and sub-tidal zones (Hughes 2008). The Pacific oyster, Japanese oyster, or Miyagi oyster (Magallana gigas), previously and currently also known as Crassostrea gigas, considered by part of the scientific community to be the proper denomination as an accepted alternative in WoRMS, is an oyster native to the Pacific coast of Asia.It has become an introduced species in North America, Australia, Europe, and New Zealand. Pacific oyster (Crassostrea gigas) is a sessile bivalve living in the intertidal zone. Annual production of the Pacific oyster, Crassostrea gigas, in Korea, is 3.5 million ton, which occupies 90% of the total shellfish production (MIFAFF, 2012).Production of diverse lines through a breeding program and management of mother shell for the production of artificial seeds are essential to increase volume and quality of the oysters.
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