Identification of the differentially expressed genes of Pinctada maxima individuals with different sizes through transcriptome analysis

Wang, Ziman; Liang, Fang; Huang, Ronglian; Deng, Yuewen; Li, Junhui

doi:10.1016/j.rsma.2019.100512

Cited by 16 publications

(15 citation statements)

References 44 publications

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“…RNA-seq is a method of large-scale screening that reflects trends in gene expression in whole samples, but it does not guarantee that trends for each gene are consistent between RNA-seq and qPCR methods. Previous research reported that the majority of differentially expressed metabolites are up-regulated in small individuals [ 24 , 51 ]. Additionally, some genes related to growth and development, shell formation, and reproduction are expressed more highly in S groups compared with L groups in pearl oyster [ 26 ].…”

Section: Discussionmentioning

confidence: 99%

“…In shellfish, understanding the differences between individuals is very important for developing strategies in breeding. Screening for growth-related candidate genes has helped advance molecular genetics and breeding [ 23 , 24 ]. Growth of oysters were regulated by a series of genes associated with protein synthesis, signal transduction and metabolism [ 9 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

“…Thus, identification of various differentially expressed genes involved in individual differences can provide insights into the growth mechanism, and develop suitable molecular markers for breeding [ 25 ]. Because growth mechanisms are complex and relate to many physiological processes, growth-related molecules derived from oysters have been studied using Illumina sequencing [ 11 , 24 , 26 ]. However, PacBio sequencing can provide further information on transcript diversity, including alternative splicing and alternative polyadenylation [ 15 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

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PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome

Zhang

Liu

et al. 2020

BMC Genomics

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Background The pearl oyster Pinctada fucata martensii is an economically valuable shellfish for seawater pearl production, and production of pearls depends on its growth. To date, the molecular mechanisms of the growth of this species remain poorly understood. The transcriptome sequencing has been considered to understanding of the complexity of mechanisms of the growth of P. f. martensii. The recently released genome sequences of P. f. martensii , as well as emerging Pacific Bioscience (PacBio) single-molecular sequencing technologies, provide an opportunity to thoroughly investigate these molecular mechanisms. Results Herein, the full-length transcriptome was analysed by combining PacBio single-molecule long-read sequencing (PacBio sequencing) and Illumina sequencing. A total of 20.65 Gb of clean data were generated, including 574,561 circular consensus reads, among which 443,944 full-length non-chimeric (FLNC) sequences were identified. Through transcript clustering analysis of FLNC reads, 32,755 consensus isoforms were identified, including 32,095 high-quality consensus sequences. After removing redundant reads, 16,388 transcripts were obtained, and 641 fusion transcripts were derived by performing fusion transcript prediction of consensus sequences. Alternative splicing analysis of the 16,388 transcripts was performed after accounting for redundancy, and 9097 gene loci were detected, including 1607 new gene loci and 14,946 newly discovered transcripts. The original boundary of 11,235 genes on the chromosomes was corrected, 12,025 complete open reading frame sequences and 635 long non-coding RNAs (LncRNAs) were predicted, and functional annotation of 13,482 new transcripts was achieved. Two thousand three hundred eighteen alternative splicing events were detected. A total of 228 differentially expressed transcripts (DETs) were identified between the largest (L) and smallest (S) pearl oysters. Compared with the S, the L showed 99 and 129 significantly up-and down-regulated DETs, respectively. Six of these DETs were further confirmed by quantitative real-time RT-PCR (RT-qPCR) in independent experiment. Conclusions Our results significantly improve existing gene models and genome annotations, optimise the genome structure, and in-depth understanding of the complexity and diversity of the differential growth patterns of P. f. martensii .

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome

Zhang

Liu

et al. 2020

BMC Genomics

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“…One major problem found in pearl oyster stocks is the variability in growth performance when pearl oysters are cultured under same environmental conditions (Hao et al, ). This unsynchronized growth was related to an unexplainable variance (Tamayo, Ibarrola, Urrutia, & Navarro, ) and in an attempt to understand and explain the variance, transcriptome and metabolomics studies have been used to investigate this mechanism in pearl oysters (Hao et al, , ; Wang et al, ). The results have provided insights into candidate genes and vital pathways involved in controlling the physiology of phenotypic traits.…”

Section: Unsynchronized Growth In Pearl Oystersmentioning

confidence: 99%

“…Various genes are involved in pearl oyster growth. Although the information and roles of the genes are limited due to their involvement in other biological processes, transcriptomic studies have screened and reported to some extent molecular mechanism and possible genes involved in regulating the growth of pearl oyster (Deng et al, ; Guan, He, & Wu, ; Shi & He, ; Wang, Liang, Huang, Deng, & Li, ; Yang et al, ). Understanding the functional mechanisms of these genes in growth is essential in improving the pearl industry.…”

Section: Introductionmentioning

confidence: 99%

Growth in pearl oysters: A review of genetic and environmental influences

et al. 2019

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Pearl oysters have high economic value. These species have gained much interest of research in growth, producing disease resistant and viable stocks for aquaculture facilities. Growth‐related genes, such as insulin‐related peptide receptor and the IGF system, and its components ERKs and MKK4 have been documented to influence growth in pearl oysters. Temperature, salinity, culture condition among other environmental factors were also reported to influence growth by influencing the physiological functions of pearl oysters such as clearance rate, oxygen consumption, respiration rate, excretion rate and expressed in parameters such as the scope of growth and the net growth efficiency. Genetic and artificial breeding techniques have been utilized in breeding programmes to improve growth and pearl quality in pearl oysters with mass selection and hybridization documented as efficient methods to improve growth traits. One problem observed during the growth of pearl oysters is the unsynchronized growth. Transcriptome and metabolomics studies have been undertaken to understand the underlying mechanism of this problem. The pearl oyster immune response to stress has also been reported to cause growth differences and needs to be thoroughly investigated to help produce viable stocks with synchronized growth for the aquaculture industry.

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Mantle Transcriptome Provides Insights into Biomineralization and Growth Regulation in the Eastern Oyster (Crassostrea virginica)

Zhang

2022

Mar Biotechnol

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Identification of the differentially expressed genes of Pinctada maxima individuals with different sizes through transcriptome analysis

Cited by 16 publications

References 44 publications

PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome

PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome

Growth in pearl oysters: A review of genetic and environmental influences

Mantle Transcriptome Provides Insights into Biomineralization and Growth Regulation in the Eastern Oyster (Crassostrea virginica)

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