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Marine biotechnology (New York, N.Y.)
Apr, 2021;23 (2): 233-241.

Whole-Genome Re-sequencing and Transcriptome Reveal Oogenesis-Related Genes in Autotetraploid Carassius auratus.

Chongqing Wang, Huan Qin, Chun Zhao, Li Yang, Tingting Yu, Yuxin Zhang, Xiang Luo, Qinbo Qin, Shaojun Liu
Author Information
  1. Chongqing Wang: State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
  2. Huan Qin: State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
  3. Chun Zhao: State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
  4. Li Yang: State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
  5. Tingting Yu: State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
  6. Yuxin Zhang: State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
  7. Xiang Luo: State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
  8. Qinbo Qin: State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China. 30055776@qq.com.
  9. Shaojun Liu: State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China. lsj@hunnu.edu.cn. ORCID
PMID: 33675430 DOI: 10.1007/s10126-021-10018-7

Abstract

Oogenesis involves a series of biochemical and physiological transformations and numerous regulated genes. The autotetraploid Carassius auratus (4nRR) originated from whole-genome duplication of Carassius auratus red var. (RCC), which produces diploid eggs through pairing of diploid-like chromosome during female meiosis. To explore the molecular mechanisms underlying oogenesis in 4nRR, we used the Illumina sequencing platform to characterize the ovaries of 4nRR and RCC. Transcriptome and whole-genome re-sequencing were performed to uncover the key genes and potential genetic mutations related to oogenesis. Each sample produced paired-end reads in the range of 66.97 to 98.36 million via Illumina HiSeq™ 2500. After comparing of the transcriptome profiles between the 4nRR and RCC, we uncovered 8562 differentially expressed genes (DEGs). The DEGs were enriched in oogenesis-related processes, including oogenesis, oocyte development, ubiquitin-mediated proteolysis, the signaling pathways of MAPK and calcium, and oocyte meiosis as investigated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Additionally, whole-genome re-sequencing revealed 34,058,834 SNPs and 6,153,711 InDels, including 6,677,638 non-synonymous variations (SNPs) and 706,210 frame-shift InDels in the 8510 DEGs of 4nRR fish. Subsequently, whole-genome re-sequencing and transcriptomatic analyses revealed the genes that participate in oogenesis associated processes. Specifically, genes involved in ubiquitin-mediated proteolysis (SMURF1, UBE2I), calcium transport (CALM3, CAMK4), and meiosis (MAPK3, GRB2, CPEB1, CCNB2, YWHAE) were related to oogenesis in 4nRR. These findings enrich our understanding of oogenesis in the autopolyploid fish.

Keywords

Autotetraploid Oogenesis Transcriptome Whole-genome re-sequencing

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Grants

  1. 2017JJ1022/Natural Science Foundation for Distinguished Young Scholars of Hunan Province
  2. 31730098/National Natural Science Foundation of China
  3. U19A2040/National Natural Science Foundation of China
  4. CARS-45/Earmarked Fund for China Agriculture Research System
  5. 2019RS5001/Hunan Provincial Science and Technology Department
  6. 2020YFD0900104/National Key Research and Development Program of China

MeSH Term

Animals
Female
Goldfish
INDEL Mutation
Oogenesis
Ovary
Polymorphism, Single Nucleotide
Signal Transduction
Tetraploidy
Transcriptome
Whole Genome Sequencing
Journal Article
Article has an altmetric score of 3

Word Cloud

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