title: Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish × common carp cross.
abstract: Polyploidy is much rarer in animals than in plants but it is not known why. The outcome of combining two genomes in vertebrates remains unpredictable, especially because polyploidization seldom shows positive effects and more often results in lethal consequences because viable gametes fail to form during meiosis. Fortunately, the goldfish (maternal) × common carp (paternal) hybrids have reproduced successfully up to generation 22, and this hybrid lineage permits an investigation into the genomics of hybridization and tetraploidization. The first two generations of these hybrids are diploids, and subsequent generations are tetraploids. Liver transcriptomes from four generations and their progenitors reveal chimeric genes (>9%) and mutations of orthologous genes. Characterizations of 18 randomly chosen genes from genomic DNA and cDNA confirm the chimera. Some of the chimeric and differentially expressed genes relate to mutagenesis, repair, and cancer-related pathways in 2nF1. Erroneous DNA excision between homologous parental genes may drive the high percentage of chimeric genes, or even more potential mechanisms may result in this phenomenon. Meanwhile, diploid offspring show paternal-biased expression, yet tetraploids show maternal-biased expression. These discoveries reveal that fast and unstable changes are mainly deleterious at the level of transcriptomes although some offspring still survive their genomic abnormalities. In addition, the synthetic effect of genome shock might have resulted in greatly reduced viability of 2nF2 hybrid offspring. The goldfish × common carp hybrids constitute an ideal system for unveiling the consequences of intergenomic interactions in hybrid vertebrate genomes and their fertility.
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China; zhangyp@mail.kiz.ac.cn lsj@hunnu.edu.cn axel.meyer@uni-konstanz.de.
authors.forename: Shaojun
authors.initials: S
authors.lastname: Liu
authors.affiliation: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China;
authors.forename: Jing
authors.initials: J
authors.lastname: Luo
authors.affiliation: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China;
authors.forename: Jing
authors.initials: J
authors.lastname: Chai
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Li
authors.initials: L
authors.lastname: Ren
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China;
authors.forename: Feng
authors.initials: F
authors.lastname: Huang
authors.affiliation: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China;
authors.forename: Xiaochuan
authors.initials: X
authors.lastname: Liu
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Yubao
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Chun
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Min
authors.initials: M
authors.lastname: Tao
authors.affiliation: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China;
authors.forename: Bin
authors.initials: B
authors.lastname: Lu
authors.affiliation: School of Software, Yunnan University, Kunming, 650091, Yunnan, China;
authors.forename: Wei
authors.initials: W
authors.lastname: Zhou
authors.affiliation: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China;
authors.forename: Guoliang
authors.initials: G
authors.lastname: Lin
authors.affiliation: School of Software, Yunnan University, Kunming, 650091, Yunnan, China;
authors.forename: Chao
authors.initials: C
authors.lastname: Mai
authors.affiliation: School of Software, Yunnan University, Kunming, 650091, Yunnan, China;
authors.forename: Shuo
authors.initials: S
authors.lastname: Yuan
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Tao
authors.initials: T
authors.lastname: Li
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Qinbo
authors.initials: Q
authors.lastname: Qin
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Hao
authors.initials: H
authors.lastname: Feng
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Kaikun
authors.initials: K
authors.lastname: Luo
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Jun
authors.initials: J
authors.lastname: Xiao
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Huan
authors.initials: H
authors.lastname: Zhong
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Rurong
authors.initials: R
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Wei
authors.initials: W
authors.lastname: Duan
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Zhenyan
authors.initials: Z
authors.lastname: Song
authors.affiliation: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China;
authors.forename: Yanqin
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China;
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China;
authors.forename: Li
authors.initials: L
authors.lastname: Zhong
authors.affiliation: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China;
authors.forename: Lu
authors.initials: L
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China;
authors.forename: Zhaoli
authors.initials: Z
authors.lastname: Ding
authors.affiliation: Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China;
authors.forename: Zhenglin
authors.initials: Z
authors.lastname: Du
authors.affiliation: Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China;
authors.forename: Xuemei
authors.initials: X
authors.lastname: Lu
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China;
authors.forename: Yun
authors.initials: Y
authors.lastname: Gao
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China; Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada M5S 2C6;
authors.forename: Robert W
authors.initials: RW
authors.lastname: Murphy
authors.affiliation: Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
authors.forename: Yun
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Biology, University of Konstanz, 78457 Konstanz, Germany zhangyp@mail.kiz.ac.cn lsj@hunnu.edu.cn axel.meyer@uni-konstanz.de.
authors.forename: Axel
authors.initials: A
authors.lastname: Meyer
authors.affiliation: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China; zhangyp@mail.kiz.ac.cn lsj@hunnu.edu.cn axel.meyer@uni-konstanz.de.
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Zhang
mesh_terms: D000818:Animals; D002875:Chromosomes; D003433:Crosses, Genetic; D020869:Gene Expression Profiling; D006054:Goldfish / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence; D011003:Ploidies
keywords: allopolyploidization; chimeric genes; sequence validation; transcriptomes; vertebrate