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Chen P, Zhong Z, Jin WX, Sun J, Sun SC. Chromosome-scale assembly of Artemia tibetiana genome, first aquatic invertebrate genome from Tibet Plateau. Sci Data 2025; 12:777. [PMID: 40355476 PMCID: PMC12069563 DOI: 10.1038/s41597-025-05136-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Accepted: 05/01/2025] [Indexed: 05/14/2025] Open
Abstract
Genomic-level studies on the adaptive evolution of animals in the Qinghai-Tibet Plateau have been rapidly increasing. However, most studies are concentrated on vertebrates, and there are few reports on invertebrates. Here, we report the chromosome-level genome assembly for the brine shrimp Artemia tibetiana from Kyêbxang Co, a high-altitude (4620 m above sea level) salt lake on the plateau, based on the combination of Illumina, Nanopore long-reads and Hi-C sequencing data. The assembled genome is 1.69 Gb, and 94.83% of the assembled sequences are anchored to 21 pseudo-chromosomes. Approximately 75% of the genome was identified as repetitive sequences, which is higher than most crustaceans documented so far. A total of 17,988 protein-coding genes were identified, among them 14,388 were functionally annotated. This genomic resource provides the foundation for whole-genome level investigation on the genetic adaptation of Artemia to the harsh conditions in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Panpan Chen
- Fisheries College, Ocean University of China, Qingdao, 266000, China
- MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266000, China
| | - Zhaoyan Zhong
- MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266000, China
| | - Wei-Xin Jin
- Fisheries College, Ocean University of China, Qingdao, 266000, China
- MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266000, China
| | - Jin Sun
- MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266000, China.
| | - Shi-Chun Sun
- Fisheries College, Ocean University of China, Qingdao, 266000, China.
- MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266000, China.
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Liu B, Gao L, Liu Y, He K, Li H, Feng T, Han M, Zhang C. The First Genome-Wide Survey Analysis of the Tibetan Plateau Tetraploid Schizothorax curvilabiatus Reveals Its Microsatellite Characteristics and Phylogenetic Relationships. Genes (Basel) 2025; 16:491. [PMID: 40428313 PMCID: PMC12111650 DOI: 10.3390/genes16050491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2025] [Revised: 04/23/2025] [Accepted: 04/23/2025] [Indexed: 05/29/2025] Open
Abstract
Background/Objectives: Schizothorax curvilabiatus, a typical highland polyploid species within the subfamily Schizothoracinae, holds economic value and ecological research significance. Currently, there are no related genomic studies. To obtain its genetic information and lay the foundation for subsequent whole-genome map construction, this study conducted a genome survey analysis, preliminary genome assembly, microsatellite identification, repeat sequence annotation, mitochondrial genome characterization, and phylogenetic relationship research. Methods: DNA was sequenced on a DNBSEQ-T7 platform to obtain paired-end genomic data. The genome was analyzed using GCE, and the draft genome was assembled with SOAPdenovo. Microsatellites were identified using MISA, and the mitochondrial genome was assembled with NOVOPlasty. Genome features were analyzed, and phylogenetic trees were constructed using PhyloSuite and MEGA. Results: The genome size was estimated at 2.53 Gb, with a heterozygosity of 6.55% and 47.66% repeat sequences. A 1.324 Gb preliminary genome draft was obtained, with repeat sequences comprising 47.17%, the majority being DNA transposons (24.64%). Dinucleotide repeats were most abundant (46.91%), followed by mononucleotide repeats (38.31%), with A/T and AC/GT being the most frequent. A complete mitochondrial genome of 16,589 bp was assembled, and a 939 bp D-loop was annotated. Phylogenetic relationships among genera in the Schizothoracinae subfamily were also clarified. Conclusions: This study provides the latest molecular data for analysis of the S. curvilabiatus genome and its related populations, and for the first time offers genomic resources for research on genomic adaptive evolution and polyploidization in high-altitude environments.
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Affiliation(s)
- Bingjian Liu
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (B.L.); (L.G.); (Y.L.); (T.F.); (M.H.)
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan 316022, China
| | - Luxiu Gao
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (B.L.); (L.G.); (Y.L.); (T.F.); (M.H.)
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yifan Liu
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (B.L.); (L.G.); (Y.L.); (T.F.); (M.H.)
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan 316022, China
| | - Kai He
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China; (K.H.); (H.L.)
| | - Hongchi Li
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China; (K.H.); (H.L.)
| | - Taobo Feng
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (B.L.); (L.G.); (Y.L.); (T.F.); (M.H.)
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan 316022, China
| | - Mingzhe Han
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (B.L.); (L.G.); (Y.L.); (T.F.); (M.H.)
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan 316022, China
| | - Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China; (K.H.); (H.L.)
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Liang X, Wang W, Huang J, Luo M, Wangdui N, Sun C, Lu J. A chromosome-level genome assembly of big-barbel schizothorcin, Schizothorax macropogon. Sci Data 2024; 11:1402. [PMID: 39702420 DOI: 10.1038/s41597-024-04266-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 12/09/2024] [Indexed: 12/21/2024] Open
Abstract
Big-barbel schizothorcin (Schizothorax macropogon), an endemic and vulnerable species to the mid-reaches of the Yarlung Zangbo River, epitomizes survival in harsh conditions yet suffers significant population contractions due to human activities. This species was the subject of our study in which we leveraged PacBio, MGI-Seq, and Hi-C data to assemble a chromosome-scale genome. This assembly comprises 25 pseudo-chromosomes, yielding a genome size of 1.42 Gb with a scaffold N50 length of 59.4 Mb, indicative of a highly contiguous assembly. A BUSCO assessment ascertained the comprehensiveness of the genome at 97.9%. Annotation efforts identified 46,246 putative protein-coding genes, with 49.61% of the assembled genome annotated as repetitive sequences. This genome assembly is instrumental for advancing conservation of the giant whiskered schizothoracines and related species, and for illuminating the evolution and ecology of schizothoracine fishes in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Xuanguang Liang
- School of Marine Sciences, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, Guangdong, China
| | - Wenhao Wang
- School of Marine Sciences, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, Guangdong, China
| | - Junrou Huang
- School of Marine Sciences, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, Guangdong, China
| | - Mingfei Luo
- Zhuhai Modern Agricultural Development Center, Zhuhai, 519082, Guangdong, China
| | - Nima Wangdui
- Nyingchi agriculture Kema Agriculture Co., LTD, Nyingchi, 860000, Xizang, China
| | - Caiyun Sun
- Nyingchi agriculture Kema Agriculture Co., LTD, Nyingchi, 860000, Xizang, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, Guangdong, China.
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Kim KR, Park SY, Jeong JH, Hwang Y, Kim H, Sung MS, Yu JN. Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly. Int J Mol Sci 2024; 25:6689. [PMID: 38928393 PMCID: PMC11203500 DOI: 10.3390/ijms25126689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
This study is the first report to characterize the Rhodus uyekii genome and study the development of microsatellite markers and their markers applied to the genetic structure of the wild population. Genome assembly was based on PacBio HiFi and Illumina HiSeq paired-end sequencing, resulting in a draft genome assembly of R. uyekii. The draft genome was assembled into 2652 contigs. The integrity assessment of the assemblies indicates that the quality of the draft assemblies is high, with 3259 complete BUSCOs (97.2%) in the database of Verbrata. A total of 31,166 predicted protein-coding genes were annotated in the protein database. The phylogenetic tree showed that R. uyekii is a close but distinct relative of Onychostoma macrolepis. Among the 10 fish genomes, there were significant gene family expansions (8-2387) and contractions (16-2886). The average number of alleles amplified by the 21 polymorphic markers ranged from 6 to 23, and the average PIC value was 0.753, which will be useful for evolutionary and genetic analysis. Using population genetic analysis, we analyzed genetic diversity and the genetic structures of 120 individuals from 6 populations. The average number of alleles per population ranged from 7.6 to 9.9, observed heterozygosity ranged from 0.496 to 0.642, and expected heterozygosity ranged from 0.587 to 0.783. Discriminant analysis of principal components According to the analysis method, the population was divided into three populations (BS vs. DC vs. GG, GC, MS, DC). In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of R. uyekii.
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Affiliation(s)
- Kang-Rae Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (K.-R.K.); (S.Y.P.); (J.H.J.); (Y.H.); (H.K.)
| | - So Young Park
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (K.-R.K.); (S.Y.P.); (J.H.J.); (Y.H.); (H.K.)
| | - Ju Hui Jeong
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (K.-R.K.); (S.Y.P.); (J.H.J.); (Y.H.); (H.K.)
| | - Yujin Hwang
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (K.-R.K.); (S.Y.P.); (J.H.J.); (Y.H.); (H.K.)
| | - Heesoo Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (K.-R.K.); (S.Y.P.); (J.H.J.); (Y.H.); (H.K.)
| | - Mu-Sung Sung
- Muldeuli Research, Icheon 12607, Republic of Korea;
| | - Jeong-Nam Yu
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (K.-R.K.); (S.Y.P.); (J.H.J.); (Y.H.); (H.K.)
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Chen L, Li C, Li B, Zhou X, Bai Y, Zou X, Zhou Z, He Q, Chen B, Wang M, Xue Y, Jiang Z, Feng J, Zhou T, Liu Z, Xu P. Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success. FUNDAMENTAL RESEARCH 2024; 4:589-602. [PMID: 38933191 PMCID: PMC11197550 DOI: 10.1016/j.fmre.2023.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 06/28/2024] Open
Abstract
Hybridization and polyploidization have made great contributions to speciation, heterosis, and agricultural production within plants, but there is still limited understanding and utilization in animals. Subgenome structure and expression reorganization and cooperation post hybridization and polyploidization are essential for speciation and allopolyploid success. However, the mechanisms have not yet been comprehensively assessed in animals. Here, we produced a high-fidelity reference genome sequence for common carp, a typical allotetraploid fish species cultured worldwide. This genome enabled in-depth analysis of the evolution of subgenome architecture and expression responses. Most genes were expressed with subgenome biases, with a trend of transition from the expression of subgenome A during the early stages to that of subgenome B during the late stages of embryonic development. While subgenome A evolved more rapidly, subgenome B contributed to a greater level of expression during development and under stressful conditions. Stable dominant patterns for homoeologous gene pairs both during development and under thermal stress suggest a potential fixed heterosis in the allotetraploid genome. Preferentially expressing either copy of a homoeologous gene at higher levels to confer development and response to stress indicates the dominant effect of heterosis. The plasticity of subgenomes and their shifting of dominant expression during early development, and in response to stressful conditions, provide novel insights into the molecular basis of the successful speciation, evolution, and heterosis of the allotetraploid common carp.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Chengyu Li
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Bijun Li
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaofan Zhou
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yulin Bai
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaoqing Zou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Zhixiong Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Qian He
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Baohua Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Mei Wang
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yaguo Xue
- College of Fisheries, Henan Normal University, Xinxiang 453007, China
| | - Zhou Jiang
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Jianxin Feng
- Henan Academy of Fishery Science, Zhengzhou 450044, China
| | - Tao Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse 13244, USA
| | - Peng Xu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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Zhang S, Song Y, Liu M, Yuan Z, Zhang M, Zhang H, Seim I, Fan G, Liu S, Liu X. Chromosome-level genome of butterflyfish unveils genomic features of unique colour patterns and morphological traits. DNA Res 2023; 30:dsad018. [PMID: 37590994 PMCID: PMC10468729 DOI: 10.1093/dnares/dsad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/06/2023] [Accepted: 08/17/2023] [Indexed: 08/19/2023] Open
Abstract
Chaetodontidae, known as butterflyfishes, are typical fish in coral ecosystems, exhibiting remarkable interspecific differences including body colour patterns and feeding ecology. In this study, we report genomes of three butterflyfish species (Chelmon rostratus, Chaetodon trifasciatus and Chaetodon auriga) and a closely related species from the Pomacanthidae family, Centropyge bicolour, with an average genome size of 65,611 Mb. Chelmon rostratus, comprising 24 chromosomes assembled to the chromosome level, could be served as a reference genome for butterflyfish. By conducting a collinearity analysis between butterflyfishes and several fishes, we elucidated the specific and conserved genomic features of butterflyfish, with particular emphasis on novel genes arising from tandem duplications and their potential functions. In addition to the two melanocyte-specific tyr genes commonly found in fish, we found the gene tyrp3, a new tyrosinase-related proteins gene in the reef fish, including butterflyfish and clownfish, implicating their involvement in the pigmentation diversity of fish. Additionally, we observed a tandem duplication expansion of three copies of nell1 gene in C. rostratus genome, which likely contribute to its unique jaw development and distinctive morphology of its sharp mouth. These results provided valuable genomic resources for further investigations into the genetic diversity and evolutionary adaptations of reef fish.
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Affiliation(s)
- Suyu Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Meiru Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Zengbao Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane 4102, Queensland, Australia
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
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He J, He Z, Yang D, Ma Z, Chen H, Zhang Q, Deng F, Ye L, Pu Y, Zhang M, Yang S, Yang S, Yan T. Genetic Variation in Schizothorax kozlovi Nikolsky in the Upper Reaches of the Chinese Yangtze River Based on Genotyping for Simplified Genome Sequencing. Animals (Basel) 2022; 12:ani12172181. [PMID: 36077902 PMCID: PMC9454844 DOI: 10.3390/ani12172181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Schizothorax kozlovi Nikolsky is a unique cold−water fish in the upper reaches of the Yangtze River in China and has high economic value. In our study, genetic diversity and population structure analyses were performed on seven wild populations in the upper reaches of the Yangtze River by GBS. The above results indicate that the populations of S. kozlovi have different degrees of tolerance and selection pressure in response to temperature and altitude. The Wujiang population was genetically differentiated from the Jinsha River and Yalong River populations. The Wujiang intrapopulation has greater genetic diversity and differentiation than the Jinsha River and Yalong River populations, which demonstrates that the Jinsha and Yalong populations require more attention and resources for their protection. The results of this study will increase our understanding of the diversity of S. kozlovi in the upper reaches of the Yangtze River and provide a basis for the conservation and utilization of wild resources. Abstract Schizothorax kozlovi Nikolsky is a unique cold−water fish in the upper reaches of the Yangtze River in China and has high economic value. In our study, genetic diversity and population structure analyses were performed on seven wild populations (originating from the Jinsha River, Yalong River, and Wujiang River) in the upper reaches of the Yangtze River by genotyping by sequencing (GBS). The results indicated that a total of 303,970 single−nucleotide polymorphisms (SNPs) were identified from the seven wild populations. Lower genetic diversity was exhibited among the intrapopulations of the three tributaries, and the Wujiang River population had significant genetic differentiation when compared to the Jinsha River and Yalong River populations. Furthermore, the selected SNPs were enriched in cellular processes, environmental adaptation, signal transduction, and related metabolic processes between the Wujiang population and the other two populations. The above results indicate that the populations of S. kozlovi have different degrees of tolerance and selection pressure in response to temperature and altitude. The Wujiang intrapopulation has greater genetic diversity and differentiation than the Jinsha River and Yalong River populations, which demonstrates that the Jinsha and Yalong populations require more attention and resources for their protection. The results of this study will increase our understanding of the diversity of S. kozlovi in the upper reaches of the Yangtze River and provide a basis for the conservation and utilization of wild resources.
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Tian F, Liu S, Zhou B, Tang Y, Zhang Y, Zhang C, Zhao K. Chromosome-level genome of Tibetan naked carp ( Gymnocypris przewalskii) provides insights into Tibetan highland adaptation. DNA Res 2022; 29:6647840. [PMID: 35861387 PMCID: PMC9326183 DOI: 10.1093/dnares/dsac025] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Gymnocypris przewalskii, a cyprinid fish endemic to the Qinghai-Tibetan Plateau, has evolved unique morphological, physiological and genetic characteristics to adapt to the highland environment. Herein, we assembled a high-quality G. przewalskii tetraploid genome with a size of 2.03 Gb and scaffold N50 of 44.93 Mb, which was anchored onto 46 chromosomes. The comparative analysis suggested that gene families related to highland adaptation were significantly expanded in G. przewalskii. According to the G. przewalskii genome, we evaluated the phylogenetic relationship of 13 schizothoracine fishes, and inferred that the demographic history of G. przewalskii was strongly associated with geographic and eco-environmental alterations. We noticed that G. przewalskii experienced whole-genome duplication, and genes preserved post duplication were functionally associated with adaptation to high salinity and alkalinity. In conclusion, a chromosome-scale G. przewalskii genome provides an important genomic resource for teleost fish, and will particularly promote our understanding of the molecular evolution and speciation of fish in the highland environment.
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Affiliation(s)
- Fei Tian
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining, Qinghai, China
- University of Chinese Academy of Sciences , Beijing, China
| | - Sijia Liu
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining, Qinghai, China
| | - Bingzheng Zhou
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining, Qinghai, China
- University of Chinese Academy of Sciences , Beijing, China
| | - Yongtao Tang
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining, Qinghai, China
- Henan Normal University , Xinxiang, China
| | - Yu Zhang
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining, Qinghai, China
- University of Chinese Academy of Sciences , Beijing, China
| | - Cunfang Zhang
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University , Xining, Qinghai, China
| | - Kai Zhao
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining, Qinghai, China
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Zhu T, Li X, Wu X, Yang D. Temperature Acclimation Alters the Thermal Tolerance and Intestinal Heat Stress Response in a Tibetan Fish Oxygymnocypris stewarti. Front Microbiol 2022; 13:898145. [PMID: 35814681 PMCID: PMC9261780 DOI: 10.3389/fmicb.2022.898145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous studies have shown that thermal tolerance and intestinal heat resistance are strongly associated with temperature acclimation. However, few reports have successfully conducted similar research on fishes from the Qinghai–Tibetan Plateau, an area that is facing the threat of climate warming. Therefore, the present study determined the growth, thermal tolerance, and intestinal heat stress (exposure to 30°C) responses in juveniles of a Tibetan fish, Oxygymnocypris stewarti, acclimated to three temperature levels (10°C, 15°C, and 20°C, named as T10, T15, and T20, respectively) for 30 days. The fastest growth was recorded in the T15 group. At 1°C/30 min heating rate, the critical thermal maximum (CTMax) ranged from 31.3°C to 32.3°C, and the lethal thermal maximum (LTMax) ranged from 31.8°C to 32.6°C among the three acclimation temperatures. According to the results of thermal tolerance tests, the heat stress temperature was set to 30°C. When the water temperature reached 30°C, the expression of the intestinal heat shock protein 70 (HSP70) gene as well as the intestinal microbiome and histology of experimental fish were monitored at 0, 2, 6, and 12 h. The expression of HSP70 reached the highest level at 2 h in all three temperature treatments. The histological analysis showed damage to intestinal cells, including diffuse infiltration of lymphocytes, villi epithelial cell swelling, decrease of intestinal villi length, and cytoplasmic light staining at 2 h in all three temperature treatments. In terms of the intestinal microbiome, phyla Proteobacteria and Firmicutes dominated the treatments at each monitored time in the T10 and T15 groups and at 0 h in T20 group, while phyla Fusobacteria, Proteobacteria, and Cyanobacteria were dominant in treatments at 2, 6, and 12 h in the T20 group. The overall results indicated that acclimation temperature could affect the growth, thermal tolerance, and intestinal heat stress response of O. stewarti juveniles. As the first report on intestinal heat stress response associated with temperature acclimation in a Tibetan fish, this study will help to understand the potential effects of climate change on highland fishes.
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10
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Li R, Wang X, Bian C, Gao Z, Zhang Y, Jiang W, Wang M, You X, Cheng L, Pan X, Yang J, Shi Q. Whole-Genome Sequencing of Sinocyclocheilus maitianheensis Reveals Phylogenetic Evolution and Immunological Variances in Various Sinocyclocheilus Fishes. Front Genet 2021; 12:736500. [PMID: 34675964 PMCID: PMC8523889 DOI: 10.3389/fgene.2021.736500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/06/2021] [Indexed: 12/02/2022] Open
Abstract
An adult Sinocyclocheilus maitianheensis, a surface-dwelling golden-line barbel fish, was collected from Maitian river (Kunming City, Yunnan Province, China) for whole-genome sequencing, assembly, and annotation. We obtained a genome assembly of 1.7 Gb with a scaffold N50 of 1.4 Mb and a contig N50 of 24.7 kb. A total of 39,977 protein-coding genes were annotated. Based on a comparative phylogenetic analysis of five Sinocyclocheilus species and other five representative vertebrates with published genome sequences, we found that S. maitianheensis is close to Sinocyclocheilus anophthalmus (a cave-restricted species with similar locality). Moreover, the assembled genomes of S. maitianheensis and other four Sinocyclocheilus counterparts were used for a fourfold degenerative third-codon transversion (4dTv) analysis. The recent whole-genome duplication (WGD) event was therefore estimated to occur about 18.1 million years ago. Our results also revealed a decreased tendency of copy number in many important genes related to immunity and apoptosis in cave-restricted Sinocyclocheilus species. In summary, we report the first genome assembly of S. maitianheensis, which provides a valuable genetic resource for comparative studies on cavefish biology, species protection, and practical aquaculture of this potentially economical fish.
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Affiliation(s)
- Ruihan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, The Innovative Academy of Seed Design, Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Chao Bian
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Zijian Gao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Yuanwei Zhang
- State Key Laboratory of Genetic Resources and Evolution, The Innovative Academy of Seed Design, Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wansheng Jiang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest and Chemical Industry Engineering, Jishou University, Zhangjiajie, China
| | - Mo Wang
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Faculty of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Xinxin You
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | | | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, The Innovative Academy of Seed Design, Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, The Innovative Academy of Seed Design, Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qiong Shi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
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11
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Yang L, Wang Y, Sun N, Chen J, He S. Genomic and functional evidence reveals convergent evolution in fishes on the Tibetan Plateau. Mol Ecol 2021; 30:5752-5764. [PMID: 34516715 DOI: 10.1111/mec.16171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 08/18/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022]
Abstract
High-altitude environments are strong drivers of adaptive evolution in endemic organisms. However, little is known about the genetic mechanisms of convergent adaptation among different lineages, especially in fishes. There are three independent fish groups on the Tibetan Plateau: Tibetan Loaches, Schizothoracine fishes and Glyptosternoid fishes; all are well adapted to the harsh environmental conditions. They represent an excellent example of convergent evolution but with an unclear genetic basis. We used comparative genomic analyses between Tibetan fishes and fishes from low altitudes and detected genomic signatures of convergent evolution in fishes on the Tibetan Plateau. The Tibetan fishes exhibited genome-wide accelerated evolution in comparison with a control set of fishes from low altitudes. A total of 368 positively selected genes were identified in Tibetan fishes, which were enriched in functional categories related to energy metabolism and hypoxia response. Widespread parallel amino acid substitutions were detected among the Tibetan fishes and a subset of these substitutions occurred in positively selected genes associated with high-altitude adaptation. Functional assays suggested that von Hippel-Lindau (VHL) tumour suppressor genes from Tibetan fishes enhance hypoxia-inducible factor (HIF) activity convergently under hypoxia compared to low-altitude fishes. The results provide genomic and functional evidence supporting convergent genetic mechanisms for high-altitude adaptation in fishes on the Tibetan Plateau.
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Affiliation(s)
- Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China.,Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ying Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, College of Life Sciences, Jianghan University, Wuhan, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Juan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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12
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Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomes. Sci Rep 2021; 11:13797. [PMID: 34226617 PMCID: PMC8257616 DOI: 10.1038/s41598-021-93257-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/16/2021] [Indexed: 01/27/2023] Open
Abstract
Genome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.
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13
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Lei Y, Yang L, Zhou Y, Wang C, Lv W, Li L, He S. Hb adaptation to hypoxia in high-altitude fishes: Fresh evidence from schizothoracinae fishes in the Qinghai-Tibetan Plateau. Int J Biol Macromol 2021; 185:471-484. [PMID: 34214574 DOI: 10.1016/j.ijbiomac.2021.06.186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/27/2021] [Indexed: 10/21/2022]
Abstract
Uncovering the genetic basis of hypoxic adaptation is one of the most active research areas in evolutionary biology. Among air-breathing vertebrates, modifications of hemoglobin (Hb) play a pivotal role in mediating an adaptive response to high-altitude hypoxia. However, the relative contributions in water-breathing organisms are still unclear. Here, we tested the Hb concentration of fish at different altitudes. All species showed species-specific Hb concentration, which has a non-positive correlation with altitude. Moreover, we investigated the expression of Hb genes by the RNA-seq and quantitative real-time PCR (qRT-PCR), and Hb composition by two-dimensional electrophoresis (2-DE). The results showed that the multiple Hb genes and isoforms are co-expressed in schizothoracinae fishes endemic to the Qinghai-Tibetan Plateau (QTP). Phylogenetic analyses of Hb genes indicated that the evolutionary relationships are not easily reconciled with the organismal phylogeny. Furthermore, evidence of positive selection was found in the Hb genes of schizothoracinae fishes through the selection pressure analysis. We demonstrated that positively selected sites likely facilitated the functional divergence of Hb isoforms. Taken together, this study indicated that the long-term maintenance of high Hb concentration may be a disadvantage for physiologically acclimating to high altitude hypoxia. Meanwhile, the genetically based modification of Hb-O2 affinity in schizothoracinae fishes might facilitate the evolutionary adaptation to Tibetan aqueous environments.
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Affiliation(s)
- Yi Lei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhou
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqi Lv
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Li
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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14
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Tong C, Li M, Tang Y, Zhao K. Genomic Signature of Shifts in Selection and Alkaline Adaptation in Highland Fish. Genome Biol Evol 2021; 13:evab086. [PMID: 33892511 PMCID: PMC8126726 DOI: 10.1093/gbe/evab086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2021] [Indexed: 12/19/2022] Open
Abstract
Understanding how organisms adapt to aquatic life at high altitude is fundamental in evolutionary biology. This objective has been addressed primarily related to hypoxia adaptation by recent comparative studies, whereas highland fish has also long suffered extreme alkaline environment, insight into the genomic basis of alkaline adaptation has rarely been provided. Here, we compared the genomes or transcriptomes of 15 fish species, including two alkaline tolerant highland fish species and their six alkaline intolerant relatives, three alkaline tolerant lowland fish species, and four alkaline intolerant species. We found putatively consistent patterns of molecular evolution in alkaline tolerant species in a large number of shared orthologs within highland and lowland fish taxa. Remarkably, we identified consistent signatures of accelerated evolution and positive selection in a set of shared genes associated with ion transport, apoptosis, immune response, and energy metabolisms in alkaline tolerant species within both highland and lowland fish taxa. This is one of the first comparative studies that began to elucidate the consistent genomic signature of alkaline adaptation shared by highland and lowland fish. This finding also highlights the adaptive molecular evolution changes that support fish adapting to extreme environments at high altitude.
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Affiliation(s)
- Chao Tong
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Miao Li
- Center for Advanced Retinal and Ocular Therapeutics, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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15
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Chen C, Fu R, Wang J, Li X, Chen X, Li Q, Lu D. Genome sequence and transcriptome profiles of pathogenic fungus Paecilomyces penicillatus reveal its interactions with edible fungus Morchella importuna. Comput Struct Biotechnol J 2021; 19:2607-2617. [PMID: 34025947 PMCID: PMC8120865 DOI: 10.1016/j.csbj.2021.04.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 12/15/2022] Open
Abstract
Paecilomyces penicillatus is one of the pathogens of morels, which greatly affects the yield and quality of Morchella spp.. In the present study, we de novo assembled the genome sequence of the fungus P. penicillatus SAAS_ppe1. We analyzed the transcriptional profile of P. penicillatus SAAS_ppe1 infection of Morchella importuna at different stages (3 days and 6 days after infection) and the response of M. importuna using the transcriptome. The assembled genome sequence of P. penicillatus SAAS_ppe1 was 39.78 Mb in length (11 scaffolds; scaffold N50, 6.50 Mb), in which 99.7% of the expected genes were detected. A total of 7.48% and 19.83% clean transcriptional reads from the infected sites were mapped to the P. penicillatus genome at the early and late stages of infection, respectively. There were 3,943 genes differently expressed in P. penicillatus at different stages of infection, of which 24 genes had increased expression with the infection and infection stage, including diphthamide biosynthesis, aldehyde reductase, and NAD (P)H-hydrate epimerase (P < 0.05). Several genes had variable expression trends at different stages of infection, indicating P. penicillatus had diverse regulation patterns to infect M. importuna. GO function, involving cellular components, and KEGG pathways, involving glycerolipid metabolism, and plant-pathogen interaction were significantly enriched during infection by P. penicillatus. The expression of ten genes in M. importuna increased during the infection and infection stage, and these may regulate the response of M. importuna to P. penicillatus infection. This is the first comprehensive study on P. penicillatus infection mechanism and M. importuna response mechanism, which will lay a foundation for understanding the fungus-fungus interactions, gene functions, and variety breeding of pathogenic and edible fungi.
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Affiliation(s)
- Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, PR China
| | - Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, PR China
| | - Jian Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, PR China
| | - Xingyue Li
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, PR China
| | - Xiaojuan Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, PR China
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, PR China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, PR China
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16
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Peng Y, Li H, Liu Z, Zhang C, Li K, Gong Y, Geng L, Su J, Guan X, Liu L, Zhou R, Zhao Z, Guo J, Liang Q, Li X. Chromosome-level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi-C technology. Mol Ecol Resour 2021; 21:2093-2108. [PMID: 33829635 DOI: 10.1111/1755-0998.13397] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
The Arctic fox (Vulpes lagopus) is the only fox species occurring in the Arctic and has adapted to its extreme climatic conditions. Currently, the molecular basis of its adaptation to the extreme climate has not been characterized. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first V. lagopus genome assembly, which is assembled into chromosome fragments. The genome assembly has a total length of 2.345 Gb with a contig N50 of 31.848 Mb and a scaffold N50 of 131.537 Mb, consisting of 25 pseudochromosomal scaffolds. The V. lagopus genome had approximately 32.33% repeat sequences. In total, 21,278 protein-coding genes were predicted, of which 99.14% were functionally annotated. Compared with 12 other mammals, V. lagopus was most closely related to V. Vulpes with an estimated divergence time of ~7.1 Ma. The expanded gene families and positively selected genes potentially play roles in the adaptation of V. lagopus to Arctic extreme environment. This high-quality assembled genome will not only promote future studies of genetic diversity and evolution in foxes and other canids but also provide important resources for conservation of Arctic species.
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Affiliation(s)
- Yongdong Peng
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhengzhu Liu
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Chuansheng Zhang
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Keqiang Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Mathematics and Information Science, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yuanfang Gong
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Liying Geng
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jingjing Su
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, China
| | - Xuemin Guan
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Lei Liu
- College of Animal Science and Technology, Shandong Agricultural University, Tai-an, China
| | - Ruihong Zhou
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Ziya Zhao
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jianxu Guo
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing, China
| | - Xianglong Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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17
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Chen L, Li B, Chen B, Li C, Zhou Z, Zhou T, Yang W, Xu P. Chromosome-level genome of Poropuntius huangchuchieni provides a diploid progenitor-like reference genome for the allotetraploid Cyprinus carpio. Mol Ecol Resour 2021; 21:1658-1669. [PMID: 33624395 DOI: 10.1111/1755-0998.13365] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/27/2021] [Accepted: 02/16/2021] [Indexed: 11/27/2022]
Abstract
The diploid Poropuntius huangchuchieni in the cyprinid family, which is widely distributed in the Mekong and Red River basins, is one of the most closely related diploid progenitor-like species of allotetraploid common carp, which was generated by merging of two diploid genomes during evolution. Therefore, the P. huangchuchieni genome is essential for polyploid evolution studies in Cyprinidae. Here, we report a high-quality chromosome-level genome assembly of P. huangchuchieni by integrating Oxford Nanopore and Hi-C technologies. The assembled genome size was 1,021.38 Mb, 895.66 Mb of which was anchored onto 25 chromosomes with a N50 of 32.93 Mb. The genome contained 486.28 Mb repetitive elements and 24,099 protein-coding genes. Approximately 95.9% of the complete BUSCOs were detected, suggesting a high completeness of the genome. Evolutionary analysis revealed that P. huangchuchieni diverged from Cyprinus carpio at approximately 12 Mya. Genome comparison between P. huangchuchieni and the B subgenome of C. carpio provided insights into chromosomal rearrangements during the allotetraploid speciation. With the complete gene set, 17,474 orthologous genes were identified between P. huangchuchieni and C. carpio, providing a broad view of the gene component in the allotetraploid genome, which is critical for future genetic analyses. The high-quality genomic data set created for P. huangchuchieni provides a diploid progenitor-like reference for the evolution and adaptation of allotetraploid carps.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Bijun Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Baohua Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Chengyu Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Zhixiong Zhou
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Tao Zhou
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Weidi Yang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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18
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Feng X, Jia Y, Zhu R, Li K, Guan Z, Chen Y. Comparative transcriptome analysis of scaled and scaleless skins in Gymnocypris eckloni provides insights into the molecular mechanism of scale degeneration. BMC Genomics 2020; 21:835. [PMID: 33246415 PMCID: PMC7694923 DOI: 10.1186/s12864-020-07247-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/18/2020] [Indexed: 11/30/2022] Open
Abstract
Background The scale degeneration is thought to be related to the adaptation to the extreme environment with cold climate and high-altitude in schizothoracine fishes. Gymnocypris eckloni, a schizothoracine fish living in plateau waters with the elevation above 2500 m, is nearly esquamate and only covered with shoulder scales and anal scales, making it a good model species to study the molecular mechanism of scale degeneration. Results The transcriptomes of shoulder scaled skins (SSS), anal scaled skins (ASS) and scaleless skins (NSS) were sequenced and analyzed in G. eckloni at the age of 1 year. Histological examination showed that shoulder scale had completed its differentiation and anal scale just initiated the differentiation. A total of 578,046 unigenes were obtained from the transcriptomes, with 407,799 unigenes annotated in public databases. A total of 428 and 142 differentially expressed unigenes (DEUs) were identified between SSS and NSS, and between ASS and NSS, respectively, with 45 DEUs that were overlapped. Annotation analysis indicated that these DEUs were mainly enriched in Gene Ontology (GO) terms and KEGG pathways associated with bone and muscle formation, such as myofibril, contractile fiber, cytoskeletal protein binding, muscle structure development, cardiac muscle contraction, hypertrophic cardiomyopathy (HCM) and calcium signaling pathway. Conclusions Our results would provide insights into the molecular mechanisms of scale degeneration in G. eckloni and other congeneric fishes. In addition, the transcriptome data provides candidate genes and markers for future studies.
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Affiliation(s)
- Xiu Feng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yintao Jia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ren Zhu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kemao Li
- QingHai Provincial Fishery Environmental Monitoring Center, Xining, 810012, China
| | - Zhongzhi Guan
- QingHai Provincial Fishery Environmental Monitoring Center, Xining, 810012, China
| | - Yifeng Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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19
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Yuan D, Chen X, Gu H, Zou M, Zou Y, Fang J, Tao W, Dai X, Xiao S, Wang Z. Chromosomal genome of Triplophysa bleekeri provides insights into its evolution and environmental adaptation. Gigascience 2020; 9:giaa132. [PMID: 33231676 PMCID: PMC7684707 DOI: 10.1093/gigascience/giaa132] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/18/2020] [Accepted: 10/30/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Intense stresses caused by high-altitude environments may result in noticeable genetic adaptions in native species. Studies of genetic adaptations to high elevations have been largely limited to terrestrial animals. How fish adapt to high-elevation environments is largely unknown. Triplophysa bleekeri, an endemic fish inhabiting high-altitude regions, is an excellent model to investigate the genetic mechanisms of adaptation to the local environment. Here, we assembled a chromosomal genome sequence of T. bleekeri, with a size of ∼628 Mb (contig and scaffold N50 of 3.1 and 22.9 Mb, respectively). We investigated the origin and environmental adaptation of T. bleekeri based on 21,198 protein-coding genes in the genome. RESULTS Compared with fish species living at low altitudes, gene families associated with lipid metabolism and immune response were significantly expanded in the T. bleekeri genome. Genes involved in DNA repair exhibit positive selection for T. bleekeri, Triplophysa siluroides, and Triplophysa tibetana, indicating that adaptive convergence in Triplophysa species occurred at the positively selected genes. We also analyzed whole-genome variants among samples from 3 populations. The results showed that populations separated by geological and artificial barriers exhibited obvious differences in genetic structures, indicating that gene flow is restricted between populations. CONCLUSIONS These results will help us expand our understanding of environmental adaptation and genetic diversity of T. bleekeri and provide valuable genetic resources for future studies on the evolution and conservation of high-altitude fish species such as T. bleekeri.
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Affiliation(s)
- Dengyue Yuan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xuehui Chen
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haoran Gu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ming Zou
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
| | - Yu Zou
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
| | - Jian Fang
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiangyan Dai
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Shijun Xiao
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
- College of Plant Protection, Jilin Agriculture University, Changchun, Jilin 130118, China
| | - Zhijian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
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20
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Lei Y, Yang L, Jiang H, Chen J, Sun N, Lv W, He S. Recent genome duplications facilitate the phenotypic diversity of Hb repertoire in the Cyprinidae. SCIENCE CHINA-LIFE SCIENCES 2020; 64:1149-1164. [PMID: 33051703 DOI: 10.1007/s11427-020-1809-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022]
Abstract
Whole-genome duplications (WGDs) are an important contributor to phenotypic innovations in evolutionary history. The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for evolutionary success among vertebrates. In this study, the evolutionary changes of hemoglobin (Hb) repertoire driven by the recent genome duplications were detected in representative Cyprinidae fish, including eight diploid and four tetraploid species. Comparative genomic analysis revealed a substantial variation in both membership composition and intragenomic organization of Hb genes in these species. Phylogenetic reconstruction analyses were conducted to characterize the evolutionary history of these genes. Data were integrated with the expression profiles of the genes during ontogeny. Our results indicated that genome duplications facilitated the phenotypic diversity of the Hb gene family; each was associated with species-specific changes in gene content via gene loss and fusion after genome duplications. This led to repeated evolutionary transitions in the ontogenic regulation of Hb gene expression. Our results revealed that genome duplications helped to generate phenotypic changes in Cyprinidae Hb systems.
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Affiliation(s)
- Yi Lei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haifeng Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Sun
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenqi Lv
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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21
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Liu Q, Wang X, Xiao Y, Zhao H, Xu S, Wang Y, Wu L, Zhou L, Du T, Lv X, Li J. Sequencing of the black rockfish chromosomal genome provides insight into sperm storage in the female ovary. DNA Res 2020; 26:453-464. [PMID: 31711192 PMCID: PMC6993816 DOI: 10.1093/dnares/dsz023] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 11/09/2019] [Indexed: 01/09/2023] Open
Abstract
Black rockfish (Sebastes schlegelii) is an economically important viviparous marine teleost in Japan, Korea, and China. It is characterized by internal fertilization, long-term sperm storage in the female ovary, and a high abortion rate. For better understanding the mechanism of fertilization and gestation, it is essential to establish a reference genome for viviparous teleosts. Herein, we used a combination of Pacific Biosciences sequel, Illumina sequencing platforms, 10× Genomics, and Hi-C technology to obtain a genome assembly size of 848.31 Mb comprising 24 chromosomes, and contig and scaffold N50 lengths of 2.96 and 35.63 Mb, respectively. We predicted 39.98% repetitive elements, and 26,979 protein-coding genes. S. schlegelii diverged from Gasterosteus aculeatus ∼32.1-56.8 million years ago. Furthermore, sperm remained viable within the ovary for up to 6 months. The glucose transporter SLC2 showed significantly positive genomic selection, and carbohydrate metabolism-related KEGG pathways were significantly up-regulated in ovaries after copulation. In vitro suppression of glycolysis with sodium iodoacetate reduced sperm longevity significantly. The results indicated the importance of carbohydrates in maintaining sperm survivability. Decoding the S. schlegelii genome not only provides new insights into sperm storage; additionally, it is highly valuable for marine researchers and reproduction biologists.
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Affiliation(s)
- Qinghua Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xueying Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yongshuang Xiao
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Haixia Zhao
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shihong Xu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yanfeng Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lele Wu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Zhou
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tengfei Du
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuejiao Lv
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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22
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Genomic signature of accelerated evolution in a saline-alkaline lake-dwelling Schizothoracine fish. Int J Biol Macromol 2020; 149:341-347. [DOI: 10.1016/j.ijbiomac.2020.01.207] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/21/2019] [Accepted: 01/15/2020] [Indexed: 12/18/2022]
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23
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Zhou C, Xiao S, Liu Y, Mou Z, Zhou J, Pan Y, Zhang C, Wang J, Deng X, Zou M, Liu H. Comprehensive transcriptome data for endemic Schizothoracinae fish in the Tibetan Plateau. Sci Data 2020; 7:28. [PMID: 31964888 PMCID: PMC6972879 DOI: 10.1038/s41597-020-0361-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/18/2019] [Indexed: 01/05/2023] Open
Abstract
The Schizothoracinae fishes, endemic species in the Tibetan Plateau, are considered as ideal models for highland adaptation and speciation investigation. Despite several transcriptome studies for highland fishes have been reported before, the transcriptome information of Schizothoracinae is still lacking. To obtain comprehensive transcriptome data for Schizothoracinae, the transcriptome of a total of 183 samples from 14 representative Schizothoracinae species, were sequenced and de novo assembled. As a result, about 1,363 Gb transcriptome clean data was obtained. After the assembly, we obtain 76,602-154,860 unigenes for each species with sequence N50 length of 1,564-2,143 bp. More than half of the unigenes were functionally annotated by public databases. The Schizothoracinae fishes in this work exhibited diversified ecological distributions, phenotype characters and feeding habits; therefore, the comprehensive transcriptome data of those species provided valuable information for the environmental adaptation and speciation of Schizothoracinae in the Tibetan Plateau.
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Affiliation(s)
- Chaowei Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
- Departments of Aquaculture, College of Animal Science, Southwest University, Chongqing, 402460, China
| | - Shijun Xiao
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, 430000, China
| | - Yanchao Liu
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Zhenbo Mou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Jianshe Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Yingzi Pan
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Jiu Wang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China
| | - Xingxing Deng
- Departments of Aquaculture, College of Animal Science, Southwest University, Chongqing, 402460, China
| | - Ming Zou
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, 430000, China
| | - Haiping Liu
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, China.
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