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Zhou C, Li J, Duan Y, Fu S, Li H, Zhou Y, Gao H, Zhou X, Liu H, Lei L, Chen J, Yuan D. Genome sequencing and transcriptome analysis provide an insight into the hypoxia resistance of Channa asiatica. Int J Biol Macromol 2024; 282:137306. [PMID: 39515710 DOI: 10.1016/j.ijbiomac.2024.137306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 11/02/2024] [Accepted: 11/04/2024] [Indexed: 11/16/2024]
Abstract
Channa asiatica is an economically valuable fish species and excellent model for studying hypoxic tolerance. However, the underlying genetic and molecular mechanisms are poorly understood. In this study, we assembled a high-quality C. asiatica genome (23 chromosomes, totaling 722 Mb) using a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing. Repetitive elements accounted for 28.39%of the C. asiatica genome, and 23,949 protein-coding genes were predicted, with 96.63 % of these functionally annotated. Moreover, a comparative genomic analysis of 12 fish genomes showed that gene families associated with oxygen binding and transport were expanded in C. asiatica. In addition, transcriptome analysis revealed that multiple oxidative stress pathways were activated when C. asiatica was exposed to air. In conclusion, this study provided high-quality genome assembly and transcriptome data, both serving as critical resources for researching the genetic basis of hypoxic tolerance in C. asiatica.
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Affiliation(s)
- Chaowei Zhou
- College of Fisheries, Southwest University, Chongqing 402460, China; Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatics Science of Chongqing, Chongqing 400700, China
| | - Junting Li
- College of Fisheries, Southwest University, Chongqing 402460, China; Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatics Science of Chongqing, Chongqing 400700, China
| | - Yuting Duan
- College of Fisheries, Southwest University, Chongqing 402460, China; Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatics Science of Chongqing, Chongqing 400700, China
| | - Suxing Fu
- College of Fisheries, Southwest University, Chongqing 402460, China; Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatics Science of Chongqing, Chongqing 400700, China
| | - Hejiao Li
- College of Fisheries, Southwest University, Chongqing 402460, China; Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatics Science of Chongqing, Chongqing 400700, China
| | - Yinhua Zhou
- College of Fisheries, Southwest University, Chongqing 402460, China; Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatics Science of Chongqing, Chongqing 400700, China
| | - He Gao
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatics Science of Chongqing, Chongqing 400700, China; Key Laboratory of Aquatic Science of Chongqing, College of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xinghua Zhou
- College of Fisheries, Southwest University, Chongqing 402460, China; Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatics Science of Chongqing, Chongqing 400700, China
| | - Haiping Liu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatics Science of Chongqing, Chongqing 400700, China; Key Laboratory of Aquatic Science of Chongqing, College of Life Sciences, Southwest University, Chongqing 400715, China
| | - Luo Lei
- College of Fisheries, Southwest University, Chongqing 402460, China; Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatics Science of Chongqing, Chongqing 400700, China.
| | - Jie Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
| | - Dengyue Yuan
- College of Fisheries, Southwest University, Chongqing 402460, China; Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Key Laboratory of Aquatics Science of Chongqing, Chongqing 400700, China.
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2
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Bista B, González-Rodelas L, Álvarez-González L, Wu ZQ, Montiel EE, Lee LS, Badenhorst DB, Radhakrishnan S, Literman R, Navarro-Dominguez B, Iverson JB, Orozco-Arias S, González J, Ruiz-Herrera A, Valenzuela N. De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes. Genome Res 2024; 34:1553-1569. [PMID: 39414368 PMCID: PMC11529993 DOI: 10.1101/gr.279443.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 09/20/2024] [Indexed: 10/18/2024]
Abstract
Understanding the evolution of chromatin conformation among species is fundamental to elucidate the architecture and plasticity of genomes. Nonrandom interactions of linearly distant loci regulate gene function in species-specific patterns, affecting genome function, evolution, and, ultimately, speciation. Yet, data from nonmodel organisms are scarce. To capture the macroevolutionary diversity of vertebrate chromatin conformation, here we generate de novo genome assemblies for two cryptodiran (hidden-neck) turtles via Illumina sequencing, chromosome conformation capture, and RNA-seq: Apalone spinifera (ZZ/ZW, 2n = 66) and Staurotypus triporcatus (XX/XY, 2n = 54). We detected differences in the three-dimensional (3D) chromatin structure in turtles compared to other amniotes beyond the fusion/fission events detected in the linear genomes. Namely, whole-genome comparisons revealed distinct trends of chromosome rearrangements in turtles: (1) a low rate of genome reshuffling in Apalone (Trionychidae) whose karyotype is highly conserved when compared to chicken (likely ancestral for turtles), and (2) a moderate rate of fusions/fissions in Staurotypus (Kinosternidae) and Trachemys scripta (Emydidae). Furthermore, we identified a chromosome folding pattern that enables "centromere-telomere interactions" previously undetected in turtles. The combined turtle pattern of "centromere-telomere interactions" (discovered here) plus "centromere clustering" (previously reported in sauropsids) is novel for amniotes and it counters previous hypotheses about amniote 3D chromatin structure. We hypothesize that the divergent pattern found in turtles originated from an amniote ancestral state defined by a nuclear configuration with extensive associations among microchromosomes that were preserved upon the reshuffling of the linear genome.
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Affiliation(s)
- Basanta Bista
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Laura González-Rodelas
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Lucía Álvarez-González
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Zhi-Qiang Wu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
- Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Eugenia E Montiel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Ling Sze Lee
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Daleen B Badenhorst
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Srihari Radhakrishnan
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Beatriz Navarro-Dominguez
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - John B Iverson
- Department of Biology, Earlham College, Richmond, Indiana 47374, USA
| | | | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, 080003 Barcelona, Spain
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain;
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA;
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3
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Sachslehner AP, Surbek M, Holthaus KB, Steinbinder J, Golabi B, Hess C, Eckhart L. The Evolution of Transglutaminases Underlies the Origin and Loss of Cornified Skin Appendages in Vertebrates. Mol Biol Evol 2024; 41:msae100. [PMID: 38781495 PMCID: PMC11152450 DOI: 10.1093/molbev/msae100] [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: 02/13/2024] [Revised: 04/11/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024] Open
Abstract
Transglutaminases (TGMs) cross-link proteins by introducing covalent bonds between glutamine and lysine residues. These cross-links are essential for epithelial cornification which enables tetrapods to live on land. Here, we investigated which evolutionary adaptations of vertebrates were associated with specific changes in the family of TGM genes. We determined the catalog of TGMs in the main clades of vertebrates, performed a comprehensive phylogenetic analysis of TGMs, and localized the distribution of selected TGMs in tissues. Our data suggest that TGM1 is the phylogenetically oldest epithelial TGM, with orthologs being expressed in the cornified teeth of the lamprey, a basal vertebrate. Gene duplications led to the origin of TGM10 in stem vertebrates, the origin of TGM2 in jawed vertebrates, and an increasing number of epithelium-associated TGM genes in the lineage leading to terrestrial vertebrates. TGM9 is expressed in the epithelial egg tooth, and its evolutionary origin in stem amniotes coincided with the evolution of embryonic development in eggs that are surrounded by a protective shell. Conversely, viviparous mammals have lost both the epithelial egg tooth and TGM9. TGM3 and TGM6 evolved as regulators of cornification in hair follicles and underwent pseudogenization upon the evolutionary loss of hair in cetaceans. Taken together, this study reveals the gain and loss of vertebrate TGM genes in association with the evolution of cornified skin appendages and suggests an important role of TGM9 in the evolution of amniotes.
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Affiliation(s)
| | - Marta Surbek
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Julia Steinbinder
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Bahar Golabi
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Claudia Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Leopold Eckhart
- Department of Dermatology, Medical University of Vienna, 1090 Vienna, Austria
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4
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Kato A, Pipil S, Ota C, Kusakabe M, Watanabe T, Nagashima A, Chen AP, Islam Z, Hayashi N, Wong MKS, Komada M, Romero MF, Takei Y. Convergent gene losses and pseudogenizations in multiple lineages of stomachless fishes. Commun Biol 2024; 7:408. [PMID: 38570609 PMCID: PMC10991444 DOI: 10.1038/s42003-024-06103-x] [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: 04/03/2023] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
The regressive evolution of independent lineages often results in convergent phenotypes. Several teleost groups display secondary loss of the stomach, and four gastric genes, atp4a, atp4b, pgc, and pga2 have been co-deleted in agastric (stomachless) fish. Analyses of genotypic convergence among agastric fishes showed that four genes, slc26a9, kcne2, cldn18a, and vsig1, were co-deleted or pseudogenized in most agastric fishes of the four major groups. kcne2 and vsig1 were also deleted or pseudogenized in the agastric monotreme echidna and platypus, respectively. In the stomachs of sticklebacks, these genes are expressed in gastric gland cells or surface epithelial cells. An ohnolog of cldn18 was retained in some agastric teleosts but exhibited an increased non-synonymous substitution when compared with gastric species. These results revealed novel convergent gene losses at multiple loci among the four major groups of agastric fish, as well as a single gene loss in the echidna and platypus.
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Affiliation(s)
- Akira Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan.
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Japan.
- Department of Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, USA.
| | - Supriya Pipil
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Chihiro Ota
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Makoto Kusakabe
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Department of Biological Sciences, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Taro Watanabe
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Ayumi Nagashima
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - An-Ping Chen
- Department of Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, USA
| | - Zinia Islam
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan
| | - Naoko Hayashi
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan
| | - Marty Kwok-Shing Wong
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Department of Biomolecular Science, Toho University, Funabashi, Japan
| | - Masayuki Komada
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Michael F Romero
- Department of Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, USA
- Department of Nephrology & Hypertension, Mayo Clinic College of Medicine & Science, Rochester, MN, USA
| | - Yoshio Takei
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
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5
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Zhou R, Jenkins JW, Zeng Y, Shu S, Jang H, Harding SA, Williams M, Plott C, Barry KW, Koriabine M, Amirebrahimi M, Talag J, Rajasekar S, Grimwood J, Schmitz RJ, Dawe RK, Schmutz J, Tsai CJ. Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1003-1017. [PMID: 37675609 DOI: 10.1111/tpj.16454] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023]
Abstract
Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen Populus tremula × P. alba INRA 717-1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence-sensitive analyses. Here we report a telomere-to-telomere genome for this hybrid aspen with two chromosome-scale, haplotype-resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array-based and array-less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span >1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section Populus) but PtaM147-like sequences occur in LTR-retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis-driven research to probe into the function of the abundant and aspen-specific PtaM147 satellite DNA.
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Affiliation(s)
- Ran Zhou
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Shengqiang Shu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Scott A Harding
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Melissa Williams
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | | | - Kerrie W Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Maxim Koriabine
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Mojgan Amirebrahimi
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Chung-Jui Tsai
- School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
- Department of Genetics, University of Georgia, Athens, Georgia, USA
- Department of Plant Biology, University of Georgia, Athens, Georgia, USA
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6
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Dong J, Pei K, Xu W, Gong M, Zhu W, Liu S, Tang M, Liu J, Xia X, Bu X, Nie L. Zona pellucida family genes in Chinese pond turtle: identification, expression profiles, and role in the spermatozoa acrosome reaction†. Biol Reprod 2023; 109:97-106. [PMID: 37140246 DOI: 10.1093/biolre/ioad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/12/2023] [Accepted: 04/28/2023] [Indexed: 05/05/2023] Open
Abstract
The zona pellucida (ZP) is an extracellular matrix that surrounds all vertebrate eggs, and it is involved in fertilization and species-specific recognition. Numerous in-depth studies of the ZP proteins of mammals, birds, amphibians, and fishes have been conducted, but systematic investigation of the ZP family genes and their role during fertilization in reptiles has not been reported to date. In this study, we identified six turtle ZP (Tu-ZP) gene subfamilies (Tu-ZP1, Tu-ZP2, Tu-ZP3, Tu-ZP4, Tu-ZPD, and Tu-ZPAX) based on whole genome sequence data from Mauremys reevesii. We found that Tu-ZP4 had large segmental duplication and was distributed on three chromosomes, and we also detected gene duplication in the other Tu-ZP genes. To evaluate the role of Tu-ZP proteins in sperm-egg binding, we assessed the expression pattern of these Tu-ZP proteins and their ability to induce the spermatozoa acrosome reaction in M. reevesii. In conclusion, this is the first report of the existence of gene duplication of Tu-ZP genes and that Tu-ZP2, Tu-ZP3, and Tu-ZPD can induce acrosome exocytosis of spermatogenesis in the reptile.
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Affiliation(s)
- Jinxiu Dong
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Kejiao Pei
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Wannan Xu
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Mengmeng Gong
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Wenrui Zhu
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Siqi Liu
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Min Tang
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Jianjun Liu
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Xingquan Xia
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Xinjiang Bu
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Liuwang Nie
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
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7
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Luo M, Feng G, Chen M, Ke H. Probiotics and Immunostimulant modulate intestinal flora diversity in Reeves pond tortoise (Mauremys reevesii) and effects of Clostridium butyricum on its spleen transcriptome. FISH & SHELLFISH IMMUNOLOGY 2023:108908. [PMID: 37380116 DOI: 10.1016/j.fsi.2023.108908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023]
Abstract
In this study, we investigated the effects of Clostridium butyricum (group A), Bacillus subtilis (group B), and the immune enhancer algal β-1,3 glucan (group C) on the intestinal flora of Mauremys reevesii and the effects of C. butyricum on the transcriptome of M. reevesii splenic immune tissues. M. reevesii were assigened to four groups, each containing three replicates from 18 samples. Juvenile turtles with an initial weight of 106.35 ± 0.03 g were fed a basic diet containing no probiotics (control group D), or a basic diet containing the A, B, or C supplement. After the turtles had been fed for 60, 90, and 120 d of the experimental period, high-throughput sequencing of the 16S rRNA gene revealed no significant difference in alpha diversity among the four groups at 60 days of feeding (P > 0.05), and at 90 days, the alpha diversity in group A was significantly different (P < 0.05), with an increase of 26.62% in the Shannon index and a decrease of 83.33% in the Simpson index; at 120 d, the alpha diversity (Shannon index)showed a decreasing trend in order for groups A, B, and C, At the phylum level, the abundance of Bacteroidetes, Proteobacteria, and Fusobacteria in group A increased significantly with increasing feeding time (P < 0.05),At the genus level, the abundance of Ruminococcaceae and Anaerotruncus in group A increased significantly compared with that in the other three groups (P < 0.05). Transcriptome analysis showed that 384 genes were differentially expressed in the spleen of M. reevesii, 195 genes were upregulated and 189 genes were downregulated, and C. butyricum TF201120 regulated the hematopoietic cell lineage signaling pathway in the spleen of M. reevesii (P < 0.05). The regulation of several identified immune-related genes was confirmed by qPCR, These results showed that C. butyricum, B. subtilis and the immune enhancer algal β-1,3 glucan can improve the intestinal flora of M. reevesii, with C. butyricum TF20 being the most effective and significantly enhancing the immunity of M. reevesii.
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Affiliation(s)
- Meng Luo
- Aquatic Disease Research Laboratory, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510000, China; College of Aquatic and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Guoqing Feng
- Aquatic Disease Research Laboratory, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510000, China; Guangdong Scientific Observation Experimental Station of Veterinary Drugs and Diagnostic Technology, Ministry of Agriculture and Rural Affairs, Guangzhou, 510000, China
| | - Mingjie Chen
- Aquatic Disease Research Laboratory, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510000, China; College of Aquatic and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Hao Ke
- Aquatic Disease Research Laboratory, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510000, China; Guangdong Scientific Observation Experimental Station of Veterinary Drugs and Diagnostic Technology, Ministry of Agriculture and Rural Affairs, Guangzhou, 510000, China; Key Laboratory of Animal and Poultry Disease Control Research, Guangdong Province, Guangzhou, 510000, China.
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8
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Chen W, Chen H, Liao J, Tang M, Qin H, Zhao Z, Liu X, Wu Y, Jiang L, Zhang L, Fang B, Feng X, Zhang B, Reid K, Merilä J. Chromosome-level genome assembly of a high-altitude-adapted frog (Rana kukunoris) from the Tibetan plateau provides insight into amphibian genome evolution and adaptation. Front Zool 2023; 20:1. [PMID: 36604706 PMCID: PMC9817415 DOI: 10.1186/s12983-022-00482-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The high-altitude-adapted frog Rana kukunoris, occurring on the Tibetan plateau, is an excellent model to study life history evolution and adaptation to harsh high-altitude environments. However, genomic resources for this species are still underdeveloped constraining attempts to investigate the underpinnings of adaptation. RESULTS The R. kukunoris genome was assembled to a size of 4.83 Gb and the contig N50 was 1.80 Mb. The 6555 contigs were clustered and ordered into 12 pseudo-chromosomes covering ~ 93.07% of the assembled genome. In total, 32,304 genes were functionally annotated. Synteny analysis between the genomes of R. kukunoris and a low latitude species Rana temporaria showed a high degree of chromosome level synteny with one fusion event between chr11 and chr13 forming pseudo-chromosome 11 in R. kukunoris. Characterization of features of the R. kukunoris genome identified that 61.5% consisted of transposable elements and expansions of gene families related to cell nucleus structure and taste sense were identified. Ninety-five single-copy orthologous genes were identified as being under positive selection and had functions associated with the positive regulation of proteins in the catabolic process and negative regulation of developmental growth. These gene family expansions and positively selected genes indicate regions for further interrogation to understand adaptation to high altitude. CONCLUSIONS Here, we reported a high-quality chromosome-level genome assembly of a high-altitude amphibian species using a combination of Illumina, PacBio and Hi-C sequencing technologies. This genome assembly provides a valuable resource for subsequent research on R. kukunoris genomics and amphibian genome evolution in general.
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Affiliation(s)
- Wei Chen
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China.
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Dongzhi, 247230, China.
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei, 230601, China.
| | - Hongzhou Chen
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Jiahong Liao
- School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000, Sichuan, China
| | - Min Tang
- School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000, Sichuan, China
| | - Haifen Qin
- School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000, Sichuan, China
| | - Zhenkun Zhao
- School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000, Sichuan, China
| | - Xueyan Liu
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Yanfang Wu
- School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Lichun Jiang
- School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000, Sichuan, China
| | - Lixia Zhang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Bohao Fang
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, USA
| | - Xueyun Feng
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Baowei Zhang
- School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Kerry Reid
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Juha Merilä
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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Lu R, Liu J, Wang X, Song Z, Ji X, Li N, Ma G, Sun X. Chromosome-Level Genome Assembly of a Fragrant Japonica Rice Cultivar 'Changxianggeng 1813' Provides Insights into Genomic Variations between Fragrant and Non-Fragrant Japonica Rice. Int J Mol Sci 2022; 23:9705. [PMID: 36077110 PMCID: PMC9456513 DOI: 10.3390/ijms23179705] [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: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
East Asia has an abundant resource of fragrant japonica rice that is gaining increasing interest among both consumers and producers. However, genomic resources and in particular complete genome sequences currently available for the breeding of fragrant japonica rice are still scarce. Here, integrating Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods, we presented a high-quality chromosome-level genome assembly (~378.78 Mb) for a new fragrant japonica cultivar ‘Changxianggeng 1813’, with 31,671 predicated protein-coding genes. Based on the annotated genome sequence, we demonstrated that it was the badh2-E2 type of deletion (a 7-bp deletion in the second exon) that caused fragrance in ‘Changxianggeng 1813’. Comparative genomic analyses revealed that multiple gene families involved in the abiotic stress response were expanded in the ‘Changxianggeng 1813’ genome, which further supported the previous finding that no generalized loss of abiotic stress tolerance associated with the fragrance phenotype. Although the ‘Changxianggeng 1813’ genome showed high genomic synteny with the genome of the non-fragrant japonica rice cultivar Nipponbare, a total of 289,970 single nucleotide polymorphisms (SNPs), 96,093 small insertion-deletion polymorphisms (InDels), and 8690 large structure variants (SVs, >1000 bp) were identified between them. Together, these genomic resources will be valuable for elucidating the mechanisms underlying economically important traits and have wide-ranging implications for genomics-assisted breeding in fragrant japonica rice.
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Affiliation(s)
- Ruisen Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Jia Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Xuegang Wang
- Changshu Agricultural Science Research Institute, Changshu 215500, China
| | - Zhao Song
- Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Xiangdong Ji
- Changshu Agricultural Science Research Institute, Changshu 215500, China
| | - Naiwei Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Gang Ma
- Changshu Agricultural Science Research Institute, Changshu 215500, China
| | - Xiaoqin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
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10
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Chronology of embryonic and gonadal development in the Reeves' turtle, Mauremys reevesii. Sci Rep 2022; 12:11619. [PMID: 35804180 PMCID: PMC9270433 DOI: 10.1038/s41598-022-15515-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/24/2022] [Indexed: 11/08/2022] Open
Abstract
Temperature-dependent sex determination (TSD) is a mechanism in which environmental temperature, rather than innate zygotic genotype, determines the fate of sexual differentiation during embryonic development. Reeves' turtle (also known as the Chinese three-keeled pond turtle, Mauremys reevesii) exhibits TSD and is the only species whose genome has been determined in Geoemydidae to date. Thus, M. reevesii occupy phylogenetically important position for the study of TSD and can be compared to other TSD species to elucidate the underlying molecular mechanism of this process. Nevertheless, neither embryogenesis nor gonadogenesis has been described in this species. Therefore, herein, we investigated the chronology of normal embryonic development and gonadal structures in M. reevesii under both female- and male-producing incubation temperatures (FPT 31 °C or MPT 26 °C, respectively). External morphology remains indistinct between the two temperature regimes throughout the studied embryonic stages. However, the gonadal ridges present on the mesonephros at stage 16 develop and sexually differentiate at FPT and MPT. Ovarian and testicular structures begin to develop at stages 18-19 at FPT and stages 20-21 at MPT, respectively, and thus, the sexual differentiation of gonadal structures began earlier in the embryos at FPT than at MPT. Our results suggest that temperature sensitive period, at which the gonadal structures remain sexually undifferentiated, spans from stage 16 (or earlier) to stages 18-19 at FPT and to stages 20-21 at MPT. Understanding the temperature-dependent differentiation in gonadal structures during embryonic development is a prerequisite for investigating molecular basis underlying TSD. Thus, the result of the present study will facilitate further developmental studies on TSD in M. reevesii.
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