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Sun B, Li Q, Mei Y, Zhang Y, Zheng Y, Huang Y, Xiao X, Zhang J, Jian G, Cao X. Chromosome-scale and haplotype-resolved genome assembly of the autotetraploid Misgurnus anguillicaudatus. Sci Data 2024; 11:1059. [PMID: 39341798 PMCID: PMC11438953 DOI: 10.1038/s41597-024-03891-z] [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: 04/09/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
In nature, diploids and tetraploids are two common types of polyploid evolution. Misgurnus anguillicaudatus (mud loach) is a remarkable fish species that exhibits both diploid and tetraploid forms. However, reconstructing the four haplotypes of its autotetraploid genome remains unresolved. Here, we generated the first haplotype-resolved, chromosome-level genome of autotetraploid M. anguillicaudatus with a size of 4.76 Gb, contig N50 of 6.78 Mb, and scaffold N50 of 44.11 Mb. We identified approximately 2.9 Gb (61.03% of genome) of repetitive sequences and predicted 91,485 protein-coding genes. Moreover, allelic gene expression levels indicated the absence of significant dominant haplotypes within the autotetraploid loach genome. This genome will provide a valuable biological model for unraveling the mechanisms of polyploid formation and evolution, adaptation to environmental changes, and benefit for aquaculture applications and biodiversity conservation.
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Affiliation(s)
- Bing Sun
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingshan Li
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yihui Mei
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunbang Zhang
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuxuan Zheng
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuwei Huang
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinxin Xiao
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gao Jian
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaojuan Cao
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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2
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Quinn CB, Preckler-Quisquater S, Buchalski MR, Sacks BN. Whole Genomes Inform Genetic Rescue Strategy for Montane Red Foxes in North America. Mol Biol Evol 2024; 41:msae193. [PMID: 39288165 PMCID: PMC11424165 DOI: 10.1093/molbev/msae193] [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: 03/12/2024] [Revised: 08/07/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024] Open
Abstract
A few iconic examples have proven the value of facilitated gene flow for counteracting inbreeding depression and staving off extinction; yet, the practice is often not implemented for fear of causing outbreeding depression. Using genomic sequencing, climatic niche modeling, and demographic reconstruction, we sought to assess the risks and benefits of using translocations as a tool for recovery of endangered montane red fox (Vulpes vulpes) populations in the western United States. We demonstrated elevated inbreeding and homozygosity of deleterious alleles across all populations, but especially those isolated in the Cascade and Sierra Nevada ranges. Consequently, translocations would be expected to increase population growth by masking deleterious recessive alleles. Demographic reconstructions further indicated shallow divergences of less than a few thousand years among montane populations, suggesting low risk of outbreeding depression. These genomic-guided findings set the stage for future management, the documentation of which will provide a roadmap for recovery of other data-deficient taxa.
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Affiliation(s)
- Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
- California Department of Fish and Wildlife, Wildlife Genetics Research Unit, Wildlife Health Laboratory, Sacramento, CA, USA
- National Genomics Center for Wildlife and Fish Conservation, USDA Forest Service, Rocky Mountain Research Station, Missoula, MT, USA
| | - Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Michael R Buchalski
- California Department of Fish and Wildlife, Wildlife Genetics Research Unit, Wildlife Health Laboratory, Sacramento, CA, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
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3
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Zhu Y, Yuan Y, Si H, Li S, Zhao F, Mu R, Lin Z, Wang X, Qiu Q, Xu C, Ji L, Li Z. Lipidomic and transcriptomic profiles provide new insights into the triacylglycerol and glucose handling capacities of the Arctic fox. Front Vet Sci 2024; 11:1388532. [PMID: 38988981 PMCID: PMC11233799 DOI: 10.3389/fvets.2024.1388532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/10/2024] [Indexed: 07/12/2024] Open
Abstract
The Arctic fox (Vulpes lagopus) is a species indigenous to the Arctic and has developed unique lipid metabolism, but the mechanisms remain unclear. Here, the significantly increased body weight of Arctic foxes was consistent with the significantly increased serum very-low-density lipoprotein (VLDL), and the 40% crude fat diet further increased the Arctic fox body weight. The enhanced body weight gain stems primarily from increased subcutaneous adipose tissue accumulation. The adipose triacylglycerol and phosphatidylethanolamine were significantly greater in Arctic foxes. The adipose fatty-acid synthase content was significantly lower in Arctic foxes, highlighting the main role of exogenous fatty-acids in fat accumulation. Considering the same diet, liver-derived fat dominates adipose expansion in Arctic foxes. Liver transcriptome analysis revealed greater fat and VLDL synthesis in Arctic foxes, consistent with the greater VLDL. Glucose homeostasis wasn't impacted in Arctic foxes. And the free fatty-acids in adipose, which promote insulin resistance, also did not differ between groups. However, the hepatic glycogen was greater in Arctic foxes and transcriptome analysis revealed upregulated glycogen synthesis, improving glucose homeostasis. These results suggest that the superior fat accumulation capacity and distinct characteristics of hepatic and adipose lipid and glucose metabolism facilitate glucose homeostasis and massive fat accumulation in Arctic foxes.
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Affiliation(s)
- Yuhang Zhu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yuan Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Huazhe Si
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Songze Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Fei Zhao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Ruina Mu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Zihan Lin
- College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Xiaoxu Wang
- Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Chao Xu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Lele Ji
- National Demonstration Center for Experimental Preclinical Medicine Education, The Fourth Military Medical University, Xi'an, China
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, China
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4
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Armstrong EE, Bissell KL, Fatima HS, Heikkinen MA, Jessup A, Junaid MO, Lee DH, Lieb EC, Liem JT, Martin EM, Moreno M, Otgonbayar K, Romans BW, Royar K, Adler MB, Needle DB, Harkess A, Kelley JL, Mooney JA, Mychajliw AM. Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae. G3 (BETHESDA, MD.) 2024; 14:jkae034. [PMID: 38366575 PMCID: PMC10989890 DOI: 10.1093/g3journal/jkae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Reference genome assemblies have been created from multiple lineages within the Canidae family; however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases, respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern United States and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of PRDM9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago.
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Affiliation(s)
- Ellie E Armstrong
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Ky L Bissell
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - H Sophia Fatima
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Maya A Heikkinen
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Anika Jessup
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Maryam O Junaid
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Dong H Lee
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Emily C Lieb
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Josef T Liem
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Estelle M Martin
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Mauricio Moreno
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | | | - Betsy W Romans
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Kim Royar
- Vermont Department of Fish and Wildlife, Montpelier, VT 05620, USA
| | - Mary Beth Adler
- Vermont Department of Fish and Wildlife, Montpelier, VT 05620, USA
| | - David B Needle
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jazlyn A Mooney
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90007, USA
| | - Alexis M Mychajliw
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
- Program in Environmental Studies, Middlebury College, Middlebury, VT 05753, USA
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5
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Patra SK, Douglas J, Wills PR, Bouckeart R, Betts L, Qing TG, Carter CW. Genomic database furnishes a spontaneous example of a functional Class II glycyl-tRNA synthetase urzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575260. [PMID: 38260702 PMCID: PMC10802616 DOI: 10.1101/2024.01.11.575260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The chief barrier to studies of how genetic coding emerged is the lack of experimental models for ancestral aminoacyl-tRNA synthetases (AARS). We hypothesized that conserved core catalytic sites could represent such ancestors. That hypothesis enabled engineering functional "urzymes" from TrpRS, LeuRS, and HisRS. We describe here a fourth urzyme, GlyCA, detected in an open reading frame from the genomic record of the arctic fox, Vulpes lagopus. GlyCA is homologous to a bacterial heterotetrameric Class II GlyRS-B. Alphafold2 predicted that the N-terminal 81 amino acids would adopt a 3D structure nearly identical to the HisRS urzyme (HisCA1). We expressed and purified that N-terminal segment. Enzymatic characterization revealed a robust single-turnover burst size and a catalytic rate for ATP consumption well in excess of that previously published for HisCA1. Time-dependent aminoacylation of tRNAGly proceeds at a rate consistent with that observed for amino acid activation. In fact, GlyCA is actually 35 times more active in glycine activation by ATP than the full-length GlyRS-B α-subunit dimer. ATP-dependent activation of the 20 canonical amino acids favors Class II amino acids that complement those favored by HisCA and LeuAC. These properties reinforce the notion that urzymes represent the requisite ancestral catalytic activities to implement a reduced genetic coding alphabet.
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Affiliation(s)
- Sourav Kumar Patra
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260
| | - Jordan Douglas
- Department of Physics, The University of Auckland, New Zealand
- Centre for Computational Evolution, University of Auckland, New Zealand
| | - Peter R. Wills
- Department of Physics, The University of Auckland, New Zealand
| | - Remco Bouckeart
- Centre for Computational Evolution, University of Auckland, New Zealand
- Department of Computer Science, The University of Auckland, New Zealand
| | - Laurie Betts
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260
| | | | - Charles W. Carter
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260
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6
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She J, Chen S, Liu X, Huo B. Chromosome-level assembly of Triplophysa yarkandensis genome based on the single molecule real-time sequencing. Sci Data 2024; 11:39. [PMID: 38182618 PMCID: PMC10770143 DOI: 10.1038/s41597-023-02900-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: 07/24/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024] Open
Abstract
Triplophysa yarkandensis, a species of freshwater fish endemic to Xinjiang, China, is currently classified as endangered. The objective of this study was to obtain the chromosome-level genome of T. yarkandensis using PacBio and Hi-C techniques. The PacBio sequencing technology resulted in an assembly of 520.64 Mb, with a contig N50 size of 1.30 Mb. Hi-C data was utilized for chromosome mapping, ultimately yielding 25 chromosome sequences. The success rate of chromosome mapping was 93%, with a scaffold N50 of 19.14 Mb, and a BUSCO evaluation integrity of 94.1%. The genome of T. yarkandensis encompasses 25,505 predicted protein-coding genes, with a total of 30,673 proteins predicted. The BUSCO evaluation integrity for predicted protein-coding genes was found to be 91.5%. Additionally, the genome contained a genomic repeat sequence accounting for 27.29% of its total length. Future research employing comparative genomics holds considerable importance in elucidating the molecular mechanisms behind saline-alkali adaptation and ensuring the conservation of biological resources.
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Affiliation(s)
- Jiacheng She
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shengao Chen
- College of Life Sciences and Technology, Tarim University, Alar, 843300, China
| | - Xuan Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Huo
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
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7
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Zhang Z, Xia T, Zhou S, Yang X, Lyu T, Wang L, Fang J, Wang Q, Dou H, Zhang H. High-Quality Chromosome-Level Genome Assembly of the Corsac Fox ( Vulpes corsac) Reveals Adaptation to Semiarid and Harsh Environments. Int J Mol Sci 2023; 24:ijms24119599. [PMID: 37298549 DOI: 10.3390/ijms24119599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
The Corsac fox (Vulpes corsac) is a species of fox distributed in the arid prairie regions of Central and Northern Asia, with distinct adaptations to dry environments. Here, we applied Oxford-Nanopore sequencing and a chromosome structure capture technique to assemble the first Corsac fox genome, which was then assembled into chromosome fragments. The genome assembly has a total length of 2.2 Gb with a contig N50 of 41.62 Mb and a scaffold N50 of 132.2 Mb over 18 pseudo-chromosomal scaffolds. The genome contained approximately 32.67% of repeat sequences. A total of 20,511 protein-coding genes were predicted, of which 88.9% were functionally annotated. Phylogenetic analyses indicated a close relation to the Red fox (Vulpes vulpes) with an estimated divergence time of ~3.7 million years ago (MYA). We performed separate enrichment analyses of species-unique genes, the expanded and contracted gene families, and positively selected genes. The results suggest an enrichment of pathways related to protein synthesis and response and an evolutionary mechanism by which cells respond to protein denaturation in response to heat stress. The enrichment of pathways related to lipid and glucose metabolism, potentially preventing stress from dehydration, and positive selection of genes related to vision, as well as stress responses in harsh environments, may reveal adaptive evolutionary mechanisms in the Corsac fox under harsh drought conditions. Additional detection of positive selection for genes associated with gustatory receptors may reveal a unique desert diet strategy for the species. This high-quality genome provides a valuable resource for studying mammalian drought adaptation and evolution in the genus Vulpes.
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Affiliation(s)
- Zhihao Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tian Xia
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Shengyang Zhou
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Xiufeng Yang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tianshu Lyu
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lidong Wang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Jiaohui Fang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Qi Wang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir 021000, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir 021000, China
| | - Honghai Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China
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8
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Lyu T, Zhou S, Fang J, Wang L, Shi L, Dong Y, Zhang H. Convergent Genomic Signatures of High-Altitude Adaptation among Six Independently Evolved Mammals. Animals (Basel) 2022; 12:ani12243572. [PMID: 36552492 PMCID: PMC9774524 DOI: 10.3390/ani12243572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The species living in the Qinghai-Tibet Plateau provide an excellent model system for studying the relationship between molecular convergent evolution and adaptation. Distant species experiencing the same selection pressure (i.e., hypoxia, low temperature and strong ultraviolet radiation) are likely to evolve similar genetic adaptations independently. Here, we performed comparative genomics studies on six independently evolved high-altitude species. The results also showed that the convergent evolution of the six species was mainly reflected at the level of rapidly evolving genes, and the functions of these rapidly evolving genes were mainly related to hypoxia response and DNA damage repair. In addition, we found that high-altitude species had more gene family changes than their low-altitude relatives, except for the order Lagomorpha. The results also show that the convergence of the gene family contraction of high-altitude species is much greater than that of expansion, revealing a possible pattern of species in adapting to high-altitude. Furthermore, we detected a positive selection signature in four genes related to hypoxia response and ultraviolet radiation damage in these six species (FYCO1, ERBIN, SCAMP1 and CXCL10). Our study reveals that hypoxia response might play an important role in the adaptation of independently evolved species to a high-altitude environment, providing a basic perspective for further exploring the high-altitude adaptation mechanism of different related species in the future.
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Affiliation(s)
- Tianshu Lyu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150000, China
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Shengyang Zhou
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Jiaohui Fang
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lidong Wang
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lupeng Shi
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Yuehuan Dong
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu 273165, China
- Correspondence:
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9
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Lan T, Li H, Yang S, Shi M, Han L, Sahu SK, Lu Y, Wang J, Zhou M, Liu H, Huang J, Wang Q, Zhu Y, Wang L, Xu Y, Lin C, Liu H, Hou Z. The chromosome-scale genome of the raccoon dog: Insights into its evolutionary characteristics. iScience 2022; 25:105117. [PMID: 36185367 PMCID: PMC9523411 DOI: 10.1016/j.isci.2022.105117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/07/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Tianming Lan
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shangchen Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yaxian Lu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Jiangang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Mengchao Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Hui Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou 570228, China
| | - Junxuan Huang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Zhu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanchun Xu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Corresponding author
| | - Chuyu Lin
- Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518120, China
- Corresponding author
| | - Huan Liu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- Corresponding author
| | - Zhijun Hou
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Corresponding author
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10
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Lyu T, Yang X, Zhao C, Wang L, Zhou S, Shi L, Dong Y, Dou H, Zhang H. Comparative transcriptomics of high-altitude Vulpes and their low-altitude relatives. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.999411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The harsh environment of Qinghai-Tibet Plateau (QTP) imposes strong selective stresses (e.g., hypoxia, high UV-radiation, and extreme temperature) to the native species, which have driven striking phenotypic and genetic adaptations. Although the mechanisms of high-altitude adaptation have been explored for many plateau species, how the phylogenetic background contributes to genetic adaption to high-altitude of Vulpes is largely unknown. In this study, we sequenced transcriptomic data across multiple tissues of two high-altitude Vulpes (Vulpes vulpes montana and Vulpes ferrilata) and their low-altitude relatives (Vulpes corsac and Vulpes lagopus) to search the genetic and gene expression changes caused by high-altitude environment. The results indicated that the positive selection genes (PSGs) identified by both high-altitude Vulpes are related to angiogenesis, suggesting that angiogenesis may be the result of convergent evolution of Vulpes in the face of hypoxic selection pressure. In addition, more PSGs were detected in V. ferrilata than in V. v. montana, which may be related to the longer adaptation time of V. ferrilata to plateau environment and thus more genetic changes. Besides, more PSGs associated with high-altitude adaptation were identified in V. ferrilata compared with V. v. montana, indicating that the longer the adaptation time to the high-altitude environment, the more genetic alterations of the species. Furthermore, the result of expression profiles revealed a tissue-specific pattern between Vulpes. We also observed that differential expressed genes in the high-altitude group exhibited species-specific expression patterns, revealed a convergent expression pattern of Vulpes in high-altitude environment. In general, our research provides a valuable transcriptomic resource for further studies, and expands our understanding of high-altitude adaptation within a phylogenetic context.
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Wang F, Wang L, Liu D, Gao Q, Nie M, Zhu S, Chao Y, Yang C, Zhang C, Yi R, Ni W, Tian F, Zhao K, Qi D. Chromosome-level assembly of Gymnocypris eckloni genome. Sci Data 2022; 9:464. [PMID: 35918339 PMCID: PMC9346132 DOI: 10.1038/s41597-022-01595-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/25/2022] [Indexed: 11/27/2022] Open
Abstract
Gymnocypris eckloni is widely distributed in isolated lakes and the upper reaches of the Yellow River and play significant roles in the trophic web of freshwater communities. In this study, we generated a chromosome-level genome of G. eckloni using PacBio, Illumina and Hi-C sequencing data. The genome consists of 23 pseudo-chromosomes that contain 918.68 Mb of sequence, with a scaffold N50 length of 43.54 Mb. In total, 23,157 genes were annotated, representing 94.80% of the total predicted protein-coding genes. The phylogenetic analysis showed that G. eckloni was most closely related to C. carpio with an estimated divergence time of ~34.8 million years ago. For G. eckloni, we identified a high-quality genome at the chromosome level. This genome will serve as a valuable genomic resource for future research on the evolution and ecology of the schizothoracine fish in the Qinghai-Tibetan Plateau.
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Affiliation(s)
- Fayan Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Lihan Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Dan Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Miaomiao Nie
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Shihai Zhu
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Yan Chao
- Animal Science Department of Agriculture and Animal Husbandry College, Qinghai University, Xining, 810016, China
| | - Chaojie Yang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Rigui Yi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Weilin Ni
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China.
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Yang X, Sun G, Xia T, Cha M, Zhang L, Pang B, Tang Q, Dou H, Zhang H. Transcriptome analysis provides new insights into cold adaptation of corsac fox (
Vulpes Corsac
). Ecol Evol 2022; 12:e8866. [PMID: 35462974 PMCID: PMC9019142 DOI: 10.1002/ece3.8866] [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: 11/09/2021] [Revised: 12/10/2021] [Accepted: 04/06/2022] [Indexed: 11/11/2022] Open
Abstract
Vulpesare widely distributed throughout the world and have undergone drastic physiological and phenotypic changes in response to their environment. However, little is known about the underlying genetic causes of these traits, especially Vulpes corsac. In this study, RNA‐Seq was used to obtain a comprehensive dataset for multiple pooled tissues of corsac fox, and selection analysis of orthologous genes was performed to identify the genes that may be influenced by the low‐temperature environment. More than 6.32 Gb clean reads were obtained and assembled into a total of 173,353 unigenes with an average length of 557 bp for corsac fox. Selective pressure analysis showed that 16 positively selected genes (PSGs) were identified in corsac fox, red fox, and arctic fox. Enrichment analysis of PSGs showed that the LRP11 gene was enriched in several pathways related to the low‐temperature response and might play a key role in response to environmental stimuli of foxes. In addition, several positively selected genes were related to DNA damage repair (ELP2 and CHAF1A), innate immunity (ARRDC4 and S100A12), and the respiratory chain (NDUFA5), and these positively selected genes might play a role in adaptation to harsh wild fox environments. The results of common orthologous gene analysis showed that gene flow or convergent evolution might be an important factor in promoting regional differentiation of foxes. Our study provides a valuable transcriptomic resource for the evolutionary history of the corsac fox and the adaptations to the extreme environments.
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Affiliation(s)
- Xiufeng Yang
- College of Life Science Qufu Normal University Qufu China
| | - Guolei Sun
- College of Life Science Qufu Normal University Qufu China
| | - Tian Xia
- College of Life Science Qufu Normal University Qufu China
| | - Muha Cha
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas Hulunbuir China
| | - Lei Zhang
- College of Life Science Qufu Normal University Qufu China
| | - Bo Pang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas Hulunbuir China
| | - Qingming Tang
- Hulun Buir Forestry and Grassland Business Development Center Hulunbuir China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas Hulunbuir China
| | - Honghai Zhang
- College of Life Science Qufu Normal University Qufu China
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Chen D, Zheng X, Huang Z, Chen Y, Xue T, Li K, Rao X, Lin G. Chromosome Genome Assembly and Annotation of the Capitulum mitella With PacBio and Hi-C Sequencing Data. Front Genet 2021; 12:707546. [PMID: 34484300 PMCID: PMC8416341 DOI: 10.3389/fgene.2021.707546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/12/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Duo Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xuehai Zheng
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Zhen Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Youqiang Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Ting Xue
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Ke Li
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xiaozhen Rao
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Gang Lin
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, China
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