1
|
An ZX, Shi LG, Hou GY, Zhou HL, Xun WJ. Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data. Animal 2024; 18:101147. [PMID: 38843669 DOI: 10.1016/j.animal.2024.101147] [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: 10/30/2023] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 06/22/2024] Open
Abstract
Understanding the genetic characteristics of indigenous goat breeds is crucial for their conservation and breeding efforts. Hainan black goats, as a native breed of south China's tropical island province of Hainan, possess distinctive traits such as black hair, a moderate growth rate, good meat quality, and small body size. However, they exhibit exceptional resilience to rough feeding conditions, possess high-quality meat, and show remarkable resistance to stress and heat. In this study, we resequenced the whole genome of Hainan black goats to study the economic traits and genetic basis of these goats, we leveraged whole-genome sequencing data from 33 Hainan black goats to analyze single nucleotide polymorphism (SNP) density, Runs of homozygosity (ROH), Integrated Haplotype Score (iHS), effective population size (Ne), Nucleotide diversity Analysis (Pi) and selection characteristics. Our findings revealed that Hainan black goats harbor a substantial degree of genetic variation, with a total of 23 608 983 SNPs identified. Analysis of ROHs identified 53 710 segments, predominantly composed of short fragments, with inbreeding events mainly occurring in ancient ancestors, the estimates of inbreeding based on ROH in Hainan black goats typically exhibit moderate values ranging from 0.107 to 0.186. This is primarily attributed to significant declines in the effective population size over recent generations. Moreover, we identified 921 candidate genes within the intersection candidate region of ROH and iHS. Several of these genes are associated with crucial traits such as immunity (PTPRC, HYAL1, HYAL2, HYAL3, CENPE and PKN1), heat tolerance (GNG2, MAPK8, CAPN2, SLC1A1 and LEPR), meat quality (ACOX1, SSTR1, CAMK2B, PPP2CA and PGM1), cashmere production (AKT4, CHRM2, OXTR, AKT3, HMCN1 and CDK19), and stress resistance (TLR2, IFI44, ENPP1, STK3 and NFATC1). The presence of these genes may be attributed to the genetic adaptation of Hainan black goats to local climate conditions. The insights gained from this study provide valuable references and a solid foundation for the preservation, breeding, and utilization of Hainan black goats and their valuable genetic resources.
Collapse
Affiliation(s)
- Z X An
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China
| | - L G Shi
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China
| | - G Y Hou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China
| | - H L Zhou
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524000, China
| | - W J Xun
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| |
Collapse
|
2
|
Wang D, Ji X, Jiang B, Yuan Y, Liang B, Sun S, Zhu L, Liu J, Guo X, Yin Y, Sun Y. Prevalence of Antibiotic Resistance and Virulence Genes in Escherichia coli Carried by Migratory Birds on the Inner Mongolia Plateau of Northern China from 2018 to 2023. Microorganisms 2024; 12:1076. [PMID: 38930458 PMCID: PMC11205581 DOI: 10.3390/microorganisms12061076] [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: 04/22/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
(1) Background: Antibiotic resistance in bacteria is an urgent global threat to public health. Migratory birds can acquire antibiotic-resistant and pathogenic bacteria from the environment or through contact with each other and spread them over long distances. The objectives of this study were to explore the relationship between migratory birds and the transmission of drug-resistant pathogenic Escherichia coli. (2) Methods: Faeces and swab samples from migratory birds were collected for isolating E. coli on the Inner Mongolia Plateau of northern China from 2018 to 2023. The resistant phenotypes and spectra of isolates were determined using a BD Phoenix 100 System. Conjugation assays were performed on extended-spectrum β-lactamase (ESBL)-producing strains, and the genomes of multidrug-resistant (MDR) and ESBL-producing isolates were sequenced and analysed. (3) Results: Overall, 179 isolates were antibiotic-resistant, with 49.7% MDR and 14.0% ESBL. Plasmids were successfully transferred from 32% of ESBL-producing strains. Genome sequencing analysis of 91 MDR E. coli strains identified 57 acquired resistance genes of 13 classes, and extraintestinal pathogenic E. coli and avian pathogenic E. coli accounted for 26.4% and 9.9%, respectively. There were 52 serotypes and 54 sequence types (STs), including ST48 (4.4%), ST69 (4.4%), ST131 (2.2%) and ST10 (2.2%). The international high-risk clonal strains ST131 and ST10 primarily carried blaCTX-M-27 and blaTEM-176. (4) Conclusions: There is a high prevalence of multidrug-resistant virulent E. coli in migratory birds on the Inner Mongolian Plateau. This indicates a risk of intercontinental transmission from migratory birds to livestock and humans.
Collapse
Affiliation(s)
- Danhong Wang
- School of Chemistry and Life Science, Changchun University of Technology, Changchun 130012, China;
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130121, China; (X.J.); (B.J.); (Y.Y.); (B.L.); (S.S.); (L.Z.); (J.L.); (X.G.)
| | - Xue Ji
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130121, China; (X.J.); (B.J.); (Y.Y.); (B.L.); (S.S.); (L.Z.); (J.L.); (X.G.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130121, China
| | - Bowen Jiang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130121, China; (X.J.); (B.J.); (Y.Y.); (B.L.); (S.S.); (L.Z.); (J.L.); (X.G.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130121, China
| | - Yue Yuan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130121, China; (X.J.); (B.J.); (Y.Y.); (B.L.); (S.S.); (L.Z.); (J.L.); (X.G.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130121, China
| | - Bing Liang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130121, China; (X.J.); (B.J.); (Y.Y.); (B.L.); (S.S.); (L.Z.); (J.L.); (X.G.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130121, China
| | - Shiwen Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130121, China; (X.J.); (B.J.); (Y.Y.); (B.L.); (S.S.); (L.Z.); (J.L.); (X.G.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130121, China
| | - Lingwei Zhu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130121, China; (X.J.); (B.J.); (Y.Y.); (B.L.); (S.S.); (L.Z.); (J.L.); (X.G.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130121, China
| | - Jun Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130121, China; (X.J.); (B.J.); (Y.Y.); (B.L.); (S.S.); (L.Z.); (J.L.); (X.G.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130121, China
| | - Xuejun Guo
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130121, China; (X.J.); (B.J.); (Y.Y.); (B.L.); (S.S.); (L.Z.); (J.L.); (X.G.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130121, China
| | - Yuhe Yin
- School of Chemistry and Life Science, Changchun University of Technology, Changchun 130012, China;
| | - Yang Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130121, China; (X.J.); (B.J.); (Y.Y.); (B.L.); (S.S.); (L.Z.); (J.L.); (X.G.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130121, China
| |
Collapse
|
3
|
Huang R, Ji X, Zhu L, Zhang C, Luo T, Liang B, Jiang B, Zhou A, Du C, Sun Y. Metagenomic and Antibiotic Resistance Analysis of the Gut Microbiota in Larus relictus and Anatidae Species Inhabiting the Honghaizi Wetland of Ordos, Inner Mongolia, from 2021 to 2023. Microorganisms 2024; 12:978. [PMID: 38792807 PMCID: PMC11123678 DOI: 10.3390/microorganisms12050978] [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: 03/06/2024] [Revised: 04/11/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Gut microbes thrive by utilising host energy and, in return, provide valuable benefits, akin to a symbiotic relationship. Here, metagenomic sequencing was performed to characterise and compare the community composition, diversity and antibiotic resistance of the gut microbiota of Relict gull (Larus relictus) and Anatidae species. Alpha diversity analysis revealed that the intestinal microbial richness of L. relictus was significantly lower than that of Anatidae, with distinct differences observed in microbial composition. Notably, the intestines of L. relictus harboured more pathogenic bacteria such as clostridium, which may contribute to the decline in their population and endangered status. A total of 117 strains of Escherichia coli were isolated, with 90.60% exhibiting full susceptibility to 21 antibiotics, while 25.3% exhibited significant biofilm formation. Comprehensive Antibiotic Resistance Database data indicated that glycopeptide resistance genes were the most prevalent type carried by migratory birds, alongside quinolone, tetracycline and lincosamide resistance genes. The abundance of resistance genes carried by migratory birds decreased over time. This metagenomic analysis provides valuable insights into the intestinal microbial composition of these wild bird species, offering important guidance for their conservation efforts, particularly for L. relictus, and contributing to our understanding of pathogen spread and antibiotic-resistant bacteria.
Collapse
Affiliation(s)
- Ronglei Huang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (R.H.); (C.Z.); (A.Z.)
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.J.); (L.Z.); (B.L.); (B.J.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
| | - Xue Ji
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.J.); (L.Z.); (B.L.); (B.J.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
| | - Lingwei Zhu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.J.); (L.Z.); (B.L.); (B.J.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
| | - Chengyang Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (R.H.); (C.Z.); (A.Z.)
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.J.); (L.Z.); (B.L.); (B.J.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
| | - Tingting Luo
- College of Animal Sciences, Jilin University, Changchun 130062, China;
| | - Bing Liang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.J.); (L.Z.); (B.L.); (B.J.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
| | - Bowen Jiang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.J.); (L.Z.); (B.L.); (B.J.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
| | - Ang Zhou
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (R.H.); (C.Z.); (A.Z.)
| | - Chongtao Du
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (R.H.); (C.Z.); (A.Z.)
| | - Yang Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (X.J.); (L.Z.); (B.L.); (B.J.)
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun 130122, China
| |
Collapse
|
4
|
Li X, Wang X, Yu X, Yang C, Lin L, Huang Y. The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications. BMC Genomics 2023; 24:751. [PMID: 38062370 PMCID: PMC10702090 DOI: 10.1186/s12864-023-09857-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND High-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The absence of a sequenced genome has restricted previous evolutionary trait studies of this taxa. RESULTS The whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three methods, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The results indicated that T. temminckii was the first species to branch off from the clade containing Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in the list of positively selected genes (PSGs). CONCLUSIONS A genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.
Collapse
Affiliation(s)
- Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaoyang Wang
- School of Biological and Environmental Engineering, Xi'an University, Xi'an, China
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chao Yang
- Shaanxi Institute of Zoology, Xi'an, China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
| |
Collapse
|
5
|
Sozzoni M, Ferrer Obiol J, Formenti G, Tigano A, Paris JR, Balacco JR, Jain N, Tilley T, Collins J, Sims Y, Wood J, Benowitz-Fredericks ZM, Field KA, Seyoum E, Gatt MC, Léandri-Breton DJ, Nakajima C, Whelan S, Gianfranceschi L, Hatch SA, Elliott KH, Shoji A, Cecere JG, Jarvis ED, Pilastro A, Rubolini D. A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (Rissa tridactyla), a Declining Circumpolar Seabird. Genome Biol Evol 2023; 15:evad153. [PMID: 37590950 PMCID: PMC10457150 DOI: 10.1093/gbe/evad153] [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: 07/12/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/19/2023] Open
Abstract
Amidst the current biodiversity crisis, the availability of genomic resources for declining species can provide important insights into the factors driving population decline. In the early 1990s, the black-legged kittiwake (Rissa tridactyla), a pelagic gull widely distributed across the arctic, subarctic, and temperate zones, suffered a steep population decline following an abrupt warming of sea surface temperature across its distribution range and is currently listed as Vulnerable by the International Union for the Conservation of Nature. Kittiwakes have long been the focus for field studies of physiology, ecology, and ecotoxicology and are primary indicators of fluctuating ecological conditions in arctic and subarctic marine ecosystems. We present a high-quality chromosome-level reference genome and annotation for the black-legged kittiwake using a combination of Pacific Biosciences HiFi sequencing, Bionano optical maps, Hi-C reads, and RNA-Seq data. The final assembly spans 1.35 Gb across 32 chromosomes, with a scaffold N50 of 88.21 Mb and a BUSCO completeness of 97.4%. This genome assembly substantially improves the quality of a previous draft genome, showing an approximately 5× increase in contiguity and a more complete annotation. Using this new chromosome-level reference genome and three more chromosome-level assemblies of Charadriiformes, we uncover several lineage-specific chromosome fusions and fissions, but find no shared rearrangements, suggesting that interchromosomal rearrangements have been commonplace throughout the diversification of Charadriiformes. This new high-quality genome assembly will enable population genomic, transcriptomic, and phenotype-genotype association studies in a widely studied sentinel species, which may provide important insights into the impacts of global change on marine systems.
Collapse
Affiliation(s)
- Marcella Sozzoni
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Joan Ferrer Obiol
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
| | - Anna Tigano
- Department of Biology, Queen’s University, Kingston, Ontario, Canada
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Josephine R Paris
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Jennifer R Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
| | - Nivesh Jain
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
| | - Tatiana Tilley
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
| | - Joanna Collins
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Ying Sims
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Jonathan Wood
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Kenneth A Field
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Eyuel Seyoum
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Marie Claire Gatt
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Don-Jean Léandri-Breton
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
- Centre d’Études Biologiques de Chizé (CEBC), UMR 7372 - CNRS & Université de La Rochelle, Villiers-en-Bois, France
| | - Chinatsu Nakajima
- Department of Life and Environmental Science, University of Tsukuba, Tsukuba, Japan
| | - Shannon Whelan
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
| | | | - Scott A Hatch
- Institute for Seabird Research and Conservation, Anchorage, Alaska, USA
| | - Kyle H Elliott
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
| | - Akiko Shoji
- Department of Life and Environmental Science, University of Tsukuba, Tsukuba, Japan
| | | | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | | | - Diego Rubolini
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Water Research Institute, IRSA-CNR, Brugherio, Monza and Brianza, Italy
| |
Collapse
|
6
|
Li X, Wang X, Yang C, Lin L, Yuan H, Lei F, Huang Y. A de novo assembled genome of the Tibetan Partridge (Perdix hodgsoniae) and its high-altitude adaptation. Integr Zool 2023; 18:225-236. [PMID: 36049502 DOI: 10.1111/1749-4877.12673] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Tibetan Partridge (Perdix hodgsoniae) is an endemic species distributed in high-altitude areas of 3600-5600 m on the Qinghai-Tibet Plateau. To explore how the species is adapted to the high elevation environment, we assembled a draft genome based on both the Illumina and PacBio sequencing platforms with its population genetics and genomics analysis. In total, 134.74 Gb short reads and 30.81 Gb long reads raw data were generated. The 1.05-Gb assembled genome had a contig N50 of 4.56 Mb, with 91.94% complete BUSCOs. The 17 457 genes were annotated, and 11.35% of the genome was composed of repeat sequences. The phylogenetic tree showed that P. hodgsoniae was located at the basal position of the clade, including Golden Pheasant (Chrysolophus pictus), Common Pheasant (Phasianus colchicus), and Mikado Pheasant (Syrmaticus mikado). We found that 1014, 2595, and 2732 of the 6641 one-to-one orthologous genes were under positive selection in P. hodgsoniae, detected using PAML, BUSTED, and aBSREL programs, respectively, of which 965 genes were common under positive selection with 3 different programs. Several positively selected genes and immunity pathways relevant to high-altitude adaptation were detected. Gene family evolution showed that 99 gene families experienced significant expansion events, while 6 gene families were under contraction. The total number of olfactory receptor genes was relatively low in P. hodgsoniae. Genomic data provide an important resource for a further study on the evolutionary history of P. hodgsoniae, which provides a new insight into its high-altitude adaptation mechanisms.
Collapse
Affiliation(s)
- Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaoyang Wang
- School of Biological and Environmental Engeering, Xi'an University, Xi'an, China
| | - Chao Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Shaanxi Institute of Zoology, Xi'an, China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Fumin Lei
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, the Chinese Academy of Sciences, Beijing, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| |
Collapse
|
7
|
Yuan H, Huang Y, Mao Y, Zhang N, Nie Y, Zhang X, Zhou Y, Mao S. The Evolutionary Patterns of Genome Size in Ensifera (Insecta: Orthoptera). Front Genet 2021; 12:693541. [PMID: 34249107 PMCID: PMC8261143 DOI: 10.3389/fgene.2021.693541] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Genomic size variation has long been a focus for biologists. However, due to the lack of genome size data, the mechanisms behind this variation and the biological significance of insect genome size are rarely studied systematically. The detailed taxonomy and phylogeny of the Ensifera, as well as the extensive documentation concerning their morphological, ecological, behavioral, and distributional characteristics, make them a strong model for studying the important scientific problem of genome size variation. However, data on the genome size of Ensifera are rather sparse. In our study, we used flow cytometry to determine the genome size of 32 species of Ensifera, the smallest one being only 1C = 0.952 pg with the largest species up to 1C = 19.135 pg, representing a 20-fold range. This provides a broader blueprint for the genome size variation of Orthoptera than was previously available. We also completed the assembly of nine mitochondrial genomes and combined mitochondrial genome data from public databases to construct phylogenetic trees containing 32 species of Ensifera and three outgroups. Based on these inferred phylogenetic trees, we detected the phylogenetic signal of genome size variation in Ensifera and found that it was strong in both males and females. Phylogenetic comparative analyses revealed that there were no correlations between genome size and body size or flight ability in Tettigoniidae. Reconstruction of ancestral genome size revealed that the genome size of Ensifera evolved in a complex pattern, in which the genome size of the grylloid clade tended to decrease while that of the non-grylloid clade expanded significantly albeit with fluctuations. However, the evolutionary mechanisms underlying variation of genome size in Ensifera are still unknown.
Collapse
Affiliation(s)
- Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Ying Mao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Nan Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yimeng Nie
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xue Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yafu Zhou
- Xi'an Botanical Garden of Shaanxi Province/Institute of Botany of Shaanxi Province, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an, China
| | - Shaoli Mao
- Xi'an Botanical Garden of Shaanxi Province/Institute of Botany of Shaanxi Province, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an, China
| |
Collapse
|