1
|
Ahmad K, Shankar Pacha A, Yahya Naqash R, Kumar Peddamma S, Yellapu S, Hudson S, Singh Baghel D, Nigam P, Mondol S. Evolutionary insights on critically endangered Kashmir red deer or hangul ( Cervus hanglu hanglu) through a mitogenomic lens. PeerJ 2023; 11:e15746. [PMID: 37872949 PMCID: PMC10590573 DOI: 10.7717/peerj.15746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 06/22/2023] [Indexed: 10/25/2023] Open
Abstract
Background The Kashmir red deer or Hangul (Cervus hanglu hanglu) is the only Tarim red deer species endemic to India. With a current estimated population size of fewer than 200 individuals, this critically endangered species is confined to the greater Dachigam landscape in Jammu and Kashmir. Poaching, habitat loss and fragmentation, resource competition with livestock, and small population size are the major conservation challenges for this species. Methods Blood sampling was conducted from two wild Hangul individuals during radio-collaring operations at Dachigam National Park, Kashmir in 2013 and 2020, respectively. Using next-generation sequencing approach, we sequenced the 16,351 bp long mitogenome of two wild-caught Hangul individuals (1 M:1 F at ~14× and ~10× coverage, respectively) from Dachigam National Park. Results The annotated sequences were identical with an AT-rich composition, including 13 protein-coding genes (11,354 bp), 22 tRNA genes (1,515 bp), two ribosomal genes (2,526 bp) and a non-coding control region (917 bp) in a conserved order like other red deer species. Bayesian phylogenetic reconstruction of the red deer complex revealed two major groups: the elaphoid and the wapitoid clades. Hangul formed a distinct clade with its other subspecies C. hanglu yarkandensis and is sister to the Hungarian red deer (C. elaphus hippelaphus). Divergence time analyses suggested that the Tarim deer species group separated ~1.55 Mya from their common ancestors and Hangul diverged ~0.75 Mya from closely related C. yarkandensis, corroborating with the known paleobiogeographic events related to refugia during glaciations in the Pleistocene era. This study provides baseline information on Hangul mitogenome for further research on phylogeography and other population parameters and helps in developing suitable conservation plans for this species.
Collapse
Affiliation(s)
- Khursheed Ahmad
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Ankit Shankar Pacha
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Rashid Yahya Naqash
- Department of Wildlife Protection, Jammu & Kashmir Government, Srinagar, Jammu and Kashmir, India
| | | | | | - Shenu Hudson
- Nucleome Informatics Pvt. Ltd., Hyderabad, Telangana, India
| | | | - Parag Nigam
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Samrat Mondol
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, Uttarakhand, India
| |
Collapse
|
2
|
Han R, Han L, Zhao X, Wang Q, Xia Y, Li H. Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and Chromosome Evolution. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:470-482. [PMID: 36395998 PMCID: PMC10787017 DOI: 10.1016/j.gpb.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/24/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Despite the scientific and medicinal importance of diploid sika deer (Cervus nippon), its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed. To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae, we report, for the first time, a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies, which was anchored to 32 homologous groups with a pair of sex chromosomes (XY). Several expanded genes (RET, PPP2R1A, PPP2R1B, YWHAB, YWHAZ, and RPS6) and positively selected genes (eIF4E, Wnt8A, Wnt9B, BMP4, and TP53) were identified, which could contribute to rapid antler growth without carcinogenesis. A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis. Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer (Cervus elaphus), and the olfactory sensation of sika deer might be more powerful than that of red deer. Obvious inversion regions containing olfactory receptor genes were also identified, which arose since the divergence. In conclusion, the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler, chromosome evolution, and multi-omics research of cervid animals.
Collapse
Affiliation(s)
- Ruobing Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Lei Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Xunwu Zhao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Qianghui Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yanling Xia
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Heping Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China.
| |
Collapse
|
3
|
Heckeberg NS, Zachos FE, Kierdorf U. Antler tine homologies and cervid systematics: A review of past and present controversies with special emphasis on Elaphurus davidianus. Anat Rec (Hoboken) 2023; 306:5-28. [PMID: 35578743 DOI: 10.1002/ar.24956] [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: 01/11/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 01/29/2023]
Abstract
Antlers are the most conspicuous trait of cervids and have been used in the past to establish a classification of their fossil and living representatives. Since the availability of molecular data, morphological characters have generally become less important for phylogenetic reconstructions. In recent years, however, the appreciation of morphological characters has increased, and they are now more frequently used in addition to molecular data to reconstruct the evolutionary history of cervids. A persistent challenge when using antler traits in deer systematics is finding a consensus on the homology of structures. Here, we review early and recent attempts to homologize antler structures and objections to this approach, compare and evaluate recent advances on antler homologies, and critically discuss these different views in order to offer a basis for further scientific exchange on the topic. We further present some developmental aspects of antler branching patterns and discuss their potential for reconstructing cervid systematics. The use of heterogeneous data for reconstructing phylogenies has resulted in partly conflicting hypotheses on the systematic position of certain cervid species, on which we also elaborate here. We address current discussions on the use of different molecular markers in cervid systematics and the question whether antler morphology and molecular data can provide a consistent picture on the evolutionary history of cervids. In this context, special attention is given to the antler morphology and the systematic position of the enigmatic Pere David's deer (Elaphurus davidianus).
Collapse
Affiliation(s)
- Nicola S Heckeberg
- Staatliches Museum für Naturkunde Karlsruhe, Karlsruhe, Germany.,Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Frank E Zachos
- Natural History Museum Vienna, Vienna, Austria.,Department of Genetics, University of the Free State, Bloemfontein, South Africa.,Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Uwe Kierdorf
- Department of Biology, University of Hildesheim, Hildesheim, Germany
| |
Collapse
|
4
|
Phylogeny and evolution of the genus Cervus (Cervidae, Mammalia) as revealed by complete mitochondrial genomes. Sci Rep 2022; 12:16381. [PMID: 36180508 PMCID: PMC9525267 DOI: 10.1038/s41598-022-20763-x] [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: 03/02/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial DNA (mtDNA) lineages are recognized as important components of intra- and interspecific biodiversity, and allow to reveal colonization routes and phylogeographic structure of many taxa. Among these is the genus Cervus that is widely distributed across the Holarctic. We obtained sequences of complete mitochondrial genomes from 13 Cervus taxa and included them in global phylogenetic analyses of 71 Cervinae mitogenomes. The well-resolved phylogenetic trees confirmed Cervus to be monophyletic. Molecular dating based on several fossil calibration points revealed that ca. 2.6 Mya two main mitochondrial lineages of Cervus separated in Central Asia, the Western (including C. hanglu and C. elaphus) and the Eastern (comprising C. albirostris, C. canadensis and C. nippon). We also observed convergent changes in the composition of some mitochondrial genes in C. hanglu of the Western lineage and representatives of the Eastern lineage. Several subspecies of C. nippon and C. hanglu have accumulated a large portion of deleterious substitutions in their mitochondrial protein-coding genes, probably due to drift in the wake of decreasing population size. In contrast to previous studies, we found that the relic haplogroup B of C. elaphus was sister to all other red deer lineages and that the Middle-Eastern haplogroup E shared a common ancestor with the Balkan haplogroup C. Comparison of the mtDNA phylogenetic tree with a published nuclear genome tree may imply ancient introgressions of mtDNA between different Cervus species as well as from the common ancestor of South Asian deer, Rusa timorensis and R. unicolor, to the Cervus clade.
Collapse
|
5
|
Hu P, Wang Z, Li J, Wang D, Wang Y, Zhao Q, Li C. Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome Sequencing. Animals (Basel) 2022; 12:ani12172203. [PMID: 36077923 PMCID: PMC9454627 DOI: 10.3390/ani12172203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The size of antlers varies among species; antlers of the wapiti (Cervus canadensis xanthopygus) grow much faster than those of its close relative the sika deer (Cervus nippon hortulorum) in the same growing period. This contrast provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, the reference transcriptomes of the antler reserve mesenchyme (RM) tissue of wapiti and sika deer were constructed using single molecule real time sequencing data. The expression profiling, positive selection, and alternative splicing of the antler transcripts were compared, and interactive relationships and expression patterns of hub genes were identified and analysed. We identified that RNA Binding Motif Protein X-Linked (RBMX) gene was under strongly positive selection. One gene found to interact with RBMX was methyltransferase-like 3 (METTL3), an oncogene that could promote translation of cancer cell proteins. There was a contrasting relationship in expression level between RBMX and METTL3 genes in the RM tissue. We believe our study can provide a better understanding of rapid antler growth at the molecular level in particular and endochondral ossification in general. Abstract The molecular mechanism underlying rapid antler growth has not been elucidated. The contrast of the wapiti and sika deer antler provides a potential model for comparative studies for the identification of potent growth factors and unique regulatory systems. In the present study, reference transcriptomes of antler RM tissue of wapiti and sika deer were constructed using single molecule real time sequencing data. The expression profiling, positive selection, and alternative splicing of the antler transcripts were compared. The results showed that: a total of 44,485 reference full-length transcripts of antlers were obtained; 254 highly expressed transcripts (HETs) and 1936 differentially expressed genes (DEGs) were enriched and correlated principally with translation, endochondral ossification and ribosome; 228 genes were found to be under strong positive selection and would thus be important for the evolution of wapiti and sika deer; among the alternative splicing variants, 381 genes were annotated; and 4 genes with node degree values greater than 50 were identified through interaction network analysis. We identified a negative and a positive regulator for rapid antler growth, namely RNA Binding Motif Protein X-Linked (RBMX) and methyltransferase-like 3 (METTL3), respectively. Overall, we took advantage of this significant difference in growth rate and performed the comparative analyses of the antlers to identify key specific factors that might be candidates for the positive or negative regulation of phenomenal antler growth rate.
Collapse
Affiliation(s)
- Pengfei Hu
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, China
| | - Zhen Wang
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, China
| | - Jiping Li
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, China
| | - Dongxu Wang
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, China
| | - Yusu Wang
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, China
| | - Quanmin Zhao
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun 130118, China
| | - Chunyi Li
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun 130600, China
- Correspondence: ; Tel.: +86-177-9006-7914
| |
Collapse
|
6
|
Xing X, Ai C, Wang T, Li Y, Liu H, Hu P, Wang G, Liu H, Wang H, Zhang R, Zheng J, Wang X, Wang L, Chang Y, Qian Q, Yu J, Tang L, Wu S, Shao X, Li A, Cui P, Zhan W, Zhao S, Wu Z, Shao X, Dong Y, Rong M, Tan Y, Cui X, Chang S, Song X, Yang T, Sun L, Ju Y, Zhao P, Fan H, Liu Y, Wang X, Yang W, Yang M, Wei T, Song S, Xu J, Yue Z, Liang Q, Li C, Ruan J, Yang F. The first high-quality reference genome of sika deer provides insights for high-tannin adaptation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022:S1672-0229(22)00075-4. [PMID: 35718271 PMCID: PMC10372904 DOI: 10.1016/j.gpb.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/07/2022] [Accepted: 05/08/2022] [Indexed: 10/18/2022]
Abstract
Sika deer are known to prefer oak leaves, which are rich in tannins and toxic to most mammals; however, the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear. In identifying the mechanism responsible for the tolerance of a highly toxic diet, we have made a major advancement by explaining the genomics of sika deer. We generated the first high-quality, chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments. Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of the UGT family 2 subfamily B of UGT genes. The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation. Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.
Collapse
Affiliation(s)
- Xiumei Xing
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Cheng Ai
- 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 518120, China
| | - Tianjiao Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yang Li
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Huitao Liu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Pengfei Hu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Guiwu Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Huamiao Liu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Hongliang Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Ranran Zhang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Junjun Zheng
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xiaobo Wang
- 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 518120, China
| | - Lei Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yuxiao Chang
- 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 518120, China
| | - Qian Qian
- 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 518120, China
| | - Jinghua Yu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Lixin Tang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Shigang Wu
- 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 518120, China
| | - Xiujuan Shao
- 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 518120, China
| | - Alun Li
- 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 518120, China
| | - Peng Cui
- 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 518120, China
| | - Wei Zhan
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China
| | - Sheng Zhao
- 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 518120, China
| | - Zhichao Wu
- 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 518120, China
| | - Xiqun Shao
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yimeng Dong
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Min Rong
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yihong Tan
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xuezhe Cui
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Shuzhuo Chang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xingchao Song
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Tongao Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Limin Sun
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yan Ju
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Pei Zhao
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Huanhuan Fan
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Ying Liu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xinhui Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Wanyun Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Min Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Tao Wei
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Shanshan Song
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Jiaping Xu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Zhigang Yue
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing 100083, China.
| | - Chunyi Li
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Jue Ruan
- 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 518120, China.
| | - Fuhe Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| |
Collapse
|
7
|
Integrative Analyses of Antler Cartilage Transcriptome and Proteome of Gansu Red Deer (Cervus elaphus kansuensis) at Different Growth Stages. Animals (Basel) 2022; 12:ani12070934. [PMID: 35405922 PMCID: PMC8997108 DOI: 10.3390/ani12070934] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/22/2022] [Accepted: 04/01/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Velvet antler is the only organ in mammals that can completely and circularly regenerate, which involves the co-development of a variety of tissues including cartilage. Thus, velvet antler can provide an ideal model for studying chondrogenesis, endochondral ossification and rapid tissue growth. However, the mechanism of rapid growth and regeneration of velvet antler is still unclear. In this study, we conducted integrated analysis of the transcriptome and proteome of antler cartilage tissues at different growth stages. The results showed that gene13546 and its coding protein rna13546 were annotated in Wnt signaling pathway. They may play roles in antler rapid growth and regeneration. Abstract The velvet antler is a unique model for cancer and regeneration research due to its periodic regeneration and rapid growth. Antler growth is mainly triggered by the growth center located in its tip, which consists of velvet skin, mesenchyme and cartilage. Among them, cartilage accounts for most of the growth center. We performed an integrative analysis of the antler cartilage transcriptome and proteome at different antler growth stages. RNA-seq results revealed 24,778 unigenes, 19,243 known protein-coding genes, and 5535 new predicted genes. Of these, 2722 were detected with differential expression patterns among 30 d, 60 d, and 90 d libraries, and 488 differentially expressed genes (DEGs) were screened at 30 d vs. 60 d and 60 d vs. 90 d but not at 30 d vs. 90 d. Proteomic data identified 1361 known proteins and 179 predicted novel proteins. Comparative analyses showed 382 differentially expressed proteins (DEPs), of which 16 had differential expression levels at 30 d vs. 60 d and 60 d vs. 90 d but not at 30 d vs. 90 d. An integrated analysis conducted for DEGs and DEPs showed that gene13546 and its coding protein protein13546 annotated in the Wnt signaling pathway may possess important bio-logical functions in rapid antler growth. This study provides in-depth characterization of candidate genes and proteins, providing further insights into the molecular mechanisms controlling antler development.
Collapse
|
8
|
Takagi T, Tsuda Y, Torii H, Tamate HB, Kaneko S, Nagata J. Development of paternally‐inherited Y chromosome simple sequence repeats of sika deer and their application in genetic structure, artificial introduction, and interspecific hybridization analyses. POPUL ECOL 2022. [DOI: 10.1002/1438-390x.12109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Toshihito Takagi
- Graduate School of Symbiotic Systems Science and Technology Fukushima University Kanayagawa Fukushima Japan
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center (MSC) University of Tsukuba Ueda Nagano Japan
| | - Harumi Torii
- Center for Natural Environment Education Nara University of Education Takahata‐cho Nara Japan
| | | | - Shingo Kaneko
- Faculty of Symbiotic Systems Science Fukushima University Kanayagawa Fukushima Japan
| | - Junco Nagata
- Forestry and Forest Products Research Institute (FFPRI) Tsukuba Ibaraki Japan
| |
Collapse
|
9
|
Ababaikeri B, Zhang Y, Dai H, Shan W. Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing. Front Zool 2021; 18:50. [PMID: 34565397 PMCID: PMC8474959 DOI: 10.1186/s12983-021-00432-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 09/07/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Yarkand hare (Lepus yarkandensis Günther, 1875) is endemic to oasis and desert areas around the Tarim Basin in the Xinjiang Uyghur Autonomous Region of northwest China; however, genome-wide information for this species remains limited. Moreover, the genetic variation, genetic structure, and phylogenetic relationships of Yarkand hare from the plateau mountain regions have not been reported. Thus, we used specific-length amplified fragment sequencing (SLAF-seq) technology to evaluate the genetic diversity of 76 Yarkand hares from seven geographic populations in the northern and southwestern parts of the Tarim Basin to investigate single-nucleotide polymorphism (SNP) marker-based population differentiation and evolutionary processes. Selective sweep analysis was conducted to identify genetic differences between populations. RESULTS Using SLAF-seq, a total of 1,835,504 SNPs were initially obtained, of which 308,942 high-confidence SNPs were selected for further analysis. Yarkand hares exhibited a relatively high degree of genetic diversity at the SNP level. Based on pairwise FST estimates, the north and southwest groups showed a moderate level of genetic differentiation. Phylogenetic tree and population structure analyses demonstrated evident systematic phylogeographical structure patterns consistent with the geographical distribution of the hares. Hierarchical analysis of molecular variation further indicated that genetic variation was mainly observed within populations. Low to moderate genetic differentiation also occurred among populations despite a common genomic background, likely due to geographical barriers, genetic drift, and differential selection pressure of distinct environments. Nevertheless, the observed lineage-mixing pattern, as indicated by the evolutionary tree, principal component analysis, population structure, and TreeMix analyses, suggests a certain degree of gene flow between the north and southwest groups. This may be related to the migration of hares to high-altitude water sources southwest of the basin during glacial climatic oscillations, as well as river re-diffusion and oasis restoration in the basin following the glacial period. We also identified candidate genes, and their associated gene ontology terms and pathways, related to the adaptation of Yarkand hares to different environmental habitats. CONCLUSIONS The identified genome-wide SNPs, genetic diversity, and population structure of Yarkand hares expand our understanding of the genetic background of this endemic species and provide valuable insights into its environmental adaptation, allowing for further exploration of the underlying mechanisms.
Collapse
Affiliation(s)
- Buweihailiqiemu Ababaikeri
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
- College of Xinjiang Uyghur Medicine, Hoten, 848000, Xinjiang, China
| | - Yucong Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Huiying Dai
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Wenjuan Shan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China.
| |
Collapse
|
10
|
Sohn HJ, Mitchell G, Lee YH, Kim HJ, Park KJ, Staskevicus A, Walther I, Soutyrine A, Balachandran A. Experimental oral transmission of chronic wasting disease to sika deer ( Cervus nippon). Prion 2020; 14:271-277. [PMID: 33300452 PMCID: PMC7734081 DOI: 10.1080/19336896.2020.1857038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Chronic wasting disease (CWD) affects a broad array of cervid species and continues to be detected in an expanding geographic range. Initially introduced into the Republic of Korea through the importation of CWD-infected elk (Cervus canadensis), additional cases of CWD were subsequently detected in farmed Korean elk and sika deer (Cervus nippon). Wild and farmed sika deer are found in many regions of Asia, North America, and Europe, although natural transmission to this species has not been detected outside of the Republic of Korea. In this study, the oral transmission of CWD to sika deer was investigated using material from CWD-affected elk. Pathological prion (PrPCWD) immunoreactivity was detected in oropharyngeal lymphoid tissues of one sika deer at 3.9 months post-inoculation (mpi) and was more widely distributed in a second sika deer examined at 10.9 mpi. The remaining four sika deer progressed to clinical disease between 21 and 24 mpi. Analysis of PrPCWD tissue distribution in clinical sika deer revealed widespread deposition in central and peripheral nervous systems, lymphoreticular tissues, and the gastrointestinal tract. Prion protein gene (PRNP) sequences of these sika deer were identical and consistent with those reported in natural sika deer populations. These findings demonstrate the efficient oral transmission of CWD from elk to sika deer.
Collapse
Affiliation(s)
- Hyun-Joo Sohn
- Foreign Animal Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency , Gimcheon-si, Republic of Korea
| | - Gordon Mitchell
- National and OIE Reference Laboratory for Scrapie and CWD, Canadian Food Inspection Agency , Ottawa, Canada
| | - Yoon Hee Lee
- Foreign Animal Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency , Gimcheon-si, Republic of Korea
| | - Hyo Jin Kim
- Foreign Animal Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency , Gimcheon-si, Republic of Korea
| | - Kyung-Je Park
- Foreign Animal Disease Division, Department of Animal and Plant Health Research, Animal and Plant Quarantine Agency , Gimcheon-si, Republic of Korea
| | - Antanas Staskevicus
- National and OIE Reference Laboratory for Scrapie and CWD, Canadian Food Inspection Agency , Ottawa, Canada
| | - Ines Walther
- National and OIE Reference Laboratory for Scrapie and CWD, Canadian Food Inspection Agency , Ottawa, Canada
| | - Andrei Soutyrine
- National and OIE Reference Laboratory for Scrapie and CWD, Canadian Food Inspection Agency , Ottawa, Canada
| | - Aru Balachandran
- National and OIE Reference Laboratory for Scrapie and CWD, Canadian Food Inspection Agency , Ottawa, Canada
| |
Collapse
|
11
|
Ababaikeri B, Abduriyim S, Tohetahong Y, Mamat T, Ahmat A, Halik M. Whole-genome sequencing of Tarim red deer ( Cervus elaphus yarkandensis) reveals demographic history and adaptations to an arid-desert environment. Front Zool 2020; 17:31. [PMID: 33072165 PMCID: PMC7565370 DOI: 10.1186/s12983-020-00379-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/02/2020] [Indexed: 01/08/2023] Open
Abstract
Background The initiation of desert conditions in the Tarim Basin in China since the late Miocene has led to the significant genetic structuring of local organisms. Tarim Red Deer (Cervus elaphus yarkandensis, TRD) have adapted to the harsh environmental conditions in this basin, including high solar radiation and temperature, aridity, and poor nutritional conditions. However, the underlying genetic basis of this adaptation is poorly understood. Results We sequenced the whole genomes of 13 TRD individuals, conducted comparative genomic analyses, and estimated demographic fluctuation. The ∂a∂i model estimated that the TRD and Tule elk (Cervus canadensis nannodes) populations diverged approximately 0.98 Mya. Analyses revealed a substantial influence of the Earth’s climate on the effective population size of TRD, associated with glacial advances and retreat, and human activities likely underlie a recent serious decline in population. A marked bottleneck may have profoundly affected the genetic diversity of TRD populations. We detected a set of candidate genes, pathways, and GO categories related to oxidative stress, water reabsorption, immune regulation, energy metabolism, eye protection, heat stress, respiratory system adaptation, prevention of high blood pressure, and DNA damage and repair that may directly or indirectly be involved in the adaptation of TRD to an arid-desert environment. Conclusions Our analyses highlight the role of historical global climates in the population dynamics of TRD. In light of ongoing global warming and the increasing incidence of droughts, our study offers insights into the genomic adaptations of animals, especially TRD, to extreme arid-desert environments and provides a valuable resource for future research on conservation design and biological adaptations to environmental change.
Collapse
Affiliation(s)
- Buweihailiqiemu Ababaikeri
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China.,College of Xinjiang Uyghur Medicine, Hoten, 848000 Xinjiang China
| | - Shamshidin Abduriyim
- College of Life Science, Shihezi University, Shihezi, 832003 Xinjiang China.,Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, 430072 Hubei China
| | - Yilamujiang Tohetahong
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Tayerjan Mamat
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Adil Ahmat
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| | - Mahmut Halik
- College of Life Sciences and Technology, Xinjiang University, Urumqi, 830046 Xinjiang China
| |
Collapse
|
12
|
Heckeberg NS. The systematics of the Cervidae: a total evidence approach. PeerJ 2020; 8:e8114. [PMID: 32110477 PMCID: PMC7034380 DOI: 10.7717/peerj.8114] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/28/2019] [Indexed: 11/22/2022] Open
Abstract
Systematic relationships of cervids have been controversial for decades. Despite new input from molecular systematics, consensus could only be partially reached. The initial, gross (sub) classification based on morphology and comparative anatomy was mostly supported by molecular data. The rich fossil record of cervids has never been extensively tested in phylogenetic frameworks concerning potential systematic relationships of fossil cervids to extant cervids. The aim of this work was to investigate the systematic relationships of extant and fossil cervids using molecular and morphological characters and make implications about their evolutionary history based on the phylogenetic reconstructions. To achieve these objectives, molecular data were compiled consisting of five nuclear markers and the complete mitochondrial genome of 50 extant and one fossil cervids. Several analyses using different data partitions, taxon sampling, partitioning schemes, and optimality criteria were undertaken. In addition, the most extensive morphological character matrix for such a broad cervid taxon sampling was compiled including 168 cranial and dental characters of 41 extant and 29 fossil cervids. The morphological and molecular data were analysed in a combined approach and other comprehensive phylogenetic reconstructions. The results showed that most Miocene cervids were more closely related to each other than to any other cervids. They were often positioned between the outgroup and all other cervids or as the sister taxon to Muntiacini. Two Miocene cervids were frequently placed within Muntiacini. Plio- and Pleistocene cervids could often be affiliated to Cervini, Odocoileini or Capreolini. The phylogenetic analyses provide new insights into the evolutionary history of cervids. Several fossil cervids could be successfully related to living representatives, confirming previously assumed affiliations based on comparative morphology and introducing new hypotheses. New systematic relationships were observed, some uncertainties persisted and resolving systematics within certain taxa remained challenging.
Collapse
Affiliation(s)
- Nicola S. Heckeberg
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Berlin, Germany
| |
Collapse
|