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Shi L, Wang X, Yang X, Lyu T, Wang L, Zhou S, Dong Y, Wu X, Shang Y, Zhang H. Effect of locomotor preference on the evolution of mitochondrial genes in Bovidae. Sci Rep 2024; 14:12944. [PMID: 38839875 PMCID: PMC11153648 DOI: 10.1038/s41598-024-63937-5] [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: 11/20/2023] [Accepted: 06/03/2024] [Indexed: 06/07/2024] Open
Abstract
Locomotor preferences and habitat types may drive animal evolution. In this study, we speculated that locomotor preference and habitat type may have diverse influences on Bovidae mitochondrial genes. We used selection pressure and statistical analysis to explore the evolution of mitochondrial DNA (mtDNA) protein-coding genes (PCGs) from diverse locomotor preferences and habitat types. Our study demonstrates that locomotor preference (energy demand) drives the evolution of Bovidae in mtDNA PCGs. The habitat types had no significant effect on the rate of evolution in Bovidae mitochondrial genes. Our study provides deep insight into the adaptation of Bovidae.
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Affiliation(s)
- Lupeng Shi
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xiufeng Yang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Tianshu Lyu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Lidong Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Shengyang Zhou
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yuehuan Dong
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China.
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2
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Wang X, Zhou S, Wu X, Wei Q, Shang Y, Sun G, Mei X, Dong Y, Sha W, Zhang H. High-altitude adaptation in vertebrates as revealed by mitochondrial genome analyses. Ecol Evol 2021; 11:15077-15084. [PMID: 34765161 PMCID: PMC8571627 DOI: 10.1002/ece3.8189] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 12/25/2022] Open
Abstract
The high-altitude environment may drive vertebrate evolution in a certain way, and vertebrates living in different altitude environments might have different energy requirements. We hypothesized that the high-altitude environment might impose different influences on vertebrate mitochondrial genomes (mtDNA). We used selection pressure analyses and PIC (phylogenetic independent contrasts) analysis to detect the evolutionary rate of vertebrate mtDNA protein-coding genes (PCGs) from different altitudes. The results showed that the ratio of nonsynonymous/synonymous substitutions (dN/dS) in the mtDNA PCGs was significantly higher in high-altitude vertebrates than in low-altitude vertebrates. The seven rapidly evolving genes were shared by the high-altitude vertebrates, and only one positive selection gene (ND5 gene) was detected in the high-altitude vertebrates. Our results suggest the mtDNA evolutionary rate in high-altitude vertebrates was higher than in low-altitude vertebrates as their evolution requires more energy in a high-altitude environment. Our study demonstrates the high-altitude environment (low atmospheric O2 levels) drives vertebrate evolution in mtDNA PCGs.
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Affiliation(s)
- Xibao Wang
- College of Life ScienceQufu Normal UniversityQufuChina
| | | | - Xiaoyang Wu
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Qinguo Wei
- College of Life ScienceQufu Normal UniversityQufuChina
| | | | - Guolei Sun
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Xuesong Mei
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Yuehuan Dong
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Weilai Sha
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Honghai Zhang
- College of Life ScienceQufu Normal UniversityQufuChina
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3
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Yang J, Ding H, Kan X. Codon usage patterns and evolution of HSP60 in birds. Int J Biol Macromol 2021; 183:1002-1012. [PMID: 33971236 DOI: 10.1016/j.ijbiomac.2021.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 11/27/2022]
Abstract
Heat shock protein 60 (HSP60) is highly conserved from prokaryotic to eukaryotic organisms, acting as molecular chaperone and other vital biological functions. In spite of increasing knowledge of HSP60, its evolutionary mechanism on functional adaption is still far from completely understood. Moreover, analysis of codon usage bias (CUB) is a powerful tool to understand evolutionary association studies. However, so far, as we know, no scientific work on CUB of HSP60 in birds has been reported. In this study, we provide a comprehensive analysis on the codon usage and molecular evolution of HSP60 across birds. The results indicated that HSP60 had a weak codon usage bias with high ENC values (range from 52.66 to 61), low RSCU, and A/T-ending codons were mostly preferred. Meanwhile, it was considered that mutation, natural selection, and genetic drift combined to shape codon usage patterns with different strength proportions among various birds for HSP60. Then, the LRT tests suggested that different lineages of birds might be under similar selective pressures. Besides, the two positive selection sites (151 and 131) were detected and might undergo radical changes. These findings would contribute to understand function diversity and molecular evolution of HSP60 in birds.
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Affiliation(s)
- Jianke Yang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China; School of Preclinical Medicine, Wannan Medical College, Wuhu, Anhui, China
| | - Hengwu Ding
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, Anhui, China
| | - Xianzhao Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu, Anhui, China.
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4
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Insights into the Mechanism of Bovine Spermiogenesis Based on Comparative Transcriptomic Studies. Animals (Basel) 2021; 11:ani11010080. [PMID: 33466297 PMCID: PMC7824766 DOI: 10.3390/ani11010080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Any irregularity in spermiogenesis reduces the quality of semen and may lead to male sterility in cattle and humans. Thus, we investigated the differential transcriptomics of spermatids from round spermatid to epididymal sperm and compared them with the transcriptomics of mice in the same period. We found differentially expressed genes (DEGs) involved in sperm head and tail formation, and epigenetic regulatory networks which regulated genetic material condensation, the deformation of the spermatid, and the expression of genes in it. According to the sterility report on the ART3 protein and its possible epigenetic function, we detected that it was localised outside the spermatocyte, in round and elongated spermatids. Interestingly, we observed that the ART3 protein on round and elongated spermatids was localised approximately to the lumen of seminiferous tubule. It was also localised on the head and tail part near the head in epididymal sperm, suggesting its important role in the deformation from round spermatids to sperm. Our findings provide new insights into the molecular mechanism underlying bovine spermiogenesis, thereby contributing to the improved reproductive potential of cattle and the development of strategies for the diagnosis and treatment of male infertility. Abstract To reduce subfertility caused by low semen quality and provide theoretical guidance for the eradication of human male infertility, we sequenced the bovine transcriptomes of round, elongated spermatids and epididymal sperms. The differential analysis was carried out with the reference of the mouse transcriptome, and the homology trends of gene expression to the mouse were also analysed. First, to explore the physiological mechanism of spermiogenesis that profoundly affects semen quality, homological trends of differential genes were compared during spermiogenesis in dairy cattle and mice. Next, Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment, protein–protein interaction network (PPI network), and bioinformatics analyses were performed to uncover the regulation network of acrosome formation during the transition from round to elongated spermatids. In addition, processes that regulate gene expression during spermiogenesis from elongated spermatid to epididymal sperm, such as ubiquitination, acetylation, deacetylation, and glycosylation, and the functional ART3 gene may play important roles during spermiogenesis. Therefore, its localisation in the seminiferous tubules and epididymal sperm were investigated using immunofluorescent analysis, and its structure and function were also predicted. Our findings provide a deeper understanding of the process of spermiogenesis, which involves acrosome formation, histone replacement, and the fine regulation of gene expression.
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Bentz AB, Thomas GWC, Rusch DB, Rosvall KA. Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly. Sci Rep 2019; 9:15849. [PMID: 31676844 PMCID: PMC6825141 DOI: 10.1038/s41598-019-52312-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022] Open
Abstract
Tree swallows (Tachycineta bicolor) are one of the most commonly studied wild birds in North America. They have advanced numerous research areas, including life history, physiology, and organismal responses to global change; however, transcriptomic resources are scarce. To further advance the utility of this system for biologists across disciplines, we generated a transcriptome for the tree swallow using six tissues (brain, blood, ovary, spleen, liver, and muscle) collected from breeding females. We de novo assembled 207,739 transcripts, which we aligned to 14,717 high confidence protein-coding genes. We then characterized each tissue with regard to its unique genes and processes and applied this transcriptome to two fundamental questions in evolutionary biology and endocrinology. First, we analyzed 3,015 single-copy orthologs and identified 46 genes under positive selection in the tree swallow lineage, including those with putative links to adaptations in this species. Second, we analyzed tissue-specific expression patterns of genes involved in sex steroidogenesis and processing. Enzymes capable of synthesizing these behaviorally relevant hormones were largely limited to the ovary, whereas steroid binding genes were found in nearly all other tissues, highlighting the potential for local regulation of sex steroid-mediated traits. These analyses provide new insights into potential sources of phenotypic variation in a free-living female bird and advance our understanding of fundamental questions in evolutionary and organismal biology.
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Affiliation(s)
- Alexandra B Bentz
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA. .,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA.
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Department of Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Douglas B Rusch
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Kimberly A Rosvall
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA
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Jiang L, Bi D, Ding H, Ren Q, Wang P, Kan X. Identification and comparative profiling of gonadal microRNAs in the adult pigeon ( Columba livia). Br Poult Sci 2019; 60:638-648. [PMID: 31343256 DOI: 10.1080/00071668.2019.1639140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1. MicroRNAs are small noncoding RNA molecules that play crucial roles in gene expression. However, the comparative profiling of testicular and ovarian microRNAs in birds are rarely reported, particularly in pigeon.2. In this study, Illumina next-generation sequencing technology was used to sequence miRNA libraries of the gonads from six healthy adult utility pigeons. A total of 344 conserved known miRNAs and 32 novel putative miRNAs candidates were detected. Compared with those of ovaries, 130 differentially expressed (DE) miRNAs were identified in the testes. Among them, 70 miRNAs showed down-regulation in the ovaries, while another 60 miRNAs were up-regulated.3. Combining the results of the expression of target gene measurements and pathway enrichment analyses, it was revealed that some DEmiRNAs from the gonad samples involved in sexual differentiation and development (such as cli-miR-210-3p and cli-miR-214-3p) could down-regulate AR (androgen receptor). Cli-miR-181b-5p, cli-miR-9622-3p and cli-miR-145-5p were highly expressed in both the ovaries and testes, which could co-target HOXC9, and were related to regulation of primary metabolic processes. KEGG enrichment analysis showed that DEmiRNAs may play biological and sex-related roles in pigeon gonads.4. The expression profiles of testicular and ovarian miRNA in adult pigeon gonads are presented for the first time, and the findings may contribute to a better understanding of gonadal expression in poultry.
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Affiliation(s)
- L Jiang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - D Bi
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - H Ding
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Q Ren
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - P Wang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - X Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
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Two new mitogenomes of Picidae (Aves, Piciformes): Sequence, structure and phylogenetic analyses. Int J Biol Macromol 2019; 133:683-692. [DOI: 10.1016/j.ijbiomac.2019.04.157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023]
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8
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Jiang L, Bi D, Ding H, Wu X, Zhu R, Zeng J, Yang X, Kan X. Systematic Identification and Evolution Analysis of Sox Genes in Coturnix japonica Based on Comparative Genomics. Genes (Basel) 2019; 10:genes10040314. [PMID: 31013663 PMCID: PMC6523956 DOI: 10.3390/genes10040314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/16/2019] [Accepted: 04/20/2019] [Indexed: 01/04/2023] Open
Abstract
Coturnix japonica (Japanese quail) has been extensively used as a model animal for biological studies. The Sox gene family, which was systematically characterized by a high-mobility group (HMG-box) in many animal species, encodes transcription factors that play central roles during multiple developmental processes. However, genome-wide investigations on the Sox gene family in birds are scarce. In the current study, we first performed a genome-wide study to explore the Sox gene family in galliform birds. Based on available genomic sequences retrieved from the NCBI database, we focused on the global identification of the Sox gene family in C. japonica and other species in Galliformes, and the evolutionary relationships of Sox genes. In our result, a total of 35 Sox genes in seven groups were identified in the C. japonica genome. Our results also revealed that dispersed gene duplications contributed the most to the expansion of the Sox gene family in Galliform birds. Evolutionary analyses indicated that Sox genes are an ancient gene family, and strong purifying selections played key roles in the evolution of CjSox genes of C. japonica. More interestingly, we observed that most Sox genes exhibited highly embryo-specific expression in both gonads. Our findings provided new insights into the molecular function and phylogeny of Sox gene family in birds.
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Affiliation(s)
- Lan Jiang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650000, China.
| | - De Bi
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Hengwu Ding
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, 241000, China.
| | - Xuan Wu
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Ran Zhu
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Juhua Zeng
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Xiaojun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650000, China.
| | - Xianzhao Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, 241000, China.
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