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Gutiérrez EG, Maldonado JE, Castellanos-Morales G, Eguiarte LE, Martínez-Méndez N, Ortega J. Unraveling genomic features and phylogenomics through the analysis of three Mexican endemic Myotis genomes. PeerJ 2024; 12:e17651. [PMID: 38993980 PMCID: PMC11238727 DOI: 10.7717/peerj.17651] [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: 01/19/2024] [Accepted: 06/07/2024] [Indexed: 07/13/2024] Open
Abstract
Background Genomic resource development for non-model organisms is rapidly progressing, seeking to uncover molecular mechanisms and evolutionary adaptations enabling thriving in diverse environments. Limited genomic data for bat species hinder insights into their evolutionary processes, particularly within the diverse Myotis genus of the Vespertilionidae family. In Mexico, 15 Myotis species exist, with three-M. vivesi, M. findleyi, and M. planiceps-being endemic and of conservation concern. Methods We obtained samples of Myotis vivesi, M. findleyi, and M. planiceps for genomic analysis. Each of three genomic DNA was extracted, sequenced, and assembled. The scaffolding was carried out utilizing the M. yumanensis genome via a genome-referenced approach within the ntJoin program. GapCloser was employed to fill gaps. Repeat elements were characterized, and gene prediction was done via ab initio and homology methods with MAKER pipeline. Functional annotation involved InterproScan, BLASTp, and KEGG. Non-coding RNAs were annotated with INFERNAL, and tRNAscan-SE. Orthologous genes were clustered using Orthofinder, and a phylogenomic tree was reconstructed using IQ-TREE. Results We present genome assemblies of these endemic species using Illumina NovaSeq 6000, each exceeding 2.0 Gb, with over 90% representing single-copy genes according to BUSCO analyses. Transposable elements, including LINEs and SINEs, constitute over 30% of each genome. Helitrons, consistent with Vespertilionids, were identified. Values around 20,000 genes from each of the three assemblies were derived from gene annotation and their correlation with specific functions. Comparative analysis of orthologs among eight Myotis species revealed 20,820 groups, with 4,789 being single copy orthogroups. Non-coding RNA elements were annotated. Phylogenomic tree analysis supported evolutionary chiropterans' relationships. These resources contribute significantly to understanding gene evolution, diversification patterns, and aiding conservation efforts for these endangered bat species.
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Affiliation(s)
- Edgar G. Gutiérrez
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Jesus E. Maldonado
- Center for Conservation Genomics, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, D.C., United States of America
| | - Gabriela Castellanos-Morales
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Unidad Villahermosa (ECOSUR-Villahermosa), Villahermosa, Tabasco, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Norberto Martínez-Méndez
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Jorge Ortega
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
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Liu M, Wang C, Huo L, Cao J, Mao X, He Z, Hu C, Sun H, Deng W, He W, Chen Y, Gu M, Liao J, Guo N, He X, Wu Q, Chen J, Zhang L, Wang X, Shang C, Dong J. Complexin-1 enhances ultrasound neurotransmission in the mammalian auditory pathway. Nat Genet 2024; 56:1503-1515. [PMID: 38834904 DOI: 10.1038/s41588-024-01781-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 04/25/2024] [Indexed: 06/06/2024]
Abstract
Unlike megabats, which rely on well-developed vision, microbats use ultrasonic echolocation to navigate and locate prey. To study ultrasound perception, here we compared the auditory cortices of microbats and megabats by constructing reference genomes and single-nucleus atlases for four species. We found that parvalbumin (PV)+ neurons exhibited evident cross-species differences and could respond to ultrasound signals, whereas their silencing severely affected ultrasound perception in the mouse auditory cortex. Moreover, megabat PV+ neurons expressed low levels of complexins (CPLX1-CPLX4), which can facilitate neurotransmitter release, while microbat PV+ neurons highly expressed CPLX1, which improves neurotransmission efficiency. Further perturbation of Cplx1 in PV+ neurons impaired ultrasound perception in the mouse auditory cortex. In addition, CPLX1 functioned in other parts of the auditory pathway in microbats but not megabats and exhibited convergent evolution between echolocating microbats and whales. Altogether, we conclude that CPLX1 expression throughout the entire auditory pathway can enhance mammalian ultrasound neurotransmission.
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Affiliation(s)
- Meiling Liu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Changliang Wang
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Lifang Huo
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Jie Cao
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Ziqing He
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Chuanxia Hu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Haijian Sun
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Wenjun Deng
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Weiya He
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Yifu Chen
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Meifeng Gu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Jiayu Liao
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Ning Guo
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Xiangyang He
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China.
| | - Xiaoqun Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, China.
| | - Congping Shang
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
| | - Ji Dong
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
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Wang H, Sun R, Xu N, Wang X, Bao M, Li X, Li J, Lin A, Feng J. Untargeted metabolomics of the cochleae from two laryngeally echolocating bats. Front Mol Biosci 2023; 10:1171366. [PMID: 37152899 PMCID: PMC10154556 DOI: 10.3389/fmolb.2023.1171366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023] Open
Abstract
High-frequency hearing is regarded as one of the most functionally important traits in laryngeally echolocating bats. Abundant candidate hearing-related genes have been identified to be the important genetic bases underlying high-frequency hearing for laryngeally echolocating bats, however, extensive metabolites presented in the cochleae have not been studied. In this study, we identified 4,717 annotated metabolites in the cochleae of two typical laryngeally echolocating bats using the liquid chromatography-mass spectroscopy technology, metabolites classified as amino acids, peptides, and fatty acid esters were identified as the most abundant in the cochleae of these two echolocating bat species, Rhinolophus sinicus and Vespertilio sinensis. Furthermore, 357 metabolites were identified as significant differentially accumulated (adjusted p-value <0.05) in the cochleae of these two bat species with distinct echolocating dominant frequencies. Downstream KEGG enrichment analyses indicated that multiple biological processes, including signaling pathways, nervous system, and metabolic process, were putatively different in the cochleae of R. sinicus and V. sinensis. For the first time, this study investigated the extensive metabolites and associated biological pathways in the cochleae of two laryngeal echolocating bats and expanded our knowledge of the metabolic molecular bases underlying high-frequency hearing in the cochleae of echolocating bats.
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Affiliation(s)
- Hui Wang
- College of Life Science, Jilin Agricultural University, Changchun, China
- *Correspondence: Hui Wang, ; Jiang Feng,
| | - Ruyi Sun
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Ningning Xu
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Xue Wang
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Mingyue Bao
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Xin Li
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Jiqian Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- College of Life Science, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- *Correspondence: Hui Wang, ; Jiang Feng,
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Li J, Sun K, Dai W, Leng H, Li A, Feng J. Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, Rhinolophus) Revealed by Three Organs. Animals (Basel) 2022; 12:ani12233432. [PMID: 36496954 PMCID: PMC9741297 DOI: 10.3390/ani12233432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
In the process of species differentiation and adaption, the relative influence of natural selection on gene expression variation often remains unclear (especially its impact on phenotypic divergence). In this study, we used differentially expressed genes from brain, cochlea, and liver samples collected from two species of bats to determine the gene expression variation forced by natural selection when comparing at the interspecific (Rhinolophus siamensis and R. episcopus episcopus) and the intraspecific (R. e. episcopus and R. episcopus spp.) levels. In both cases, gene expression variation was extensively adaptive (>66.0%) and mainly governed by directional selection, followed by stabilizing selection, and finally balancing selection. The expression variation related to acoustic signals (resting frequency, RF) and body size (forearm length, FA) was also widely governed by natural selection (>69.1%). Different functional patterns of RF- or FA-related adaptive expression variation were found between the two comparisons, which manifested as abundant immune-related regulations between subspecies (indicating a relationship between immune response and phenotypic adaption). Our study verifies the extensive adaptive expression variation between both species and subspecies and provides insight into the effects of natural selection on species differentiation and adaptation as well as phenotypic divergence at the expression level.
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Affiliation(s)
- Jun Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
- Correspondence: (K.S.); (J.F.)
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (K.S.); (J.F.)
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Nawae W, Sonthirod C, Yoocha T, Waiyamitra P, Soisook P, Tangphatsornruang S, Pootakham W. Genome assembly of the Pendlebury's roundleaf bat, Hipposideros pendleburyi, revealed the expansion of Tc1/Mariner DNA transposons in Rhinolophoidea. DNA Res 2022; 29:6754705. [PMID: 36214371 PMCID: PMC9549598 DOI: 10.1093/dnares/dsac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Indexed: 11/16/2022] Open
Abstract
Bats (Chiroptera) constitute the second largest order of mammals and have several distinctive features, such as true self-powered flight and strong immunity. The Pendlebury's roundleaf bat, Hipposideros pendleburyi, is endemic to Thailand and listed as a vulnerable species. We employed the 10× Genomics linked-read technology to obtain a genome assembly of H. pendleburyi. The assembly size was 2.17 Gb with a scaffold N50 length of 15,398,518 bases. Our phylogenetic analysis placed H. pendleburyi within the rhinolophoid clade of the suborder Yinpterochiroptera. A synteny analysis showed that H. pendleburyi shared conserved chromosome segments (up to 105 Mb) with Rhinolophus ferrumequinum and Phyllostomus discolor albeit having different chromosome numbers and belonging different families. We found positive selection signals in genes involved in inflammation, spermatogenesis and Wnt signalling. The analyses of transposable elements suggested the contraction of short interspersed nuclear elements (SINEs) and the accumulation of young mariner DNA transposons in the analysed hipposiderids. Distinct mariners were likely horizontally transferred to hipposiderid genomes over the evolution of this family. The lineage-specific profiles of SINEs and mariners might involve in the evolution of hipposiderids and be associated with the phylogenetic separations of these bats from other bat families.
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Affiliation(s)
- Wanapinun Nawae
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Pitchaporn Waiyamitra
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Hat Yai, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Wirulda Pootakham
- To whom correspondence should be addressed. Tel: +66 2 5646700 Ext 71445. Fax: +66 2 5646707.
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Chen Z, Liu Y, Liang R, Cui C, Zhu Y, Zhang F, Zhang J, Chen X. Comparative transcriptome analysis provides insights into the molecular mechanisms of high-frequency hearing differences between the sexes of Odorrana tormota. BMC Genomics 2022; 23:296. [PMID: 35410120 PMCID: PMC9004125 DOI: 10.1186/s12864-022-08536-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/07/2022] [Indexed: 11/15/2022] Open
Abstract
Background Acoustic communication is important for the survival and reproduction of anurans and masking background noise is a critical factor for their effective acoustic communication. Males of the concave-eared frog (Odorrana tormota) have evolved an ultrasonic communication capacity to avoid masking by the widespread background noise of local fast-flowing streams, whereas females exhibit no ultrasonic sensitivity. However, the molecular mechanisms underlying the high-frequency hearing differences between the sexes of O. tormota are still poorly understood. Results In this study, we sequenced the brain transcriptomes of male and female O. tormota, and compared their differential gene expression. A total of 4,605 differentially expressed genes (DEGs) between the sexes of O. tormota were identified and eleven of them were related to auditory based on the annotation and enrichment analysis. Most of these DEGs in males showed a higher expression trend than females in both quantity and expression quantity. The highly expressed genes in males were relatively concentrated in neurogenesis, signal transduction, ion transport and energy metabolism, whereas the up-expressed genes in females were mainly related to the growth and development regulation of specific auditory cells. Conclusions The transcriptome of male and female O. tormota has been sequenced and de novo assembled, which will provide gene reference for further genomic studies. In addition, this is the first research to reveal the molecular mechanisms of sex differences in ultrasonic hearing between the sexes of O. tormota and will provide new insights into the genetic basis of the auditory adaptation in amphibians during their transition from water to land. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08536-2.
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Affiliation(s)
- Zhuo Chen
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.,The Observation and Research Field Station of Taihang Mountain Forest Ecosystems of Henan Province, Xinxiang, 453007, China
| | - Yao Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Rui Liang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Chong Cui
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yanjun Zhu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Fang Zhang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Jie Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China.
| | - Xiaohong Chen
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China. .,The Observation and Research Field Station of Taihang Mountain Forest Ecosystems of Henan Province, Xinxiang, 453007, China.
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Farré X, Molina R, Barteri F, Timmers PRHJ, Joshi PK, Oliva B, Acosta S, Esteve-Altava B, Navarro A, Muntané G. Comparative Analysis of Mammal Genomes Unveils Key Genomic Variability for Human Life Span. Mol Biol Evol 2021; 38:4948-4961. [PMID: 34297086 PMCID: PMC8557403 DOI: 10.1093/molbev/msab219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The enormous mammal's lifespan variation is the result of each species' adaptations to their own biological trade-offs and ecological conditions. Comparative genomics have demonstrated that genomic factors underlying both, species lifespans and longevity of individuals, are in part shared across the tree of life. Here, we compared protein-coding regions across the mammalian phylogeny to detect individual amino acid (AA) changes shared by the most long-lived mammals and genes whose rates of protein evolution correlate with longevity. We discovered a total of 2,737 AA in 2,004 genes that distinguish long- and short-lived mammals, significantly more than expected by chance (P = 0.003). These genes belong to pathways involved in regulating lifespan, such as inflammatory response and hemostasis. Among them, a total 1,157 AA showed a significant association with maximum lifespan in a phylogenetic test. Interestingly, most of the detected AA positions do not vary in extant human populations (81.2%) or have allele frequencies below 1% (99.78%). Consequently, almost none of these putatively important variants could have been detected by genome-wide association studies. Additionally, we identified four more genes whose rate of protein evolution correlated with longevity in mammals. Crucially, SNPs located in the detected genes explain a larger fraction of human lifespan heritability than expected, successfully demonstrating for the first time that comparative genomics can be used to enhance interpretation of human genome-wide association studies. Finally, we show that the human longevity-associated proteins are significantly more stable than the orthologous proteins from short-lived mammals, strongly suggesting that general protein stability is linked to increased lifespan.
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Affiliation(s)
- Xavier Farré
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Ruben Molina
- Structural Bioinformatics Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Fabio Barteri
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Paul R H J Timmers
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom,Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Baldomero Oliva
- Structural Bioinformatics Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sandra Acosta
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Borja Esteve-Altava
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
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Wang H, Zhao H, Chu Y, Feng J, Sun K. Assessing evidence for adaptive evolution in two hearing-related genes important for high-frequency hearing in echolocating mammals. G3 (BETHESDA, MD.) 2021; 11:jkab069. [PMID: 33784395 PMCID: PMC8049434 DOI: 10.1093/g3journal/jkab069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/28/2021] [Indexed: 11/29/2022]
Abstract
High-frequency hearing is particularly important for echolocating bats and toothed whales. Previously, studies of the hearing-related genes Prestin, KCNQ4, and TMC1 documented that adaptive evolution of high-frequency hearing has taken place in echolocating bats and toothed whales. In this study, we present two additional candidate hearing-related genes, Shh and SK2, that may also have contributed to the evolution of echolocation in mammals. Shh is a member of the vertebrate Hedgehog gene family and is required in the specification of the mammalian cochlea. SK2 is expressed in both inner and outer hair cells, and it plays an important role in the auditory system. The coding region sequences of Shh and SK2 were obtained from a wide range of mammals with and without echolocating ability. The topologies of phylogenetic trees constructed using Shh and SK2 were different; however, multiple molecular evolutionary analyses showed that those two genes experienced different selective pressures in echolocating bats and toothed whales compared to nonecholocating mammals. In addition, several nominally significant positively selected sites were detected in the nonfunctional domain of the SK2 gene, indicating that different selective pressures were acting on different parts of the SK2 gene. This study has expanded our knowledge of the adaptive evolution of high-frequency hearing in echolocating mammals.
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Affiliation(s)
- Hui Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
| | - Yujia Chu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Jiang Feng
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
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Sun H, Chen W, Wang J, Zhang L, Rossiter SJ, Mao X. Echolocation call frequency variation in horseshoe bats: molecular basis revealed by comparative transcriptomics. Proc Biol Sci 2020; 287:20200875. [PMID: 32900318 DOI: 10.1098/rspb.2020.0875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Recently diverged taxa with contrasting phenotypes offer opportunities for unravelling the genetic basis of phenotypic variation in nature. Horseshoe bats are a speciose group that exhibit a derived form of high-duty cycle echolocation in which the inner ear is finely tuned to echoes of the narrowband call frequency. Here, by focusing on three recently diverged subspecies of the intermediate horseshoe bat (Rhinolophus affinis) that display divergent echolocation call frequencies, we aim to identify candidate loci putatively involved in hearing frequency variation. We used de novo transcriptome sequencing of two mainland taxa (himalayanus and macrurus) and one island taxon (hainanus) to compare expression profiles of thousands of genes. By comparing taxa with divergent call frequencies (around 15 kHz difference), we identified 252 differentially expressed genes, of which six have been shown to be involved in hearing or deafness in human/mouse. To obtain further validation of these results, we applied quantitative reverse transcription-PCR to the candidate gene FBXL15 and found a broad association between the level of expression and call frequency across taxa. The genes identified here represent strong candidate loci associated with hearing frequency variation in bats.
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Affiliation(s)
- Haijian Sun
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, People's Republic of China
| | - Wenli Chen
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, People's Republic of China
| | - Jiaying Wang
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, People's Republic of China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou 510260, People's Republic of China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, People's Republic of China.,Institute of Eco-Chongming (IEC), East China Normal University, Shanghai 200062, People's Republic of China
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