1
|
Yohe LR, Krell NT. An updated synthesis of and outstanding questions in the olfactory and vomeronasal systems in bats: Genetics asks questions only anatomy can answer. Anat Rec (Hoboken) 2023; 306:2765-2780. [PMID: 37523493 DOI: 10.1002/ar.25290] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023]
Abstract
The extensive diversity observed in bat nasal chemosensory systems has been well-documented at the histological level. Understanding how this diversity evolved and developing hypotheses as to why particular patterns exist require a phylogenetic perspective, which was first outlined in the work of anatomist Kunwar Bhatnagar. With the onset of genetics and genomics, it might be assumed that the puzzling patterns observed in the morphological data have been clarified. However, there is still a widespread mismatch of genetic and morphological correlations among bat chemosensory systems. Novel genomic evidence has set up new avenues to explore that demand more evidence from anatomical structures. Here, we outline the progress that has been made in both morphological and molecular studies on the olfactory and vomeronasal systems in bats since the work of Bhatnagar. Genomic data of olfactory and vomeronasal receptors demonstrate the strong need for further morphological sampling, with a particular focus on receiving brain regions, glands, and ducts.
Collapse
Affiliation(s)
- Laurel R Yohe
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
- North Carolina Research Campus, Kannapolis, North Carolina, USA
| | - Nicholas T Krell
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| |
Collapse
|
2
|
Garg KM, Lamba V, Sanyal A, Dovih P, Chattopadhyay B. Next Generation Sequencing Revolutionizes Organismal Biology Research in Bats. J Mol Evol 2023:10.1007/s00239-023-10107-2. [PMID: 37154841 PMCID: PMC10166039 DOI: 10.1007/s00239-023-10107-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/29/2023] [Indexed: 05/10/2023]
Abstract
The advent of next generation sequencing technologies (NGS) has greatly accelerated our understanding of critical aspects of organismal biology from non-model organisms. Bats form a particularly interesting group in this regard, as genomic data have helped unearth a vast spectrum of idiosyncrasies in bat genomes associated with bat biology, physiology, and evolution. Bats are important bioindicators and are keystone species to many eco-systems. They often live in proximity to humans and are frequently associated with emerging infectious diseases, including the COVID-19 pandemic. Nearly four dozen bat genomes have been published to date, ranging from drafts to chromosomal level assemblies. Genomic investigations in bats have also become critical towards our understanding of disease biology and host-pathogen coevolution. In addition to whole genome sequencing, low coverage genomic data like reduced representation libraries, resequencing data, etc. have contributed significantly towards our understanding of the evolution of natural populations, and their responses to climatic and anthropogenic perturbations. In this review, we discuss how genomic data have enhanced our understanding of physiological adaptations in bats (particularly related to ageing, immunity, diet, etc.), pathogen discovery, and host pathogen co-evolution. In comparison, the application of NGS towards population genomics, conservation, biodiversity assessment, and functional genomics has been appreciably slower. We reviewed the current areas of focus, identifying emerging topical research directions and providing a roadmap for future genomic studies in bats.
Collapse
Affiliation(s)
- Kritika M Garg
- Centre for Interdisciplinay Archaeological Research, Ashoka University, Sonipat, Haryana, 131029, India
- Department of Biology, Ashoka University, Sonipat, Haryana, 131029, India
- Centre for Climate Change and Sustainability (3CS), Ashoka University, Sonipat, Haryana, 131029, India
| | - Vinita Lamba
- Trivedi School of Biosciences, Ashoka University, Sonipat, Haryana, 131029, India
- J. William Fulbright College of Arts and Sciences, Department of Biological Sciences, University of Arkansas, Fayetteville, AR72701, USA
| | - Avirup Sanyal
- Trivedi School of Biosciences, Ashoka University, Sonipat, Haryana, 131029, India
- Ecology and Evolution, National Centre for Biological Sciences, Bangalore, 560065, India
| | - Pilot Dovih
- Centre for Climate Change and Sustainability (3CS), Ashoka University, Sonipat, Haryana, 131029, India
- Ecology and Evolution, National Centre for Biological Sciences, Bangalore, 560065, India
- School of Chemistry and Biotechnology, Sastra University, Thanjavur, Tamil Nadu, 613401, India
| | - Balaji Chattopadhyay
- Centre for Climate Change and Sustainability (3CS), Ashoka University, Sonipat, Haryana, 131029, India.
- Trivedi School of Biosciences, Ashoka University, Sonipat, Haryana, 131029, India.
| |
Collapse
|
3
|
Tian S, Zeng J, Jiao H, Zhang D, Zhang L, Lei CQ, Rossiter SJ, Zhao H. Comparative analyses of bat genomes identify distinct evolution of immunity in Old World fruit bats. SCIENCE ADVANCES 2023; 9:eadd0141. [PMID: 37146151 PMCID: PMC10162675 DOI: 10.1126/sciadv.add0141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Bats have been identified as natural reservoir hosts of several zoonotic viruses, prompting suggestions that they have unique immunological adaptations. Among bats, Old World fruit bats (Pteropodidae) have been linked to multiple spillovers. To test for lineage-specific molecular adaptations in these bats, we developed a new assembly pipeline to generate a reference-quality genome of the fruit bat Cynopterus sphinx and used this in comparative analyses of 12 bat species, including six pteropodids. Our results reveal that immunity-related genes have higher evolutionary rates in pteropodids than in other bats. Several lineage-specific genetic changes were shared across pteropodids, including the loss of NLRP1, duplications of PGLYRP1 and C5AR2, and amino acid replacements in MyD88. We introduced MyD88 transgenes containing Pteropodidae-specific residues into bat and human cell lines and found evidence of dampened inflammatory responses. By uncovering distinct immune adaptations, our results could help explain why pteropodids are frequently identified as viral hosts.
Collapse
Affiliation(s)
- Shilin Tian
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Jiaming Zeng
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Hengwu Jiao
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Dejing Zhang
- Novogene Bioinformatics Institute, Beijing 100015, China
| | - Libiao Zhang
- Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Cao-Qi Lei
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Huabin Zhao
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| |
Collapse
|
4
|
Cortez T, Montenegro H, Coutinho LL, Regitano LCA, Andrade SCS. Molecular evolution and signatures of selective pressures on Bos, focusing on the Nelore breed (Bos indicus). PLoS One 2022; 17:e0279091. [PMID: 36548260 PMCID: PMC9778527 DOI: 10.1371/journal.pone.0279091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Evolutionary history leads to genome changes over time, especially for species that have experienced intense selective pressures over a short period. Here, we investigated the genomic evolution of Bos species by searching for potential selection signatures, focusing on Nelore, an economically relevant cattle breed in Brazil. We assessed the genomic processes determining the molecular evolution across Nelore and thirteen other related taxa by evaluating (i) amino acid sequence conservation, (ii) the dN/dS ratio, and (iii) gene families' turnover rate (λ). Low conserved regions potentially associated with fatty acid metabolism seem to reflect differences in meat fat content in taxa with different evolutionary histories. All Bos species presented genes under positive selection, especially B. indicus and Nelore, which include transport protein cobalamin, glycolipid metabolism, and hormone signaling. These findings could be explained by constant selective pressures to obtain higher immune resistance and efficient metabolism. The gene contraction rate across the Nelore + B. indicus branch was almost nine times higher than that in other lineages (λ = 0.01043 vs. 0.00121), indicating gene losses during the domestication process. Amino acid biosynthesis, reproductive and innate immune system-related pathways were associated with genes recognized within the most frequent rapidly evolving gene families and in genes under positive selection, supporting the substantial relevance of such traits from a domestication perspective. Our data provide new insights into how the genome may respond to intense artificial selection in distinct taxa, and reinforces the presence of selective pressures on traits potentially relevant for future animal breeding investments.
Collapse
Affiliation(s)
- Thainá Cortez
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), São Paulo, SP, Brazil
- * E-mail: (SCSA); (TC)
| | - Horácio Montenegro
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ), Piracicaba, SP, Brazil
| | - Luiz L. Coutinho
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ), Piracicaba, SP, Brazil
| | - Luciana C. A. Regitano
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil
| | - Sónia C. S. Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), São Paulo, SP, Brazil
- * E-mail: (SCSA); (TC)
| |
Collapse
|
5
|
Page RA, ter Hofstede HM. Sensory and Cognitive Ecology of Bats. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012921-052635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We see stunning morphological diversity across the animal world. Less conspicuous but equally fascinating are the sensory and cognitive adaptations that determine animals’ interactions with their environments and each other. We discuss the development of the fields of sensory and cognitive ecology and the importance of integrating these fields to understand the evolution of adaptive behaviors. Bats, with their extraordinarily high ecological diversity, are ideal animals for this purpose. An explosion in recent research allows for better understanding of the molecular, genetic, neural, and behavioral bases for sensory ecology and cognition in bats. We give examples of studies that illuminate connections between sensory and cognitive features of information filtering, evolutionary trade-offs in sensory and cognitive processing, and multimodal sensing and integration. By investigating the selective pressures underlying information acquisition, processing, and use in bats, we aim to illuminate patterns and processes driving sensory and cognitive evolution.
Collapse
Affiliation(s)
- Rachel A. Page
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Balboa, Ancón, República de Panamá
| | - Hannah M. ter Hofstede
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Balboa, Ancón, República de Panamá
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
| |
Collapse
|
6
|
Ren Y, MacPhillamy C, To TH, Smith TPL, Williams JL, Low WY. Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes. Genomics 2021; 113:3599-3609. [PMID: 34455036 DOI: 10.1016/j.ygeno.2021.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 11/27/2022]
Abstract
River buffalo is an agriculturally important species with many traits, such as disease tolerance, which promote its use worldwide. Highly contiguous genome assemblies of the river buffalo, goat, pig, human and two cattle subspecies were aligned to study gene gains and losses and signs of positive selection. The gene families that have changed significantly in river buffalo since divergence from cattle play important roles in protein degradation, the olfactory receptor system, detoxification and the immune system. We used the branch site model in PAML to analyse single-copy orthologs to identify positively selected genes that may be involved in skin differentiation, mammary development and bone formation in the river buffalo branch. The high contiguity of the genomes enabled evaluation of differences among species in the major histocompatibility complex. We identified a Babesia-like L1 LINE insertion in the DRB1-like gene in the river buffalo and discuss the implication of this finding.
Collapse
Affiliation(s)
- Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Callum MacPhillamy
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Thu-Hien To
- Norwegian University of Life Sciences: NMBU, Universitetstunet 3, 1430 Ås, Norway
| | | | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia; Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.
| |
Collapse
|
7
|
Chattopadhyay B, Garg KM, Ray R, Mendenhall IH, Rheindt FE. Novel de Novo Genome of Cynopterus brachyotis Reveals Evolutionarily Abrupt Shifts in Gene Family Composition across Fruit Bats. Genome Biol Evol 2021; 12:259-272. [PMID: 32068833 PMCID: PMC7151552 DOI: 10.1093/gbe/evaa030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2020] [Indexed: 12/01/2022] Open
Abstract
Major novel physiological or phenotypic adaptations often require accompanying modifications at the genic level. Conversely, the detection of considerable contractions and/or expansions of gene families can be an indicator of fundamental but unrecognized physiological change. We sequenced a novel fruit bat genome (Cynopterus brachyotis) and adopted a comparative approach to reconstruct the evolution of fruit bats, mapping contractions and expansions of gene families along their evolutionary history. Despite a radical change in life history as compared with other bats (e.g., loss of echolocation, large size, and frugivory), fruit bats have undergone surprisingly limited change in their genic composition, perhaps apart from a potentially novel gene family expansion relating to telomere protection and longevity. In sharp contrast, within fruit bats, the new Cynopterus genome bears the signal of unusual gene loss and gene family contraction, despite its similar morphology and lifestyle to two other major fruit bat lineages. Most missing genes are regulatory, immune-related, and olfactory in nature, illustrating the diversity of genomic strategies employed by bats to contend with responses to viral infection and olfactory requirements. Our results underscore that significant fluctuations in gene family composition are not always associated with obvious examples of novel physiological and phenotypic adaptations but may often relate to less-obvious shifts in immune strategies.
Collapse
Affiliation(s)
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rajasri Ray
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India.,Centre for Studies in Ethnobiology, Biodiversity and Sustainability (CEiBa), Mokdumpur, Malda, West Bengal, India
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore
| |
Collapse
|
8
|
Borges R, Machado JP, Gomes C, Rocha AP, Antunes A. Measuring phylogenetic signal between categorical traits and phylogenies. Bioinformatics 2020; 35:1862-1869. [PMID: 30358816 DOI: 10.1093/bioinformatics/bty800] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 08/18/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022] Open
Abstract
MOTIVATION Determining whether a trait and phylogeny share some degree of phylogenetic signal is a flagship goal in evolutionary biology. Signatures of phylogenetic signal can assist the resolution of a broad range of evolutionary questions regarding the tempo and mode of phenotypic evolution. However, despite the considerable number of strategies to measure it, few and limited approaches exist for categorical traits. Here, we used the concept of Shannon entropy and propose the δ statistic for evaluating the degree of phylogenetic signal between a phylogeny and categorical traits. RESULTS We validated δ as a measure of phylogenetic signal: the higher the δ-value the higher the degree of phylogenetic signal between a given tree and a trait. Based on simulated data we proposed a threshold-based classification test to pinpoint cases of phylogenetic signal. The assessment of the test's specificity and sensitivity suggested that the δ approach should only be applied to 20 or more species. We have further tested the performance of δ in scenarios of branch length and topology uncertainty, unbiased and biased trait evolution and trait saturation. Our results showed that δ may be applied in a wide range of phylogenetic contexts. Finally, we investigated our method in 14 360 mammalian gene trees and found that olfactory receptor genes are significantly associated with the mammalian activity patterns, a result that is congruent with expectations and experiments from the literature. Our application shows that δ can successfully detect molecular signatures of phenotypic evolution. We conclude that δ represents a useful measure of phylogenetic signal since many phenotypes can only be measured in categories. AVAILABILITY AND IMPLEMENTATION https://github.com/mrborges23/delta_statistic. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Rui Borges
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal.,CMUP, Centre of Mathematics of the University of Porto, Porto, Portugal
| | - João Paulo Machado
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal
| | - Cidália Gomes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal
| | - Ana Paula Rocha
- Department of Biology, Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal.,CMUP, Centre of Mathematics of the University of Porto, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences of the University of Porto, FCUP, Porto, Portugal
| |
Collapse
|
9
|
Nguyen VD, Nguyen TH, Tayeen ASM, Laughinghouse HD, Sánchez-Reyes LL, Wiggins J, Pontelli E, Mozzherin D, O’Meara B, Stoltzfus A. Phylotastic: Improving Access to Tree-of-Life Knowledge With Flexible, on-the-Fly Delivery of Trees. Evol Bioinform Online 2020; 16:1176934319899384. [PMID: 32372858 PMCID: PMC7192527 DOI: 10.1177/1176934319899384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/20/2019] [Indexed: 11/15/2022] Open
Abstract
A comprehensive phylogeny of species, i.e., a tree of life, has potential uses in a variety of contexts, including research, education, and public policy. Yet, accessing the tree of life typically requires special knowledge, complex software, or long periods of training. The Phylotastic project aims make it as easy to get a phylogeny of species as it is to get driving directions from mapping software. In prior work, we presented a design for an open system to validate and manage taxon names, find phylogeny resources, extract subtrees matching a user's taxon list, scale trees to time, and integrate related resources such as species images. Here, we report the implementation of a set of tools that together represent a robust, accessible system for on-the-fly delivery of phylogenetic knowledge. This set of tools includes a web portal to execute several customizable workflows to obtain species phylogenies (scaled by geologic time and decorated with thumbnail images); more than 30 underlying web services (accessible via a common registry); and code toolkits in R and Python (allowing others to develop custom applications using Phylotastic services). The Phylotastic system, accessible via http://www.phylotastic.org, provides a unique resource to access the current state of phylogenetic knowledge, useful for a variety of cases in which a tree extracted quickly from online resources (as distinct from a tree custom-made from character data) is sufficient, as it is for many casual uses of trees identified here.
Collapse
Affiliation(s)
- Van D Nguyen
- Department of Computer Science, New Mexico State University, Las Cruces, NM, USA
| | - Thanh H Nguyen
- Department of Computer Science, New Mexico State University, Las Cruces, NM, USA
| | - Abu Saleh Md Tayeen
- Department of Computer Science, New Mexico State University, Las Cruces, NM, USA
| | - H Dail Laughinghouse
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
- Fort Lauderdale Research and Education Center, University of Florida/IFAS, Davie, FL, USA
| | - Luna L Sánchez-Reyes
- Department of Ecology and Evolutionary Biology, The University of Tennessee, Knoxville, Knoxville, TN, USA
| | - Jodie Wiggins
- Department of Ecology and Evolutionary Biology, The University of Tennessee, Knoxville, Knoxville, TN, USA
| | - Enrico Pontelli
- Department of Computer Science, New Mexico State University, Las Cruces, NM, USA
| | - Dmitry Mozzherin
- Illinois Natural History Survey, Species File Group, University of Illinois at Urbana–Champaign, Champaign, IL, USA
| | - Brian O’Meara
- Department of Ecology and Evolutionary Biology, The University of Tennessee, Knoxville, Knoxville, TN, USA
| | - Arlin Stoltzfus
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
- Office of Data and Informatics, Material Measurement Laboratory, NIST, Gaithersburg, MD, USA
| |
Collapse
|
10
|
Abstract
The Orthologous Matrix (OMA) is a method and database that allows users to identify orthologs among many genomes. OMA provides three different types of orthologs: pairwise orthologs, OMA Groups and Hierarchical Orthologous Groups (HOGs). This Primer is organized in two parts. In the first part, we provide all the necessary background information to understand the concepts of orthology, how we infer them and the different subtypes of orthology in OMA, as well as what types of analyses they should be used for. In the second part, we describe protocols for using the OMA browser to find a specific gene and its various types of orthologs. By the end of the Primer, readers should be able to (i) understand homology and the different types of orthologs reported in OMA, (ii) understand the best type of orthologs to use for a particular analysis; (iii) find particular genes of interest in the OMA browser; and (iv) identify orthologs for a given gene. The data can be freely accessed from the OMA browser at https://omabrowser.org.
Collapse
Affiliation(s)
| | - Christophe Dessimoz
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
- Department of Computer Science, University College London, London, WC1E 6BT, UK
| | - Natasha M. Glover
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| |
Collapse
|
11
|
Altenhoff AM, Levy J, Zarowiecki M, Tomiczek B, Warwick Vesztrocy A, Dalquen DA, Müller S, Telford MJ, Glover NM, Dylus D, Dessimoz C. OMA standalone: orthology inference among public and custom genomes and transcriptomes. Genome Res 2019; 29:1152-1163. [PMID: 31235654 PMCID: PMC6633268 DOI: 10.1101/gr.243212.118] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 05/24/2019] [Indexed: 11/24/2022]
Abstract
Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many analyses lies in identifying orthologs—corresponding genes across multiple species—but this is far from trivial. The Orthologous MAtrix (OMA) database is a leading resource for identifying orthologs among publicly available, complete genomes. Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a cluster, it has native support for the LSF, SGE, PBS Pro, and Slurm job schedulers and can scale up to thousands of parallel processes. Another key feature of OMA standalone is that users can combine their own data with existing public data by exporting genomes and precomputed alignments from the OMA database, which currently contains over 2100 complete genomes. We compare OMA standalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of Lophotrochozoa, a challenging clade within the protostomes. We also discuss other potential applications of OMA standalone, including identifying gene families having undergone duplications/losses in specific clades, and identifying potential drug targets in nonmodel organisms. OMA standalone is available under the permissive open source Mozilla Public License Version 2.0.
Collapse
Affiliation(s)
- Adrian M Altenhoff
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Computer Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Jeremy Levy
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT, United Kingdom.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Magdalena Zarowiecki
- Genomics England, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Bartłomiej Tomiczek
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom.,Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland
| | - Alex Warwick Vesztrocy
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Daniel A Dalquen
- Department of Computer Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Steven Müller
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Natasha M Glover
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - David Dylus
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christophe Dessimoz
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Department of Computer Science, University College London, London WC1E 6BT, United Kingdom
| |
Collapse
|
12
|
Genome-Wide Identification and Characterization of Olfactory Receptor Genes in Chinese Perch, Siniperca chuatsi. Genes (Basel) 2019; 10:genes10020178. [PMID: 30823620 PMCID: PMC6409572 DOI: 10.3390/genes10020178] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 11/29/2022] Open
Abstract
Olfaction, which is mediated by olfactory receptor (OR) genes, is essential in the daily life of fish, especially in foraging. However, Chinese perch (Siniperca chuatsi) is believed to prey with reliance on vision and lateral sensation, but not on olfaction. Therefore, understanding the evolutionary dynamics of the Chinese perch OR repertoire could provide insights into genetic evidence for adapting to a decreasing reliance on olfaction. Here, we reported a whole-genome analysis of the Chinese perch OR repertoire. Our analysis identified a total of 152 OR genes, including 123 functional genes and 29 pseudogenes, and showed their genomic organization. A phylogenetic tree was constructed, and the phylogenetic relationships of teleosts ORs was illustrated. The dN/dS (global ratios of non-synonymous to synonymous) analysis demonstrated that OR groups all appeared to be under purifying selection. Among the five Percomorpha fishes, Chinese perch only had 22 subfamilies, suggesting a decrease in OR diversities. The species-specific loss of subfamily 56 and 66 in Chinese perch, of which the genes belonged to subfamily 66, were orthologs of OR51E2, which recognized the plant odorant β-ionone, indicating that extremely piscivorous fish which might lose those receptors responded to plant-related odors. Finally, the expression profiles of OR genes in the olfactory epithelium at different developmental stages were investigated using RNA-seq data. From the aforementioned results, the evolution of the OR repertoire may be shaped by the adaption of vision-dependent specializations for foraging in Chinese perch. The first systematic study of OR genes in Chinese perch could provide valuable genomic resources for the further investigation of olfactory function in teleosts.
Collapse
|
13
|
Pavlovich SS, Lovett SP, Koroleva G, Guito JC, Arnold CE, Nagle ER, Kulcsar K, Lee A, Thibaud-Nissen F, Hume AJ, Mühlberger E, Uebelhoer LS, Towner JS, Rabadan R, Sanchez-Lockhart M, Kepler TB, Palacios G. The Egyptian Rousette Genome Reveals Unexpected Features of Bat Antiviral Immunity. Cell 2018; 173:1098-1110.e18. [PMID: 29706541 PMCID: PMC7112298 DOI: 10.1016/j.cell.2018.03.070] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/22/2018] [Accepted: 03/27/2018] [Indexed: 12/27/2022]
Abstract
Bats harbor many viruses asymptomatically, including several notorious for causing extreme virulence in humans. To identify differences between antiviral mechanisms in humans and bats, we sequenced, assembled, and analyzed the genome of Rousettus aegyptiacus, a natural reservoir of Marburg virus and the only known reservoir for any filovirus. We found an expanded and diversified KLRC/KLRD family of natural killer cell receptors, MHC class I genes, and type I interferons, which dramatically differ from their functional counterparts in other mammals. Such concerted evolution of key components of bat immunity is strongly suggestive of novel modes of antiviral defense. An evaluation of the theoretical function of these genes suggests that an inhibitory immune state may exist in bats. Based on our findings, we hypothesize that tolerance of viral infection, rather than enhanced potency of antiviral defenses, may be a key mechanism by which bats asymptomatically host viruses that are pathogenic in humans.
Collapse
Affiliation(s)
- Stephanie S Pavlovich
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sean P Lovett
- Center for Genome Sciences, United States Army Research Institute of Infectious Diseases (USAMRIID), Frederick, MD 21702, USA
| | - Galina Koroleva
- Center for Genome Sciences, United States Army Research Institute of Infectious Diseases (USAMRIID), Frederick, MD 21702, USA
| | - Jonathan C Guito
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Catherine E Arnold
- Center for Genome Sciences, United States Army Research Institute of Infectious Diseases (USAMRIID), Frederick, MD 21702, USA
| | - Elyse R Nagle
- Center for Genome Sciences, United States Army Research Institute of Infectious Diseases (USAMRIID), Frederick, MD 21702, USA
| | - Kirsten Kulcsar
- Center for Genome Sciences, United States Army Research Institute of Infectious Diseases (USAMRIID), Frederick, MD 21702, USA
| | - Albert Lee
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20892, USA
| | - Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA 02118, USA
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA 02118, USA
| | - Luke S Uebelhoer
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Raul Rabadan
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, United States Army Research Institute of Infectious Diseases (USAMRIID), Frederick, MD 21702, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; Department of Mathematics and Statistics, Boston University, Boston, MA 02215, USA; National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA 02118, USA.
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Research Institute of Infectious Diseases (USAMRIID), Frederick, MD 21702, USA.
| |
Collapse
|