1
|
Ding Y, Zou M, Guo B. Genomic signatures associated with recurrent scale loss in cyprinid fish. Integr Zool 2024. [PMID: 38816909 DOI: 10.1111/1749-4877.12851] [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] [Indexed: 06/01/2024]
Abstract
Scale morphology represents a fundamental feature of fish and a key evolutionary trait underlying fish diversification. Despite frequent and recurrent scale loss throughout fish diversification, comprehensive genome-wide analyses of the genomic signatures associated with scale loss in divergent fish lineages remain scarce. In the current study, we investigated genome-wide signatures, specifically convergent protein-coding gene loss, amino acid substitutions, and cis-regulatory sequence changes, associated with recurrent scale loss in two divergent Cypriniformes lineages based on large-scale genomic, transcriptomic, and epigenetic data. Results demonstrated convergent changes in many genes related to scale formation in divergent scaleless fish lineages, including loss of P/Q-rich scpp genes (e.g. scpp6 and scpp7), accelerated evolution of non-coding elements adjacent to the fgf and fgfr genes, and convergent amino acid changes in genes (e.g. snap29) under relaxed selection. Collectively, these findings highlight the existence of a shared genetic architecture underlying recurrent scale loss in divergent fish lineages, suggesting that evolutionary outcomes may be genetically repeatable and predictable in the convergence of scale loss in fish.
Collapse
Affiliation(s)
- Yongli Ding
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China
| |
Collapse
|
2
|
Minkin I, Salzberg SL. CONSERVATION ASSESSMENT OF HUMAN SPLICE SITE ANNOTATION BASED ON A 470-GENOME ALIGNMENT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.01.569581. [PMID: 38076842 PMCID: PMC10705407 DOI: 10.1101/2023.12.01.569581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Despite many improvements over the years, the annotation of the human genome remains imperfect, and different annotations of the human reference genome sometimes contradict one another. The use of evolutionarily conserved sequences provides a strategy for selecting a high-confidence subset of the annotation that is more likely to be related to biological functions, and the rapidly growing number of genomes from other species increases its power. Using the latest whole genome alignment, we found that splice sites from protein-coding genes in the high-quality MANE annotation are consistently conserved across more than 400 species. We also studied splice sites from the RefSeq, GENCODE, and CHESS databases that are not present in MANE. We trained a logistic regression classifier to distinguish between the conservation exhibited by sites from MANE versus sites chosen randomly from neutrally evolving sequence. We found that splice sites classified by our model as conserved have lower SNP rates and better transcriptomic support. We then computed a subset of transcripts only using either "conserved" splice sites or ones from MANE. This subset is enriched in high-confidence transcripts of the major gene catalogs that appear to be under purifying selection and are more likely to be correct and functionally relevant.
Collapse
Affiliation(s)
- Ilia Minkin
- Department of Biomedical Engineering, Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Center for Computational Biology, Department of Computer Science, Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21211, USA
| |
Collapse
|
3
|
Hundsdoerfer AK, Schell T, Patzold F, Wright CJ, Yoshido A, Marec F, Daneck H, Winkler S, Greve C, Podsiadlowski L, Hiller M, Pippel M. High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae). BMC Genomics 2023; 24:443. [PMID: 37550607 PMCID: PMC10405479 DOI: 10.1186/s12864-023-09506-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/05/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Morphological and traditional genetic studies of the young Pliocene genus Hyles have led to the understanding that despite its importance for taxonomy, phenotypic similarity of wing patterns does not correlate with phylogenetic relationship. To gain insights into various aspects of speciation in the Spurge Hawkmoth (Hyles euphorbiae), we assembled a chromosome-level genome and investigated some of its characteristics. RESULTS The genome of a male H. euphorbiae was sequenced using PacBio and Hi-C data, yielding a 504 Mb assembly (scaffold N50 of 18.2 Mb) with 99.9% of data represented by the 29 largest scaffolds forming the haploid chromosome set. Consistent with this, FISH analysis of the karyotype revealed n = 29 chromosomes and a WZ/ZZ (female/male) sex chromosome system. Estimates of chromosome length based on the karyotype image provided an additional quality metric of assembled chromosome size. Rescaffolding the published male H. vespertilio genome resulted in a high-quality assembly (651 Mb, scaffold N50 of 22 Mb) with 98% of sequence data in the 29 chromosomes. The larger genome size of H. vespertilio (average 1C DNA value of 562 Mb) was accompanied by a proportional increase in repeats from 45% in H. euphorbiae (measured as 472 Mb) to almost 55% in H. vespertilio. Several wing pattern genes were found on the same chromosomes in the two species, with varying amounts and positions of repetitive elements and inversions possibly corrupting their function. CONCLUSIONS Our two-fold comparative genomics approach revealed high gene synteny of the Hyles genomes to other Sphingidae and high correspondence to intact Merian elements, the ancestral linkage groups of Lepidoptera, with the exception of three simple fusion events. We propose a standardized approach for genome taxonomy using nucleotide homology via scaffold chaining as the primary tool combined with Oxford plots based on Merian elements to infer and visualize directionality of chromosomal rearrangements. The identification of wing pattern genes promises future understanding of the evolution of forewing patterns in the genus Hyles, although further sequencing data from more individuals are needed. The genomic data obtained provide additional reliable references for further comparative studies in hawkmoths (Sphingidae).
Collapse
Affiliation(s)
- Anna K Hundsdoerfer
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109, Dresden, Germany.
| | - Tilman Schell
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt Am Main, Germany
| | - Franziska Patzold
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109, Dresden, Germany
| | | | - Atsuo Yoshido
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Hana Daneck
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109, Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
| | - Carola Greve
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt Am Main, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113, Bonn, Germany
| | - Michael Hiller
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt Am Main, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, 751 23, Sweden
| |
Collapse
|
4
|
Langschied F, Leisegang MS, Brandes RP, Ebersberger I. ncOrtho: efficient and reliable identification of miRNA orthologs. Nucleic Acids Res 2023; 51:e71. [PMID: 37260093 PMCID: PMC10359484 DOI: 10.1093/nar/gkad467] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators that finetune gene expression via translational repression or degradation of their target mRNAs. Despite their functional relevance, frameworks for the scalable and accurate detection of miRNA orthologs are missing. Consequently, there is still no comprehensive picture of how miRNAs and their associated regulatory networks have evolved. Here we present ncOrtho, a synteny informed pipeline for the targeted search of miRNA orthologs in unannotated genome sequences. ncOrtho matches miRNA annotations from multi-tissue transcriptomes in precision, while scaling to the analysis of hundreds of custom-selected species. The presence-absence pattern of orthologs to 266 human miRNA families across 402 vertebrate species reveals four bursts of miRNA acquisition, of which the most recent event occurred in the last common ancestor of higher primates. miRNA families are rarely modified or lost, but notable exceptions for both events exist. miRNA co-ortholog numbers faithfully indicate lineage-specific whole genome duplications, and miRNAs are powerful markers for phylogenomic analyses. Their exceptionally low genetic diversity makes them suitable to resolve clades where the phylogenetic signal is blurred by incomplete lineage sorting of ancestral alleles. In summary, ncOrtho allows to routinely consider miRNAs in evolutionary analyses that were thus far reserved to protein-coding genes.
Collapse
Affiliation(s)
- Felix Langschied
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
| | - Matthias S Leisegang
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| |
Collapse
|
5
|
Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos DG, Hilgers L, Lindblad-Toh K, Karlsson EK, Hiller M, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Integrating gene annotation with orthology inference at scale. Science 2023; 380:eabn3107. [PMID: 37104600 DOI: 10.1126/science.abn3107] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.
Collapse
Affiliation(s)
- Bogdan M Kirilenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Chetan Munegowda
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - David Jebb
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Moritz Blumer
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Ariadna E Morales
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Alexis-Walid Ahmed
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Dimitrios-Georgios Kontopoulos
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Leon Hilgers
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 32 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Elinor K Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Goethe University Frankfurt, Faculty of Biosciences, 60438 Frankfurt, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Osipova E, Barsacchi R, Brown T, Sadanandan K, Gaede AH, Monte A, Jarrells J, Moebius C, Pippel M, Altshuler DL, Winkler S, Bickle M, Baldwin MW, Hiller M. Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds. Science 2023; 379:185-190. [PMID: 36634192 DOI: 10.1126/science.abn7050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hummingbirds possess distinct metabolic adaptations to fuel their energy-demanding hovering flight, but the underlying genomic changes are largely unknown. Here, we generated a chromosome-level genome assembly of the long-tailed hermit and screened for genes that have been specifically inactivated in the ancestral hummingbird lineage. We discovered that FBP2 (fructose-bisphosphatase 2), which encodes a gluconeogenic muscle enzyme, was lost during a time period when hovering flight evolved. We show that FBP2 knockdown in an avian muscle cell line up-regulates glycolysis and enhances mitochondrial respiration, coincident with an increased mitochondria number. Furthermore, genes involved in mitochondrial respiration and organization have up-regulated expression in hummingbird flight muscle. Together, these results suggest that FBP2 loss was likely a key step in the evolution of metabolic muscle adaptations required for true hovering flight.
Collapse
Affiliation(s)
- Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.,Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.,Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Rico Barsacchi
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Tom Brown
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany.,DRESDEN concept Genome Center, Technische Universität Dresden, 01062 Dresden, Germany
| | - Keren Sadanandan
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Andrea H Gaede
- University of British Columbia, Vancouver, Vancouver, BC V6T 1Z4, Canada.,Structure and Motion Laboratory, Royal Veterinary College, University of London, London, UK
| | - Amanda Monte
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Julia Jarrells
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Claudia Moebius
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,DRESDEN concept Genome Center, Technische Universität Dresden, 01062 Dresden, Germany
| | - Marc Bickle
- Roche Institute for Translational Bioengineering, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.,Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.,Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| |
Collapse
|
7
|
Han W, Wu Y, Zeng L, Zhao S. Building the Chordata Olfactory Receptor Database using more than 400,000 receptors annotated by Genome2OR. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2539-2551. [PMID: 35696018 DOI: 10.1007/s11427-021-2081-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/20/2022] [Indexed: 06/15/2023]
Abstract
Olfactory receptors are poorly annotated for most genome-sequenced chordates. To address this deficiency, we developed a nhmmer-based olfactory receptor annotation tool Genome2OR ( https://github.com/ToHanwei/Genome2OR.git ), and used it to process 1,695 sequenced chordate genomes in the NCBI Assembly database as of January, 2021. In total, 765,248 olfactory receptor genes were annotated, with 404,426 functional genes and 360,822 pseudogenes, which represents a four-fold increase in the number of annotated olfactory receptors. Based on the annotation data, we built a database called Chordata Olfactory Receptor Database (CORD, https://cord.ihuman.shanghaitech.edu.cn ) for archiving, analysing and disseminating the data. Beyond the primary data, we offer derivative information, including pictures of species, cross references to public databases, structural models, sequence similarity networks and sequence profiles in the CORD. Furthermore, we did brief analyses on these receptors, including building a huge protein sequence similarity network covering all receptors in the database, and clustering them into 20 communities, classifying the 20 communities into three categories based on their presences/absences in ray-finned fish and/or lobe-finned fish. We infer that olfactory receptors should have unique activation and desensitization mechanisms by analysing their sequences and structural models. We believe the CORD can benefit the researchers and the general public who are interested in olfaction.
Collapse
Affiliation(s)
- Wei Han
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Liting Zeng
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| |
Collapse
|
8
|
Blumer M, Brown T, Freitas MB, Destro AL, Oliveira JA, Morales AE, Schell T, Greve C, Pippel M, Jebb D, Hecker N, Ahmed AW, Kirilenko BM, Foote M, Janke A, Lim BK, Hiller M. Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding. SCIENCE ADVANCES 2022; 8:eabm6494. [PMID: 35333583 PMCID: PMC8956264 DOI: 10.1126/sciadv.abm6494] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Vampire bats are the only mammals that feed exclusively on blood. To uncover genomic changes associated with this dietary adaptation, we generated a haplotype-resolved genome of the common vampire bat and screened 27 bat species for genes that were specifically lost in the vampire bat lineage. We found previously unknown gene losses that relate to reduced insulin secretion (FFAR1 and SLC30A8), limited glycogen stores (PPP1R3E), and a unique gastric physiology (CTSE). Other gene losses likely reflect the biased nutrient composition (ERN2 and CTRL) and distinct pathogen diversity of blood (RNASE7) and predict the complete lack of cone-based vision in these strictly nocturnal bats (PDE6H and PDE6C). Notably, REP15 loss likely helped vampire bats adapt to high dietary iron levels by enhancing iron excretion, and the loss of CYP39A1 could have contributed to their exceptional cognitive abilities. These findings enhance our understanding of vampire bat biology and the genomic underpinnings of adaptations to blood feeding.
Collapse
Affiliation(s)
- Moritz Blumer
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- Goethe University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Tom Brown
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | - Ana Luiza Destro
- Department of Animal Biology, Federal University of Viçosa, Viçosa, Brazil
| | - Juraci A. Oliveira
- Department of General Biology, Federal University of Viçosa, Viçosa, Brazil
| | - Ariadna E. Morales
- Goethe University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - David Jebb
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Alexis-Walid Ahmed
- Goethe University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Bogdan M. Kirilenko
- Goethe University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Maddy Foote
- Native Bat Conservation Program, Toronto Zoo, 361A Old Finch Avenue, Toronto, Ontario M1B 5K7, Canada
| | - Axel Janke
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Burton K. Lim
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario M5S 2C6, Canada
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- Goethe University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
- Corresponding author.
| |
Collapse
|
9
|
Saxena A, Sharma V, Muthuirulan P, Neufeld SJ, Tran MP, Gutierrez HL, Chen KD, Erberich JM, Birmingham A, Capellini TD, Cobb J, Hiller M, Cooper KL. Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas. Curr Biol 2022; 32:289-303.e6. [PMID: 34793695 PMCID: PMC8792248 DOI: 10.1016/j.cub.2021.10.063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/16/2021] [Accepted: 10/28/2021] [Indexed: 01/26/2023]
Abstract
Despite the great diversity of vertebrate limb proportion and our deep understanding of the genetic mechanisms that drive skeletal elongation, little is known about how individual bones reach different lengths in any species. Here, we directly compare the transcriptomes of homologous growth cartilages of the mouse (Mus musculus) and bipedal jerboa (Jaculus jaculus), the latter of which has "mouse-like" arms but extremely long metatarsals of the feet. Intersecting gene-expression differences in metatarsals and forearms of the two species revealed that about 10% of orthologous genes are associated with the disproportionately rapid elongation of neonatal jerboa feet. These include genes and enriched pathways not previously associated with endochondral elongation as well as those that might diversify skeletal proportion in addition to their known requirements for bone growth throughout the skeleton. We also identified transcription regulators that might act as "nodes" for sweeping differences in genome expression between species. Among these, Shox2, which is necessary for proximal limb elongation, has gained expression in jerboa metatarsals where it has not been detected in other vertebrates. We show that Shox2 is sufficient to increase mouse distal limb length, and a nearby putative cis-regulatory region is preferentially accessible in jerboa metatarsals. In addition to mechanisms that might directly promote growth, we found evidence that jerboa foot elongation may occur in part by de-repressing latent growth potential. The genes and pathways that we identified here provide a framework to understand the modular genetic control of skeletal growth and the remarkable malleability of vertebrate limb proportion.
Collapse
Affiliation(s)
- Aditya Saxena
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden 01307, Germany; Max Planck Institute for the Physics of Complex Systems, Nothnitzerstraße 38, Dresden 01187, Germany
| | - Pushpanathan Muthuirulan
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
| | - Stanley J Neufeld
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Mai P Tran
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Haydee L Gutierrez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kevin D Chen
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Joel M Erberich
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
| | - John Cobb
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden 01307, Germany; Max Planck Institute for the Physics of Complex Systems, Nothnitzerstraße 38, Dresden 01187, Germany
| | - Kimberly L Cooper
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| |
Collapse
|
10
|
Sharma V, Hecker N, Walther F, Stuckas H, Hiller M. Convergent Losses of TLR5 Suggest Altered Extracellular Flagellin Detection in Four Mammalian Lineages. Mol Biol Evol 2021; 37:1847-1854. [PMID: 32145026 DOI: 10.1093/molbev/msaa058] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Toll-like receptors (TLRs) play an important role for the innate immune system by detecting pathogen-associated molecular patterns. TLR5 encodes the major extracellular receptor for bacterial flagellin and frequently evolves under positive selection, consistent with coevolutionary arms races between the host and pathogens. Furthermore, TLR5 is inactivated in several vertebrates and a TLR5 stop codon polymorphism is widespread in human populations. Here, we analyzed the genomes of 120 mammals and discovered that TLR5 is convergently lost in four independent lineages, comprising guinea pigs, Yangtze river dolphin, pinnipeds, and pangolins. Validated inactivating mutations, absence of protein-coding transcript expression, and relaxed selection on the TLR5 remnants confirm these losses. PCR analysis further confirmed the loss of TLR5 in the pinniped stem lineage. Finally, we show that TLR11, encoding a second extracellular flagellin receptor, is also absent in these four lineages. Independent losses of TLR5 and TLR11 suggest that a major pathway for detecting flagellated bacteria is not essential for different mammals and predicts an impaired capacity to sense extracellular flagellin.
Collapse
Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,CRTD-DFG Center for Regenerative Therapies Dresden, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, Technische Universität Dresden, Dresden; German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
| | - Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Felix Walther
- Senckenberg Natural History Collections Dresden, Senckenberg - Leibniz Institution for Biodiversity and Earth System Research, Dresden, Germany
| | - Heiko Stuckas
- Senckenberg Natural History Collections Dresden, Senckenberg - Leibniz Institution for Biodiversity and Earth System Research, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| |
Collapse
|
11
|
Balaton BP, Fornes O, Wasserman WW, Brown CJ. Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing. Epigenetics Chromatin 2021; 14:12. [PMID: 33597016 PMCID: PMC7890635 DOI: 10.1186/s13072-021-00386-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Background X-chromosome inactivation (XCI) in eutherian mammals is the epigenetic inactivation of one of the two X chromosomes in XX females in order to compensate for dosage differences with XY males. Not all genes are inactivated, and the proportion escaping from inactivation varies between human and mouse (the two species that have been extensively studied). Results We used DNA methylation to predict the XCI status of X-linked genes with CpG islands across 12 different species: human, chimp, bonobo, gorilla, orangutan, mouse, cow, sheep, goat, pig, horse and dog. We determined the XCI status of 342 CpG islands on average per species, with most species having 80–90% of genes subject to XCI. Mouse was an outlier, with a higher proportion of genes subject to XCI than found in other species. Sixteen genes were found to have discordant X-chromosome inactivation statuses across multiple species, with five of these showing primate-specific escape from XCI. These discordant genes tended to cluster together within the X chromosome, along with genes with similar patterns of escape from XCI. CTCF-binding, ATAC-seq signal and LTR repeats were enriched at genes escaping XCI when compared to genes subject to XCI; however, enrichment was only observed in three or four of the species tested. LINE and DNA repeats showed enrichment around subject genes, but again not in a consistent subset of species. Conclusions In this study, we determined XCI status across 12 species, showing mouse to be an outlier with few genes that escape inactivation. Inactivation status is largely conserved across species. The clustering of genes that change XCI status across species implicates a domain-level control. In contrast, the relatively consistent, but not universal correlation of inactivation status with enrichment of repetitive elements or CTCF binding at promoters demonstrates gene-based influences on inactivation state. This study broadens enrichment analysis of regulatory elements to species beyond human and mouse.
Collapse
Affiliation(s)
- Bradley P Balaton
- Department of Medical Genetics, The University of British Columbia, Vancouver, Canada
| | - Oriol Fornes
- Department of Medical Genetics, The University of British Columbia, Vancouver, Canada.,BC Children's Hospital Research Institute, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, Canada
| | - Wyeth W Wasserman
- Department of Medical Genetics, The University of British Columbia, Vancouver, Canada.,BC Children's Hospital Research Institute, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, The University of British Columbia, Vancouver, Canada.
| |
Collapse
|
12
|
Alves LQ, Ruivo R, Fonseca MM, Lopes-Marques M, Ribeiro P, Castro L. PseudoChecker: an integrated online platform for gene inactivation inference. Nucleic Acids Res 2020; 48:W321-W331. [PMID: 32449938 PMCID: PMC7319564 DOI: 10.1093/nar/gkaa408] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/22/2020] [Accepted: 05/06/2020] [Indexed: 01/21/2023] Open
Abstract
The rapid expansion of high-quality genome assemblies, exemplified by ongoing initiatives such as the Genome-10K and i5k, demands novel automated methods to approach comparative genomics. Of these, the study of inactivating mutations in the coding region of genes, or pseudogenization, as a source of evolutionary novelty is mostly overlooked. Thus, to address such evolutionary/genomic events, a systematic, accurate and computationally automated approach is required. Here, we present PseudoChecker, the first integrated online platform for gene inactivation inference. Unlike the few existing methods, our comparative genomics-based approach displays full automation, a built-in graphical user interface and a novel index, PseudoIndex, for an empirical evaluation of the gene coding status. As a multi-platform online service, PseudoChecker simplifies access and usability, allowing a fast identification of disruptive mutations. An analysis of 30 genes previously reported to be eroded in mammals, and 30 viable genes from the same lineages, demonstrated that PseudoChecker was able to correctly infer 97% of loss events and 95% of functional genes, confirming its reliability. PseudoChecker is freely available, without login required, at http://pseudochecker.ciimar.up.pt.
Collapse
Affiliation(s)
- Luís Q Alves
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
| | - Raquel Ruivo
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
| | - Miguel M Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
| | - Mónica Lopes-Marques
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
| | - Pedro Ribeiro
- CRACS & INESC-TEC Department of Computer Science, FCUP, Porto, 4169-007, Portugal
| | - L Filipe C Castro
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
- Department of Biology, FCUP, Porto, 4169-007, Portugal
| |
Collapse
|
13
|
Hecker N, Hiller M. A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers. Gigascience 2020; 9:giz159. [PMID: 31899510 PMCID: PMC6941714 DOI: 10.1093/gigascience/giz159] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/29/2019] [Accepted: 12/13/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Multiple alignments of mammalian genomes have been the basis of many comparative genomic studies aiming at annotating genes, detecting regions under evolutionary constraint, and studying genome evolution. A key factor that affects the power of comparative analyses is the number of species included in a genome alignment. RESULTS To utilize the increased number of sequenced genomes and to provide an accessible resource for genomic studies, we generated a mammalian genome alignment comprising 120 species. We used this alignment and the CESAR method to provide protein-coding gene annotations for 119 non-human mammals. Furthermore, we illustrate the utility of this alignment by 2 exemplary analyses. First, we quantified how variable ultraconserved elements (UCEs) are among placental mammals. Leveraging the high taxonomic coverage in our alignment, we estimate that UCEs contain on average 4.7%-15.6% variable alignment columns. Furthermore, we show that the center regions of UCEs are generally most constrained. Second, we identified enhancer sequences that are only conserved in placental mammals. We found that these enhancers are significantly associated with placenta-related genes, suggesting that some of these enhancers may be involved in the evolution of placental mammal-specific aspects of the placenta. CONCLUSION The 120-mammal alignment and all other data are available for analysis and visualization in a genome browser at https://genome-public.pks.mpg.de/and for download at https://bds.mpi-cbg.de/hillerlab/120MammalAlignment/.
Collapse
Affiliation(s)
- Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Noethnitzer Str. 38, 01187 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Noethnitzer Str. 38, 01187 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
| |
Collapse
|
14
|
Pippel M, Jebb D, Patzold F, Winkler S, Vogel H, Myers G, Hiller M, Hundsdoerfer AK. A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae). Gigascience 2020; 9:giaa001. [PMID: 31972020 PMCID: PMC6977585 DOI: 10.1093/gigascience/giaa001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/20/2019] [Accepted: 01/08/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged ∼7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation. RESULTS Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51× Pacific Biosciences long reads with an average read length of 8.9 kb. Pacific Biosciences reads longer than 4 kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3%) than other Bombycoidea species such as Bombyx mori (45.7%) and Manduca sexta (27.5%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2%) and M. sexta (90%) annotations. CONCLUSIONS Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.
Collapse
Affiliation(s)
- Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - David Jebb
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany
| | - Franziska Patzold
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109 Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
| | - Gene Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany
| | - Anna K Hundsdoerfer
- Senckenberg Natural History Collections Dresden, Königsbrücker Landstr. 159, 01109 Dresden, Germany
| |
Collapse
|
15
|
Kirilenko BM, Hagey LR, Barnes S, Falany CN, Hiller M. Evolutionary Analysis of Bile Acid-Conjugating Enzymes Reveals a Complex Duplication and Reciprocal Loss History. Genome Biol Evol 2019; 11:3256-3268. [PMID: 31670760 PMCID: PMC6934887 DOI: 10.1093/gbe/evz238] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2019] [Indexed: 12/01/2022] Open
Abstract
To fulfill their physiological functions, bile acids are conjugated with amino acids. In humans, conjugation is catalyzed by bile acid coenzyme A: amino acid N-acyltransferase (BAAT), an enzyme with a highly conserved catalytic triad in its active site. Interestingly, the conjugated amino acids are highly variable among mammals, with some species conjugating bile acids with both glycine and taurine, whereas others conjugate only taurine. The genetic origin of these bile acid conjugation differences is unknown. Here, we tested whether mutations in BAAT’s catalytic triad could explain bile acid conjugation differences. Our comparative analysis of 118 mammals first revealed that the ancestor of placental mammals and marsupials possessed two genes, BAAT and BAATP1, that arose by a tandem duplication. This duplication was followed by numerous gene losses, including BAATP1 in humans. Losses of either BAAT or BAATP1 largely happened in a reciprocal fashion, suggesting that a single conjugating enzyme is generally sufficient for mammals. In intact BAAT and BAATP1 genes, we observed multiple changes in the catalytic triad between Cys and Ser residues. Surprisingly, although mutagenesis experiments with the human enzyme have shown that replacing Cys for Ser greatly diminishes the glycine-conjugating ability, across mammals we found that this residue provides little power in predicting the experimentally measured amino acids that are conjugated with bile acids. This suggests that the mechanism of BAAT’s enzymatic function is incompletely understood, despite relying on a classic catalytic triad. More generally, our evolutionary analysis indicates that results of mutagenesis experiments may not easily be extrapolatable to other species.
Collapse
Affiliation(s)
- Bogdan M Kirilenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology, Dresden, Germany
| | - Lee R Hagey
- Department of Medicine, University of California at San Diego, USA
| | - Stephen Barnes
- Department of Pharmacology and Toxicology, Targeted Metabolomics and Proteomics Laboratory, University of Alabama, Birmingham, USA
| | - Charles N Falany
- Department of Pharmacology and Toxicology, Targeted Metabolomics and Proteomics Laboratory, University of Alabama, Birmingham, USA
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology, Dresden, Germany
| |
Collapse
|
16
|
Sharma V, Hiller M. Losses of human disease-associated genes in placental mammals. NAR Genom Bioinform 2019; 2:lqz012. [PMID: 33575564 PMCID: PMC7671337 DOI: 10.1093/nargab/lqz012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/24/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023] Open
Abstract
We systematically investigate whether losses of human disease-associated genes occurred in other mammals during evolution. We first show that genes lost in any of 62 non-human mammals generally have a lower degree of pleiotropy, and are highly depleted in essential and disease-associated genes. Despite this under-representation, we discovered multiple genes implicated in human disease that are truly lost in non-human mammals. In most cases, traits resembling human disease symptoms are present but not deleterious in gene-loss species, exemplified by losses of genes causing human eye or teeth disorders in poor-vision or enamel-less mammals. We also found widespread losses of PCSK9 and CETP genes, where loss-of-function mutations in humans protect from atherosclerosis. Unexpectedly, we discovered losses of disease genes (TYMP, TBX22, ABCG5, ABCG8, MEFV, CTSE) where deleterious phenotypes do not manifest in the respective species. A remarkable example is the uric acid-degrading enzyme UOX, which we found to be inactivated in elephants and manatees. While UOX loss in hominoids led to high serum uric acid levels and a predisposition for gout, elephants and manatees exhibit low uric acid levels, suggesting alternative ways of metabolizing uric acid. Together, our results highlight numerous mammals that are 'natural knockouts' of human disease genes.
Collapse
Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany
| |
Collapse
|
17
|
Huelsmann M, Hecker N, Springer MS, Gatesy J, Sharma V, Hiller M. Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations. SCIENCE ADVANCES 2019; 5:eaaw6671. [PMID: 31579821 PMCID: PMC6760925 DOI: 10.1126/sciadv.aaw6671] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/28/2019] [Indexed: 05/22/2023]
Abstract
The transition from land to water in whales and dolphins (cetaceans) was accompanied by remarkable adaptations. To reveal genomic changes that occurred during this transition, we screened for protein-coding genes that were inactivated in the ancestral cetacean lineage. We found 85 gene losses. Some of these were likely beneficial for cetaceans, for example, by reducing the risk of thrombus formation during diving (F12 and KLKB1), erroneous DNA damage repair (POLM), and oxidative stress-induced lung inflammation (MAP3K19). Additional gene losses may reflect other diving-related adaptations, such as enhanced vasoconstriction during the diving response (mediated by SLC6A18) and altered pulmonary surfactant composition (SEC14L3), while loss of SLC4A9 relates to a reduced need for saliva. Last, loss of melatonin synthesis and receptor genes (AANAT, ASMT, and MTNR1A/B) may have been a precondition for adopting unihemispheric sleep. Our findings suggest that some genes lost in ancestral cetaceans were likely involved in adapting to a fully aquatic lifestyle.
Collapse
Affiliation(s)
- Matthias Huelsmann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Mark S. Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
| | - John Gatesy
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
- Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
- Corresponding author.
| |
Collapse
|
18
|
Hecker N, Lächele U, Stuckas H, Giere P, Hiller M. Convergent vomeronasal system reduction in mammals coincides with convergent losses of calcium signalling and odorant-degrading genes. Mol Ecol 2019; 28:3656-3668. [PMID: 31332871 DOI: 10.1111/mec.15180] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/16/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022]
Abstract
The vomeronasal system (VNS) serves crucial functions for detecting olfactory clues often related to social and sexual behaviour. Intriguingly, two of the main components of the VNS, the vomeronasal organ (VNO) and the accessory olfactory bulb, are regressed in aquatic mammals, several bats and primates, likely due to adaptations to different ecological niches. To detect genomic changes that are associated with the convergent reduction of the VNS, we performed the first systematic screen for convergently inactivated protein-coding genes associated with convergent VNS reduction, considering 106 mammalian genomes. Extending previous studies, our results support that Trpc2, a cation channel that is important for calcium signalling in the VNO, is a predictive molecular marker for the presence of a VNS. Our screen also detected the convergent inactivation of the calcium-binding protein S100z, the aldehyde oxidase Aox2 that is involved in odorant degradation, and the uncharacterized Mslnl gene that is expressed in the VNO and olfactory epithelium. Furthermore, we found that Trpc2 and S100z or Aox2 are also inactivated in otters and Phocid seals for which no morphological data about the VNS are available yet. This predicts a VNS reduction in these semi-aquatic mammals. By examining the genomes of 115 species in total, our study provides a detailed picture of how the convergent reduction of the VNS coincides with gene inactivation in placental mammals. These inactivated genes provide experimental targets for studying the evolution and biological significance of the olfactory system under different environmental conditions.
Collapse
Affiliation(s)
- Nikolai Hecker
- Center for Systems Biology Dresden, Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Ulla Lächele
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Heiko Stuckas
- Population Genetics, Senckenberg Natural History Collections Dresden, Dresden, Germany.,Leibniz Institution for Biodiversity and Earth System Research, Dresden, Germany
| | - Peter Giere
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Michael Hiller
- Center for Systems Biology Dresden, Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| |
Collapse
|
19
|
Signatures of Relaxed Selection in the CYP8B1 Gene of Birds and Mammals. J Mol Evol 2019; 87:209-220. [DOI: 10.1007/s00239-019-09903-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/25/2019] [Indexed: 01/26/2023]
|
20
|
Lopes-Marques M, Machado AM, Alves LQ, Fonseca MM, Barbosa S, Sinding MHS, Rasmussen MH, Iversen MR, Frost Bertelsen M, Campos PF, da Fonseca R, Ruivo R, Castro LFC. Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea. Mol Biol Evol 2019; 36:1270-1280. [PMID: 30895322 PMCID: PMC6526905 DOI: 10.1093/molbev/msz068] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genomes are dynamic biological units, with processes of gene duplication and loss triggering evolutionary novelty. The mammalian skin provides a remarkable case study on the occurrence of adaptive morphological innovations. Skin sebaceous glands (SGs), for instance, emerged in the ancestor of mammals serving pivotal roles, such as lubrication, waterproofing, immunity, and thermoregulation, through the secretion of sebum, a complex mixture of various neutral lipids such as triacylglycerol, free fatty acids, wax esters, cholesterol, and squalene. Remarkably, SGs are absent in a few mammalian lineages, including the iconic Cetacea. We investigated the evolution of the key molecular components responsible for skin sebum production: Dgat2l6, Awat1, Awat2, Elovl3, Mogat3, and Fabp9. We show that all analyzed genes have been rendered nonfunctional in Cetacea species (toothed and baleen whales). Transcriptomic analysis, including a novel skin transcriptome from blue whale, supports gene inactivation. The conserved mutational pattern found in most analyzed genes, indicates that pseudogenization events took place prior to the diversification of modern Cetacea lineages. Genome and skin transcriptome analysis of the common hippopotamus highlighted the convergent loss of a subset of sebum-producing genes, notably Awat1 and Mogat3. Partial loss profiles were also detected in non-Cetacea aquatic mammals, such as the Florida manatee, and in terrestrial mammals displaying specialized skin phenotypes such as the African elephant, white rhinoceros and pig. Our findings reveal a unique landscape of “gene vestiges” in the Cetacea sebum-producing compartment, with limited gene loss observed in other mammalian lineages: suggestive of specific adaptations or specializations of skin lipids.
Collapse
Affiliation(s)
- Mónica Lopes-Marques
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - André M Machado
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - Luís Q Alves
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, U. Porto-University of Porto, Porto, Portugal
| | - Miguel M Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - Susana Barbosa
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | | | | | | | | | - Paula F Campos
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Rute da Fonseca
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Raquel Ruivo
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - L Filipe C Castro
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, U. Porto-University of Porto, Porto, Portugal
| |
Collapse
|
21
|
Hecker N, Sharma V, Hiller M. Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores. Proc Natl Acad Sci U S A 2019; 116:3036-3041. [PMID: 30718421 PMCID: PMC6386725 DOI: 10.1073/pnas.1818504116] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The repeated evolution of dietary specialization represents a hallmark of mammalian ecology. To detect genomic changes that are associated with dietary adaptations, we performed a systematic screen for convergent gene losses associated with an obligate herbivorous or carnivorous diet in 31 placental mammals. For herbivores, our screen discovered the repeated loss of the triglyceride lipase inhibitor PNLIPRP1, suggesting enhanced triglyceride digestion efficiency. Furthermore, several herbivores lost the pancreatic exocytosis factor SYCN, providing an explanation for continuous pancreatic zymogen secretion in these species. For carnivores, we discovered the repeated loss of the hormone-receptor pair INSL5-RXFP4 that regulates appetite and glucose homeostasis, which likely relates to irregular feeding patterns and constant gluconeogenesis. Furthermore, reflecting the reduced need to metabolize plant-derived xenobiotics, several carnivores lost the xenobiotic receptors NR1I3 and NR1I2 Finally, the carnivore-associated loss of the gastrointestinal host defense gene NOX1 could be related to a reduced gut microbiome diversity. By revealing convergent gene losses associated with differences in dietary composition, feeding patterns, and gut microbiomes, our study contributes to understanding how similar dietary specializations evolved repeatedly in mammals.
Collapse
Affiliation(s)
- Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany;
- Max Planck Institute for the Physics of Complex Systems, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| |
Collapse
|
22
|
Abstract
Rapidly improving sequencing technology coupled with computational developments in sequence assembly are making reference-quality genome assembly economical. Hundreds of vertebrate genome assemblies are now publicly available, and projects are being proposed to sequence thousands of additional species in the next few years. Such dense sampling of the tree of life should give an unprecedented new understanding of evolution and allow a detailed determination of the events that led to the wealth of biodiversity around us. To gain this knowledge, these new genomes must be compared through genome alignment (at the sequence level) and comparative annotation (at the gene level). However, different alignment and annotation methods have different characteristics; before starting a comparative genomics analysis, it is important to understand the nature of, and biases and limitations inherent in, the chosen methods. This review is intended to act as a technical but high-level overview of the field that should provide this understanding. We briefly survey the state of the genome alignment and comparative annotation fields and potential future directions for these fields in a new, large-scale era of comparative genomics.
Collapse
Affiliation(s)
- Joel Armstrong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| | - Ian T Fiddes
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA;
- 10x Genomics, Pleasanton, California 94566, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA;
| |
Collapse
|
23
|
Springer MS, Emerling CA, Gatesy J, Randall J, Collin MA, Hecker N, Hiller M, Delsuc F. Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales. BMC Evol Biol 2019; 19:31. [PMID: 30674270 PMCID: PMC6343362 DOI: 10.1186/s12862-019-1359-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 01/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background The gene for odontogenic ameloblast-associated (ODAM) is a member of the secretory calcium-binding phosphoprotein gene family. ODAM is primarily expressed in dental tissues including the enamel organ and the junctional epithelium, and may also have pleiotropic functions that are unrelated to teeth. Here, we leverage the power of natural selection to test competing hypotheses that ODAM is tooth-specific versus pleiotropic. Specifically, we compiled and screened complete protein-coding sequences, plus sequences for flanking intronic regions, for ODAM in 165 placental mammals to determine if this gene contains inactivating mutations in lineages that either lack teeth (baleen whales, pangolins, anteaters) or lack enamel on their teeth (aardvarks, sloths, armadillos), as would be expected if the only essential functions of ODAM are related to tooth development and the adhesion of the gingival junctional epithelium to the enamel tooth surface. Results We discovered inactivating mutations in all species of placental mammals that either lack teeth or lack enamel on their teeth. A surprising result is that ODAM is also inactivated in a few additional lineages including all toothed whales that were examined. We hypothesize that ODAM inactivation is related to the simplified outer enamel surface of toothed whales. An alternate hypothesis is that ODAM inactivation in toothed whales may be related to altered antimicrobial functions of the junctional epithelium in aquatic habitats. Selection analyses on ODAM sequences revealed that the composite dN/dS value for pseudogenic branches is close to 1.0 as expected for a neutrally evolving pseudogene. DN/dS values on transitional branches were used to estimate ODAM inactivation times. In the case of pangolins, ODAM was inactivated ~ 65 million years ago, which is older than the oldest pangolin fossil (Eomanis, 47 Ma) and suggests an even more ancient loss or simplification of teeth in this lineage. Conclusion Our results validate the hypothesis that the only essential functions of ODAM that are maintained by natural selection are related to tooth development and/or the maintenance of a healthy junctional epithelium that attaches to the enamel surface of teeth. Electronic supplementary material The online version of this article (10.1186/s12862-019-1359-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA.
| | - Christopher A Emerling
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.,Department of Biology, Whittier College, Whittier, CA, 90602, USA
| | - John Gatesy
- Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - Jason Randall
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Matthew A Collin
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Frédéric Delsuc
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| |
Collapse
|
24
|
Coding Exon-Structure Aware Realigner (CESAR): Utilizing Genome Alignments for Comparative Gene Annotation. Methods Mol Biol 2019; 1962:179-191. [PMID: 31020560 DOI: 10.1007/978-1-4939-9173-0_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Alignment-based gene identification methods utilize sequence conservation between orthologous protein-coding genes to annotate genes in newly sequenced genomes. CESAR is an approach that makes use of existing genome alignments to transfer genes from one genome to other aligned genomes, and thus generates comparative gene annotations. To accurately detect conserved exons that exhibit an intact reading frame and consensus splice sites, CESAR produces a new alignment between orthologous exons, taking information about the exon's reading frame and splice site positions into account. Furthermore, CESAR is able to detect most evolutionary splice site shifts, which helps to annotate exon boundaries at high precision. Here, we describe how to apply CESAR to generate comparative gene annotations for one or many species, and discuss the strengths and limitations of this approach. CESAR is available at https://github.com/hillerlab/CESAR2.0 .
Collapse
|
25
|
Abstract
Whole-genome alignment (WGA) is the prediction of evolutionary relationships at the nucleotide level between two or more genomes. It combines aspects of both colinear sequence alignment and gene orthology prediction and is typically more challenging to address than either of these tasks due to the size and complexity of whole genomes. Despite the difficulty of this problem, numerous methods have been developed for its solution because WGAs are valuable for genome-wide analyses such as phylogenetic inference, genome annotation, and function prediction. In this chapter, we discuss the meaning and significance of WGA and present an overview of the methods that address it. We also examine the problem of evaluating whole-genome aligners and offer a set of methodological challenges that need to be tackled in order to make most effective use of our rapidly growing databases of whole genomes.
Collapse
Affiliation(s)
- Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
26
|
Roscito JG, Sameith K, Pippel M, Francoijs KJ, Winkler S, Dahl A, Papoutsoglou G, Myers G, Hiller M. The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly. Gigascience 2018; 7:5202467. [PMID: 30481296 PMCID: PMC6304105 DOI: 10.1093/gigascience/giy141] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 11/13/2018] [Indexed: 01/28/2023] Open
Abstract
Background Reptiles are a species-rich group with great phenotypic and life history diversity but are highly underrepresented among the vertebrate species with sequenced genomes. Results Here, we report a high-quality genome assembly of the tegu lizard, Salvator merianae, the first lacertoid with a sequenced genome. We combined 74X Illumina short-read, 29.8X Pacific Biosciences long-read, and optical mapping data to generate a high-quality assembly with a scaffold N50 value of 55.4 Mb. The contig N50 value of this assembly is 521 Kb, making it the most contiguous reptile assembly so far. We show that the tegu assembly has the highest completeness of coding genes and conserved non-exonic elements (CNEs) compared to other reptiles. Furthermore, the tegu assembly has the highest number of evolutionarily conserved CNE pairs, corroborating a high assembly contiguity in intergenic regions. As in other reptiles, long interspersed nuclear elements comprise the most abundant transposon class. We used transcriptomic data, homology- and de novo gene predictions to annotate 22,413 coding genes, of which 16,995 (76%) likely have human orthologs as inferred by CESAR-derived gene mappings. Finally, we generated a multiple genome alignment comprising 10 squamates and 7 other amniote species and identified conserved regions that are under evolutionary constraint. CNEs cover 38 Mb (1.8%) of the tegu genome, with 3.3 Mb in these elements being squamate specific. In contrast to placental mammal-specific CNEs, very few of these squamate-specific CNEs (<20 Kb) overlap transposons, highlighting a difference in how lineage-specific CNEs originated in these two clades. Conclusions The tegu lizard genome together with the multiple genome alignment and comprehensive conserved element datasets provide a valuable resource for comparative genomic studies of reptiles and other amniotes.
Collapse
Affiliation(s)
- Juliana G Roscito
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstr. 38, 01187, Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Katrin Sameith
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstr. 38, 01187, Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Kees-Jan Francoijs
- BioNano Genomics, Towne Centre Drive Suite, 100, 92121, San Diego, CA, USA
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Andreas Dahl
- Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Fetscherstr. 105, 01307, Dresden, Germany
| | - Georg Papoutsoglou
- BioNano Genomics, Towne Centre Drive Suite, 100, 92121, San Diego, CA, USA
| | - Gene Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstr. 38, 01187, Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
| |
Collapse
|
27
|
Sharma V, Hiller M. Loss of Enzymes in the Bile Acid Synthesis Pathway Explains Differences in Bile Composition among Mammals. Genome Biol Evol 2018; 10:3211-3217. [PMID: 30388264 PMCID: PMC6296402 DOI: 10.1093/gbe/evy243] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2018] [Indexed: 12/11/2022] Open
Abstract
Bile acids are important for absorbing nutrients. Most mammals produce cholic and chenodeoxycholic bile acids. Here, we investigated genes in the bile acid synthesis pathway in four mammals that deviate from the usual mammalian bile composition. First, we show that naked-mole rats, elephants, and manatees repeatedly inactivated CYP8B1, an enzyme uniquely required for cholic acid synthesis, which explains the absence of cholic acid in these species. Second, no gene-inactivating mutations were found in any pathway gene in the rhinoceros, a species that lacks bile acids, indicating an evolutionarily recent change in its bile composition. Third, elephants and/or manatees that also lack bile acids altogether have lost additional nonessential enzymes (SLC27A5, ACOX2). Apart from uncovering genomic differences explaining deviations in bile composition, our analysis of bile acid enzymes in bile acid-lacking species suggests that essentiality prevents gene loss, while loss of pleiotropic genes is permitted if their other functions are compensated by functionally related proteins.
Collapse
Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,CRTD-DFG Center for Regenerative Therapies Dresden, Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Dresden; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, Technische Universität Dresden, Dresden; and German Center for Diabetes Research (DZD), Munich, Neuherberg, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| |
Collapse
|
28
|
Jebb D, Hiller M. Recurrent loss of HMGCS2 shows that ketogenesis is not essential for the evolution of large mammalian brains. eLife 2018; 7:38906. [PMID: 30322448 PMCID: PMC6191284 DOI: 10.7554/elife.38906] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/09/2018] [Indexed: 12/04/2022] Open
Abstract
Apart from glucose, fatty acid-derived ketone bodies provide metabolic energy for the brain during fasting and neonatal development. We investigated the evolution of HMGCS2, the key enzyme required for ketone body biosynthesis (ketogenesis). Unexpectedly, we found that three mammalian lineages, comprising cetaceans (dolphins and whales), elephants and mastodons, and Old World fruit bats have lost this gene. Remarkably, many of these species have exceptionally large brains and signs of intelligent behavior. While fruit bats are sensitive to starvation, cetaceans and elephants can still withstand periods of fasting. This suggests that alternative strategies to fuel large brains during fasting evolved repeatedly and reveals flexibility in mammalian energy metabolism. Furthermore, we show that HMGCS2 loss preceded brain size expansion in toothed whales and elephants. Thus, while ketogenesis was likely important for brain size expansion in modern humans, ketogenesis is not a universal precondition for the evolution of large mammalian brains. Our brain requires a lot of energy to work properly. Sugars are usually the main type of fuel for the body, but when they run low – for example during a food shortage – fat, in the form of fatty acids, can be used instead. However, the brain cannot directly process these molecules; instead, fatty acids need to go through ketogenesis, a process that turns fat into ketone bodies, which the organ can then burn. Scientists believe that the ability to create ketone bodies was essential for us to evolve large brains. Yet, it is still unclear if all mammals can transform fatty acids into ketone bodies. One way to look into this question is to track whether other species have HMGCS2, the main enzyme that drives ketogenesis. Jebb and Hiller examined the genomes of 70 different species of mammals for the gene that codes for HMGCS2. The comparisons revealed that cetaceans (whales, dolphins and porpoises), Old World fruit bats and the African savanna elephant have all independently lost their working version of HMGCS2. Yet, many members of these three groups have evolved brains that are large for their body size. The genetic analyses showed that dolphins and elephants developed big brains after the enzyme became inactive, challenging the idea that HMGCS2 – and by extension ketogenesis – is always required for the evolution of large brains. These results may also be useful for conservation efforts. Many fruit bats across the world are severely threatened, and their lack of ketogenesis could explain why these animals are highly sensitive to starvation and quickly die when food becomes scarce.
Collapse
Affiliation(s)
- David Jebb
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| |
Collapse
|
29
|
Lee JH, Lewis KM, Moural TW, Kirilenko B, Borgonovo B, Prange G, Koessl M, Huggenberger S, Kang C, Hiller M. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. SCIENCE ADVANCES 2018; 4:eaat9660. [PMID: 30263960 PMCID: PMC6157964 DOI: 10.1126/sciadv.aat9660] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
Abstract
Detecting associations between genomic changes and phenotypic differences is fundamental to understanding how phenotypes evolved. By systematically screening for parallel amino acid substitutions, we detected known as well as novel cases (Strc, Tecta, and Cabp2) of parallelism between echolocating bats and toothed whales in proteins that could contribute to high-frequency hearing adaptations. Our screen also showed that echolocating mammals exhibit an unusually high number of parallel substitutions in fast-twitch muscle fiber proteins. Both echolocating bats and toothed whales produce an extremely rapid call rate when homing in on their prey, which was shown in bats to be powered by specialized superfast muscles. We show that these genes with parallel substitutions (Casq1, Atp2a1, Myh2, and Myl1) are expressed in the superfast sound-producing muscle of bats. Furthermore, we found that the calcium storage protein calsequestrin 1 of the little brown bat and the bottlenose dolphin functionally converged in its ability to form calcium-sequestering polymers at lower calcium concentrations, which may contribute to rapid calcium transients required for superfast muscle physiology. The proteins that our genomic screen detected could be involved in the convergent evolution of vocalization in echolocating mammals by potentially contributing to both rapid Ca2+ transients and increased shortening velocities in superfast muscles.
Collapse
Affiliation(s)
- Jun-Hoe Lee
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Kevin M. Lewis
- Department of Chemistry, Washington State University, Pullman, WA 99164–4630, USA
| | - Timothy W. Moural
- Department of Chemistry, Washington State University, Pullman, WA 99164–4630, USA
| | - Bogdan Kirilenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Barbara Borgonovo
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Gisa Prange
- Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Manfred Koessl
- Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Huggenberger
- Department II of Anatomy—Neuroanatomy, University of Cologne, Cologne, Germany
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA 99164–4630, USA
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| |
Collapse
|
30
|
Cetacea are natural knockouts for IL20. Immunogenetics 2018; 70:681-687. [DOI: 10.1007/s00251-018-1071-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/01/2018] [Indexed: 10/28/2022]
|
31
|
Sharma V, Lehmann T, Stuckas H, Funke L, Hiller M. Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals. PLoS Biol 2018; 16:e2005293. [PMID: 29953435 PMCID: PMC6023123 DOI: 10.1371/journal.pbio.2005293] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 05/24/2018] [Indexed: 01/13/2023] Open
Abstract
Descent of testes from a position near the kidneys into the lower abdomen or into the scrotum is an important developmental process that occurs in all placental mammals, with the exception of five afrotherian lineages. Since soft-tissue structures like testes are not preserved in the fossil record and since key parts of the placental mammal phylogeny remain controversial, it has been debated whether testicular descent is the ancestral or derived condition in placental mammals. To resolve this debate, we used genomic data of 71 mammalian species and analyzed the evolution of two key genes (relaxin/insulin-like family peptide receptor 2 [RXFP2] and insulin-like 3 [INSL3]) that induce the development of the gubernaculum, the ligament that is crucial for testicular descent. We show that both RXFP2 and INSL3 are lost or nonfunctional exclusively in four afrotherians (tenrec, cape elephant shrew, cape golden mole, and manatee) that completely lack testicular descent. The presence of remnants of once functional orthologs of both genes in these afrotherian species shows that these gene losses happened after the split from the placental mammal ancestor. These “molecular vestiges” provide strong evidence that testicular descent is the ancestral condition, irrespective of persisting phylogenetic discrepancies. Furthermore, the absence of shared gene-inactivating mutations and our estimates that the loss of RXFP2 happened at different time points strongly suggest that testicular descent was lost independently in Afrotheria. Our results provide a molecular mechanism that explains the loss of testicular descent in afrotherians and, more generally, highlight how molecular vestiges can provide insights into the evolution of soft-tissue characters. While fossils of whales with legs demonstrate that these species evolved from legged ancestors, the ancestral state of nonfossilizing soft-tissue structures can only be indirectly inferred. This difficulty is also confounded by uncertainties in the phylogenetic relationships between the animals concerned. A prime example is the case of testicular descent, a developmental process that determines the final position of testes, which occurs in most placental mammals but is absent from several afrotherian lineages. Here, we discovered that afrotherians possess remnants of genes known to be required for testicular descent. These “molecular vestiges” show that testicular descent was already present in the placental ancestor and was subsequently lost in Afrotheria. Our study highlights the potential of molecular vestiges in resolving contradictory ancestral states of soft-tissue characters.
Collapse
Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Germany
| | - Thomas Lehmann
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | | | - Liane Funke
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Germany
- * E-mail:
| |
Collapse
|
32
|
A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nat Commun 2018; 9:1215. [PMID: 29572503 PMCID: PMC5865188 DOI: 10.1038/s41467-018-03667-1] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 03/02/2018] [Indexed: 11/08/2022] Open
Abstract
Identifying the genomic changes that underlie phenotypic adaptations is a key challenge in evolutionary biology and genomics. Loss of protein-coding genes is one type of genomic change with the potential to affect phenotypic evolution. Here, we develop a genomics approach to accurately detect gene losses and investigate their importance for adaptive evolution in mammals. We discover a number of gene losses that likely contributed to morphological, physiological, and metabolic adaptations in aquatic and flying mammals. These gene losses shed light on possible molecular and cellular mechanisms that underlie these adaptive phenotypes. In addition, we show that gene loss events that occur as a consequence of relaxed selection following adaptation provide novel insights into species' biology. Our results suggest that gene loss is an evolutionary mechanism for adaptation that may be more widespread than previously anticipated. Hence, investigating gene losses has great potential to reveal the genomic basis underlying macroevolutionary changes.
Collapse
|
33
|
Florio M, Heide M, Pinson A, Brandl H, Albert M, Winkler S, Wimberger P, Huttner WB, Hiller M. Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex. eLife 2018; 7:32332. [PMID: 29561261 PMCID: PMC5898914 DOI: 10.7554/elife.32332] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/09/2018] [Indexed: 01/21/2023] Open
Abstract
Understanding the molecular basis that underlies the expansion of the neocortex during primate, and notably human, evolution requires the identification of genes that are particularly active in the neural stem and progenitor cells of the developing neocortex. Here, we have used existing transcriptome datasets to carry out a comprehensive screen for protein-coding genes preferentially expressed in progenitors of fetal human neocortex. We show that 15 human-specific genes exhibit such expression, and many of them evolved distinct neural progenitor cell-type expression profiles and levels compared to their ancestral paralogs. Functional studies on one such gene, NOTCH2NL, demonstrate its ability to promote basal progenitor proliferation in mice. An additional 35 human genes with progenitor-enriched expression are shown to have orthologs only in primates. Our study provides a resource of genes that are promising candidates to exert specific, and novel, roles in neocortical development during primate, and notably human, evolution.
Collapse
Affiliation(s)
- Marta Florio
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Heide
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Anneline Pinson
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Holger Brandl
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mareike Albert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Pauline Wimberger
- Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| |
Collapse
|
34
|
Hecker N, Sharma V, Hiller M. Transition to an Aquatic Habitat Permitted the Repeated Loss of the Pleiotropic KLK8 Gene in Mammals. Genome Biol Evol 2018; 9:3179-3188. [PMID: 29145610 PMCID: PMC5716171 DOI: 10.1093/gbe/evx239] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2017] [Indexed: 01/15/2023] Open
Abstract
Kallikrein related peptidase 8 (KLK8; also called neuropsin) is a serine protease that plays distinct roles in the skin and hippocampus. In the skin, KLK8 influences keratinocyte proliferation and desquamation, and activates antimicrobial peptides in sweat. In the hippocampus, KLK8 affects memory acquisition. Here, we examined the evolution of KLK8 in mammals and discovered that, out of 70 placental mammals, KLK8 is exclusively lost in three independent fully-aquatic lineages, comprising dolphin, killer whale, minke whale, and manatee. In addition, while the sperm whale has an intact KLK8 reading frame, the gene evolves neutrally in this species. We suggest that the distinct functions of KLK8 likely became obsolete in the aquatic environment, leading to the subsequent loss of KLK8 in several fully-aquatic mammalian lineages. First, the cetacean and manatee skin lacks sweat glands as an adaptation to the aquatic environment, which likely made the epidermal function of KLK8 obsolete. Second, cetaceans and manatees exhibit a proportionally small hippocampus, which may have rendered the hippocampal functions of KLK8 obsolete. Together, our results shed light on the genomic changes that correlate with skin and neuroanatomical differences of aquatic mammals, and show that even pleiotropic genes can be lost during evolution if an environmental change nullifies the need for the different functions of such genes.
Collapse
Affiliation(s)
- Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| |
Collapse
|
35
|
Sharma V, Hiller M. Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation. Nucleic Acids Res 2017. [PMID: 28645144 PMCID: PMC5737078 DOI: 10.1093/nar/gkx554] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0.75 substitutions per neutral site, like human and other non-placental vertebrates, benefit from increased sensitivity. To systematically test if increased sensitivity improves comparative gene annotations, we built a multiple alignment of 144 vertebrate genomes and used this alignment to map human genes to the other 143 vertebrates with CESAR. We found that higher alignment sensitivity substantially improves the completeness of comparative gene annotations by adding on average 2382 and 7440 novel exons and 117 and 317 novel genes for mammalian and non-mammalian species, respectively. Our results suggest a more sensitive alignment strategy that should generally be used for genome alignments between distantly-related species. Our 144-vertebrate genome alignment and the comparative gene annotations (https://bds.mpi-cbg.de/hillerlab/144VertebrateAlignment_CESAR/) are a valuable resource for comparative genomics.
Collapse
Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| |
Collapse
|