1
|
Petersen M, Winter S, Coimbra R, J de Jong M, Kapitonov VV, Nilsson MA. Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae. Mob DNA 2021; 12:27. [PMID: 34836553 PMCID: PMC8620236 DOI: 10.1186/s13100-021-00254-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/25/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. RESULTS The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. CONCLUSIONS The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.
Collapse
Affiliation(s)
- Malte Petersen
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Raphael Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
| | - Menno J de Jong
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Vladimir V Kapitonov
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
| |
Collapse
|
2
|
Li C, Huang R, Nie F, Li J, Zhu W, Shi X, Guo Y, Chen Y, Wang S, Zhang L, Chen L, Li R, Liu X, Zheng C, Zhang C, Ma RZ. Organization of the Addax Major Histocompatibility Complex Provides Insights Into Ruminant Evolution. Front Immunol 2020; 11:260. [PMID: 32161588 PMCID: PMC7053375 DOI: 10.3389/fimmu.2020.00260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/31/2020] [Indexed: 12/22/2022] Open
Abstract
Ruminants are critical as prey in transferring solar energy fixed by plants into carnivorous species, yet the genetic signature of the driving forces leading to the evolutionary success of the huge number of ruminant species remains largely unknown. Here we report a complete DNA map of the major histocompatibility complex (MHC) of the addax (Addax nasomaculatus) genome by sequencing a total of 47 overlapping BAC clones previously mapped to cover the MHC region. The addax MHC is composed of 3,224,151 nucleotides, harboring a total of 150 coding genes, 50 tRNA genes, and 14 non-coding RNA genes. The organization of addax MHC was found to be highly conserved to those of sheep and cattle, highlighted by a large piece of chromosome inversion that divided the MHC class II into IIa and IIb subregions. It is now highly possible that all of the ruminant species in the family of Bovidae carry the same chromosome inversion in the MHC region, inherited from a common ancestor of ruminants. Phylogenetic analysis indicated that DY, a ruminant-specific gene located at the boundary of the inversion and highly expressed in dendritic cells, was possibly evolved from DQ, with an estimated divergence time ~140 million years ago. Homology modeling showed that the overall predicted structure of addax DY was similar to that of HLA-DQ2. However, the pocket properties of P1, P4, P6, and P9, which were critical for antigen binding in the addax DY, showed certain distinctive features. Structural analysis suggested that the populations of peptide antigens presented by addax DY and HLA-DQ2 were quite diverse, which in theory could serve to promote microbial regulation in the rumen by ruminant species, contributing to enhanced grass utilization ability. In summary, the results of our study helped to enhance our understanding of the MHC evolution and provided additional supportive evidence to our previous hypothesis that an ancient chromosome inversion in the MHC region of the last common ancestor of ruminants may have contributed to the evolutionary success of current ruminants on our planet.
Collapse
Affiliation(s)
- Chaokun Li
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Rui Huang
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fangyuan Nie
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jiujie Li
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wen Zhu
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoqian Shi
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yu Guo
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan Chen
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shiyu Wang
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Limeng Zhang
- Molecular Biology Laboratory of Zhengzhou Normal University, Zhengzhou, China
| | - Longxin Chen
- Molecular Biology Laboratory of Zhengzhou Normal University, Zhengzhou, China
| | - Runting Li
- Molecular Biology Laboratory of Zhengzhou Normal University, Zhengzhou, China
| | - Xuefeng Liu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Changming Zheng
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Runlin Z Ma
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,Molecular Biology Laboratory of Zhengzhou Normal University, Zhengzhou, China
| |
Collapse
|
3
|
Chen L, Qiu Q, Jiang Y, Wang K, Lin Z, Li Z, Bibi F, Yang Y, Wang J, Nie W, Su W, Liu G, Li Q, Fu W, Pan X, Liu C, Yang J, Zhang C, Yin Y, Wang Y, Zhao Y, Zhang C, Wang Z, Qin Y, Liu W, Wang B, Ren Y, Zhang R, Zeng Y, da Fonseca RR, Wei B, Li R, Wan W, Zhao R, Zhu W, Wang Y, Duan S, Gao Y, Zhang YE, Chen C, Hvilsom C, Epps CW, Chemnick LG, Dong Y, Mirarab S, Siegismund HR, Ryder OA, Gilbert MTP, Lewin HA, Zhang G, Heller R, Wang W. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 2019; 364:364/6446/eaav6202. [DOI: 10.1126/science.aav6202] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/16/2019] [Indexed: 12/17/2022]
Abstract
The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.
Collapse
|
4
|
Farré M, Kim J, Proskuryakova AA, Zhang Y, Kulemzina AI, Li Q, Zhou Y, Xiong Y, Johnson JL, Perelman PL, Johnson WE, Warren WC, Kukekova AV, Zhang G, O'Brien SJ, Ryder OA, Graphodatsky AS, Ma J, Lewin HA, Larkin DM. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. Genome Res 2019; 29:576-589. [PMID: 30760546 PMCID: PMC6442394 DOI: 10.1101/gr.239863.118] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 02/08/2019] [Indexed: 02/02/2023]
Abstract
The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.
Collapse
Affiliation(s)
- Marta Farré
- Royal Veterinary College, University of London, London NW1 0TU, United Kingdom
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Korea
| | - Anastasia A Proskuryakova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk 630090, Russia.,Synthetic Biology Unit, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Yang Zhang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | | | - Qiye Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yang Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yingqi Xiong
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jennifer L Johnson
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk 630090, Russia.,Synthetic Biology Unit, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia 22630, USA.,Walter Reed Biosystematics Unit, Museum Support Center, Smithsonian Institution, Suitland, Maryland 20746, USA
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri 63201, USA
| | - Anna V Kukekova
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Centre for Social Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199004, Russia.,Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida 33004, USA
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo, Escondido, California 92027, USA
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk 630090, Russia.,Synthetic Biology Unit, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Harris A Lewin
- Department of Evolution and Ecology and the UC Davis Genome Center, University of California, Davis, California 95616, USA
| | - Denis M Larkin
- Royal Veterinary College, University of London, London NW1 0TU, United Kingdom.,The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
| |
Collapse
|
5
|
Scarpato M, Angelini C, Cocca E, Pallotta MM, Morescalchi MA, Capriglione T. Short interspersed DNA elements and miRNAs: a novel hidden gene regulation layer in zebrafish? Chromosome Res 2016; 23:533-44. [PMID: 26363800 DOI: 10.1007/s10577-015-9484-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In this study, we investigated by in silico analysis the possible correlation between microRNAs (miRNAs) and Anamnia V-SINEs (a superfamily of short interspersed nuclear elements), which belong to those retroposon families that have been preserved in vertebrate genomes for millions of years and are actively transcribed because they are embedded in the 3' untranslated region (UTR) of several genes. We report the results of the analysis of the genomic distribution of these mobile elements in zebrafish (Danio rerio) and discuss their involvement in generating miRNA gene loci. The computational study showed that the genes predicted to bear V-SINEs can be targeted by miRNAs with a very high hybridization E-value. Gene ontology analysis indicates that these genes are mainly involved in metabolic, membrane, and cytoplasmic signaling pathways. Nearly all the miRNAs that were predicted to target the V-SINEs of these genes, i.e., miR-338, miR-9, miR-181, miR-724, miR-735, and miR-204, have been validated in similar regulatory roles in mammals. The large number of genes bearing a V-SINE involved in metabolic and cellular processes suggests that V-SINEs may play a role in modulating cell responses to different stimuli and in preserving the metabolic balance during cell proliferation and differentiation. Although they need experimental validation, these preliminary results suggest that in the genome of D. rerio, as in other TE families in vertebrates, the preservation of V-SINE retroposons may also have been favored by their putative role in gene network modulation.
Collapse
Affiliation(s)
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo "M. Picone", CNR, via P. Castellino, 80131, Napoli, Italy
| | - Ennio Cocca
- IBBR-CNR, via P. Castellino, 80131, Napoli, Italy
| | - Maria M Pallotta
- Dipartimento di Biologia, Università di Napoli Federico II, via Cinthia 21, 80126, Napoli, Italy
| | - Maria A Morescalchi
- Dipartimento di Biologia, Università di Napoli Federico II, via Cinthia 21, 80126, Napoli, Italy
| | - Teresa Capriglione
- Dipartimento di Biologia, Università di Napoli Federico II, via Cinthia 21, 80126, Napoli, Italy.
| |
Collapse
|
6
|
Fennessy J, Bidon T, Reuss F, Kumar V, Elkan P, Nilsson M, Vamberger M, Fritz U, Janke A. Multi-locus Analyses Reveal Four Giraffe Species Instead of One. Curr Biol 2016; 26:2543-2549. [DOI: 10.1016/j.cub.2016.07.036] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/14/2016] [Accepted: 07/14/2016] [Indexed: 01/28/2023]
|