Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies
Abstract Relict species, like coelacanth, gingko, tuatara, are the remnants of formerly more ecologically and taxonomically diverse lineages. It raises the questions of why they are currently species-poor, have restrained ecology, and are often vulnerable to extinction. Estimating heterozygosity lev...
Gespeichert in:
Veröffentlicht in: | G3 : genes - genomes - genetics 2023-12, Vol.13 (12) |
---|---|
Hauptverfasser: | , , , , , , |
Format: | Artikel |
Sprache: | eng |
Schlagworte: | |
Online-Zugang: | Volltext |
Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
container_end_page | |
---|---|
container_issue | 12 |
container_start_page | |
container_title | G3 : genes - genomes - genetics |
container_volume | 13 |
creator | Marino, Alba Reboud, Eliette L Chevalier, Emmanuelle Tilak, Marie-Ka Contreras-Garduño, Jorge Nabholz, Benoit Condamine, Fabien L |
description | Abstract
Relict species, like coelacanth, gingko, tuatara, are the remnants of formerly more ecologically and taxonomically diverse lineages. It raises the questions of why they are currently species-poor, have restrained ecology, and are often vulnerable to extinction. Estimating heterozygosity level and demographic history can guide our understanding of the evolutionary history and conservation status of relict species. However, few studies have focused on relict invertebrates compared to vertebrates. We sequenced the genome of Baronia brevicornis (Lepidoptera: Papilionidae), which is an endangered species, the sister species of all swallowtail butterflies, and is the oldest lineage of all extant butterflies. From a dried specimen, we were able to generate both long-read and short-read data and assembled a genome of 406 Mb for Baronia. We found a fairly high level of heterozygosity (0.58%) compared to other swallowtail butterflies, which contrasts with its endangered and relict status. Taking into account the high ratio of recombination over mutation, demographic analyses indicated a sharp decline of the effective population size initiated in the last million years. Moreover, the Baronia genome was used to study genome size variation in Papilionidae. Genome sizes are mostly explained by transposable elements activities, suggesting that large genomes appear to be a derived feature in swallowtail butterflies as transposable elements activity is recent and involves different transposable elements classes among species. This first Baronia genome provides a resource for assisting conservation in a flagship and relict insect species as well as for understanding swallowtail genome evolution.
Sequencing the genome of Baronia brevicornis, an endangered species and the oldest butterfly lineage, revealed a high level of heterozygosity but a sharp population decline in the past million years. As the sister species of all swallowtail butterflies, this study also highlights genome size variation in Papilionidae and the role of transposable element activity in their evolution. The Baronia genome provides valuable resources for understanding swallowtail genome evolution and assisting in conservation efforts. |
doi_str_mv | 10.1093/g3journal/jkad239 |
format | Article |
fullrecord | <record><control><sourceid>gale_hal_p</sourceid><recordid>TN_cdi_hal_primary_oai_HAL_hal_04669175v1</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A779138791</galeid><oup_id>10.1093/g3journal/jkad239</oup_id><sourcerecordid>A779138791</sourcerecordid><originalsourceid>FETCH-LOGICAL-c434t-123e59970d48c8a751e503d7f7f41992db57f92b5f6e2e3de7c76ba922257f913</originalsourceid><addsrcrecordid>eNqNUcFu3CAUtKpWTZTmA3qpOLZSNzFgG_u4jZqk0kq9tGeE8cNmi8EFvFHyGf3i4niz6rEg8dBjZhi9ybL3OL_CeUOve7p3s7fCXO9_iY7Q5lV2TnCVb3BNq9f_3M-yyxD2eVplWVVF9TY7o6wuGCvq8-zPHVg3ahmQUygOgDwYLSMKE0gNAX0R3lktUOvhoKXzVgcUBugCMrofInIW6RhQB6PrvZgGLdGgQ3T-EQnboX5RBxT0EyA4ODNHnRhCeheSzoMwxj1EoQ1q5xjBK5P-fJe9UcIEuDzWi-zn7dcfN_eb3fe7bzfb3UYWtIgbTCiUTcPyrqhlLViJocxpxxRTBW4a0rUlUw1pS1UBAdoBk6xqRUMIWR4wvcg-rbqDMHzyehT-kTuh-f12x5deXlRVg1l5WLAfV-zk3e8ZQuSjDhKMERbcHDipWc1wOlmCXq3QXhjg2ioXvZBppxmlCVpQOvW3jCULNXv2gVfC81Q8qJMZnPMlan6Kmh-jTpwPRz9zO0J3YrwEmwCfV4Cbp__Q-wvFYLmQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2878712877</pqid></control><display><type>article</type><title>Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Access via Oxford University Press (Open Access Collection)</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><creator>Marino, Alba ; Reboud, Eliette L ; Chevalier, Emmanuelle ; Tilak, Marie-Ka ; Contreras-Garduño, Jorge ; Nabholz, Benoit ; Condamine, Fabien L</creator><contributor>Emerson, J J</contributor><creatorcontrib>Marino, Alba ; Reboud, Eliette L ; Chevalier, Emmanuelle ; Tilak, Marie-Ka ; Contreras-Garduño, Jorge ; Nabholz, Benoit ; Condamine, Fabien L ; Emerson, J J</creatorcontrib><description>Abstract
Relict species, like coelacanth, gingko, tuatara, are the remnants of formerly more ecologically and taxonomically diverse lineages. It raises the questions of why they are currently species-poor, have restrained ecology, and are often vulnerable to extinction. Estimating heterozygosity level and demographic history can guide our understanding of the evolutionary history and conservation status of relict species. However, few studies have focused on relict invertebrates compared to vertebrates. We sequenced the genome of Baronia brevicornis (Lepidoptera: Papilionidae), which is an endangered species, the sister species of all swallowtail butterflies, and is the oldest lineage of all extant butterflies. From a dried specimen, we were able to generate both long-read and short-read data and assembled a genome of 406 Mb for Baronia. We found a fairly high level of heterozygosity (0.58%) compared to other swallowtail butterflies, which contrasts with its endangered and relict status. Taking into account the high ratio of recombination over mutation, demographic analyses indicated a sharp decline of the effective population size initiated in the last million years. Moreover, the Baronia genome was used to study genome size variation in Papilionidae. Genome sizes are mostly explained by transposable elements activities, suggesting that large genomes appear to be a derived feature in swallowtail butterflies as transposable elements activity is recent and involves different transposable elements classes among species. This first Baronia genome provides a resource for assisting conservation in a flagship and relict insect species as well as for understanding swallowtail genome evolution.
Sequencing the genome of Baronia brevicornis, an endangered species and the oldest butterfly lineage, revealed a high level of heterozygosity but a sharp population decline in the past million years. As the sister species of all swallowtail butterflies, this study also highlights genome size variation in Papilionidae and the role of transposable element activity in their evolution. The Baronia genome provides valuable resources for understanding swallowtail genome evolution and assisting in conservation efforts.</description><identifier>ISSN: 2160-1836</identifier><identifier>EISSN: 2160-1836</identifier><identifier>DOI: 10.1093/g3journal/jkad239</identifier><identifier>PMID: 37847748</identifier><language>eng</language><publisher>US: Oxford University Press</publisher><subject>Analysis ; Animals ; Biochemistry, Molecular Biology ; Biodiversity ; Butterflies ; Butterflies - genetics ; Demography ; DNA Transposable Elements - genetics ; Ecology ; Endangered species ; Evolution ; Genome Size ; Genomes ; Genomics ; Life Sciences ; Phylogeny ; Populations and Evolution ; Transposons ; Wildlife conservation</subject><ispartof>G3 : genes - genomes - genetics, 2023-12, Vol.13 (12)</ispartof><rights>The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. 2023</rights><rights>The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.</rights><rights>COPYRIGHT 2023 Oxford University Press</rights><rights>Attribution</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c434t-123e59970d48c8a751e503d7f7f41992db57f92b5f6e2e3de7c76ba922257f913</cites><orcidid>0009-0005-0984-2524 ; 0000-0001-9079-4649 ; 0000-0002-9231-0641 ; 0000-0003-0447-1451 ; 0000-0003-1673-9910</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,864,885,1604,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37847748$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-04669175$$DView record in HAL$$Hfree_for_read</backlink></links><search><contributor>Emerson, J J</contributor><creatorcontrib>Marino, Alba</creatorcontrib><creatorcontrib>Reboud, Eliette L</creatorcontrib><creatorcontrib>Chevalier, Emmanuelle</creatorcontrib><creatorcontrib>Tilak, Marie-Ka</creatorcontrib><creatorcontrib>Contreras-Garduño, Jorge</creatorcontrib><creatorcontrib>Nabholz, Benoit</creatorcontrib><creatorcontrib>Condamine, Fabien L</creatorcontrib><title>Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies</title><title>G3 : genes - genomes - genetics</title><addtitle>G3 (Bethesda)</addtitle><description>Abstract
Relict species, like coelacanth, gingko, tuatara, are the remnants of formerly more ecologically and taxonomically diverse lineages. It raises the questions of why they are currently species-poor, have restrained ecology, and are often vulnerable to extinction. Estimating heterozygosity level and demographic history can guide our understanding of the evolutionary history and conservation status of relict species. However, few studies have focused on relict invertebrates compared to vertebrates. We sequenced the genome of Baronia brevicornis (Lepidoptera: Papilionidae), which is an endangered species, the sister species of all swallowtail butterflies, and is the oldest lineage of all extant butterflies. From a dried specimen, we were able to generate both long-read and short-read data and assembled a genome of 406 Mb for Baronia. We found a fairly high level of heterozygosity (0.58%) compared to other swallowtail butterflies, which contrasts with its endangered and relict status. Taking into account the high ratio of recombination over mutation, demographic analyses indicated a sharp decline of the effective population size initiated in the last million years. Moreover, the Baronia genome was used to study genome size variation in Papilionidae. Genome sizes are mostly explained by transposable elements activities, suggesting that large genomes appear to be a derived feature in swallowtail butterflies as transposable elements activity is recent and involves different transposable elements classes among species. This first Baronia genome provides a resource for assisting conservation in a flagship and relict insect species as well as for understanding swallowtail genome evolution.
Sequencing the genome of Baronia brevicornis, an endangered species and the oldest butterfly lineage, revealed a high level of heterozygosity but a sharp population decline in the past million years. As the sister species of all swallowtail butterflies, this study also highlights genome size variation in Papilionidae and the role of transposable element activity in their evolution. The Baronia genome provides valuable resources for understanding swallowtail genome evolution and assisting in conservation efforts.</description><subject>Analysis</subject><subject>Animals</subject><subject>Biochemistry, Molecular Biology</subject><subject>Biodiversity</subject><subject>Butterflies</subject><subject>Butterflies - genetics</subject><subject>Demography</subject><subject>DNA Transposable Elements - genetics</subject><subject>Ecology</subject><subject>Endangered species</subject><subject>Evolution</subject><subject>Genome Size</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Life Sciences</subject><subject>Phylogeny</subject><subject>Populations and Evolution</subject><subject>Transposons</subject><subject>Wildlife conservation</subject><issn>2160-1836</issn><issn>2160-1836</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqNUcFu3CAUtKpWTZTmA3qpOLZSNzFgG_u4jZqk0kq9tGeE8cNmi8EFvFHyGf3i4niz6rEg8dBjZhi9ybL3OL_CeUOve7p3s7fCXO9_iY7Q5lV2TnCVb3BNq9f_3M-yyxD2eVplWVVF9TY7o6wuGCvq8-zPHVg3ahmQUygOgDwYLSMKE0gNAX0R3lktUOvhoKXzVgcUBugCMrofInIW6RhQB6PrvZgGLdGgQ3T-EQnboX5RBxT0EyA4ODNHnRhCeheSzoMwxj1EoQ1q5xjBK5P-fJe9UcIEuDzWi-zn7dcfN_eb3fe7bzfb3UYWtIgbTCiUTcPyrqhlLViJocxpxxRTBW4a0rUlUw1pS1UBAdoBk6xqRUMIWR4wvcg-rbqDMHzyehT-kTuh-f12x5deXlRVg1l5WLAfV-zk3e8ZQuSjDhKMERbcHDipWc1wOlmCXq3QXhjg2ioXvZBppxmlCVpQOvW3jCULNXv2gVfC81Q8qJMZnPMlan6Kmh-jTpwPRz9zO0J3YrwEmwCfV4Cbp__Q-wvFYLmQ</recordid><startdate>20231206</startdate><enddate>20231206</enddate><creator>Marino, Alba</creator><creator>Reboud, Eliette L</creator><creator>Chevalier, Emmanuelle</creator><creator>Tilak, Marie-Ka</creator><creator>Contreras-Garduño, Jorge</creator><creator>Nabholz, Benoit</creator><creator>Condamine, Fabien L</creator><general>Oxford University Press</general><general>Genetics Society of America</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IAO</scope><scope>7X8</scope><scope>1XC</scope><scope>VOOES</scope><orcidid>https://orcid.org/0009-0005-0984-2524</orcidid><orcidid>https://orcid.org/0000-0001-9079-4649</orcidid><orcidid>https://orcid.org/0000-0002-9231-0641</orcidid><orcidid>https://orcid.org/0000-0003-0447-1451</orcidid><orcidid>https://orcid.org/0000-0003-1673-9910</orcidid></search><sort><creationdate>20231206</creationdate><title>Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies</title><author>Marino, Alba ; Reboud, Eliette L ; Chevalier, Emmanuelle ; Tilak, Marie-Ka ; Contreras-Garduño, Jorge ; Nabholz, Benoit ; Condamine, Fabien L</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c434t-123e59970d48c8a751e503d7f7f41992db57f92b5f6e2e3de7c76ba922257f913</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Analysis</topic><topic>Animals</topic><topic>Biochemistry, Molecular Biology</topic><topic>Biodiversity</topic><topic>Butterflies</topic><topic>Butterflies - genetics</topic><topic>Demography</topic><topic>DNA Transposable Elements - genetics</topic><topic>Ecology</topic><topic>Endangered species</topic><topic>Evolution</topic><topic>Genome Size</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Life Sciences</topic><topic>Phylogeny</topic><topic>Populations and Evolution</topic><topic>Transposons</topic><topic>Wildlife conservation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Marino, Alba</creatorcontrib><creatorcontrib>Reboud, Eliette L</creatorcontrib><creatorcontrib>Chevalier, Emmanuelle</creatorcontrib><creatorcontrib>Tilak, Marie-Ka</creatorcontrib><creatorcontrib>Contreras-Garduño, Jorge</creatorcontrib><creatorcontrib>Nabholz, Benoit</creatorcontrib><creatorcontrib>Condamine, Fabien L</creatorcontrib><collection>Access via Oxford University Press (Open Access Collection)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale Academic OneFile</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><jtitle>G3 : genes - genomes - genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Marino, Alba</au><au>Reboud, Eliette L</au><au>Chevalier, Emmanuelle</au><au>Tilak, Marie-Ka</au><au>Contreras-Garduño, Jorge</au><au>Nabholz, Benoit</au><au>Condamine, Fabien L</au><au>Emerson, J J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies</atitle><jtitle>G3 : genes - genomes - genetics</jtitle><addtitle>G3 (Bethesda)</addtitle><date>2023-12-06</date><risdate>2023</risdate><volume>13</volume><issue>12</issue><issn>2160-1836</issn><eissn>2160-1836</eissn><abstract>Abstract
Relict species, like coelacanth, gingko, tuatara, are the remnants of formerly more ecologically and taxonomically diverse lineages. It raises the questions of why they are currently species-poor, have restrained ecology, and are often vulnerable to extinction. Estimating heterozygosity level and demographic history can guide our understanding of the evolutionary history and conservation status of relict species. However, few studies have focused on relict invertebrates compared to vertebrates. We sequenced the genome of Baronia brevicornis (Lepidoptera: Papilionidae), which is an endangered species, the sister species of all swallowtail butterflies, and is the oldest lineage of all extant butterflies. From a dried specimen, we were able to generate both long-read and short-read data and assembled a genome of 406 Mb for Baronia. We found a fairly high level of heterozygosity (0.58%) compared to other swallowtail butterflies, which contrasts with its endangered and relict status. Taking into account the high ratio of recombination over mutation, demographic analyses indicated a sharp decline of the effective population size initiated in the last million years. Moreover, the Baronia genome was used to study genome size variation in Papilionidae. Genome sizes are mostly explained by transposable elements activities, suggesting that large genomes appear to be a derived feature in swallowtail butterflies as transposable elements activity is recent and involves different transposable elements classes among species. This first Baronia genome provides a resource for assisting conservation in a flagship and relict insect species as well as for understanding swallowtail genome evolution.
Sequencing the genome of Baronia brevicornis, an endangered species and the oldest butterfly lineage, revealed a high level of heterozygosity but a sharp population decline in the past million years. As the sister species of all swallowtail butterflies, this study also highlights genome size variation in Papilionidae and the role of transposable element activity in their evolution. The Baronia genome provides valuable resources for understanding swallowtail genome evolution and assisting in conservation efforts.</abstract><cop>US</cop><pub>Oxford University Press</pub><pmid>37847748</pmid><doi>10.1093/g3journal/jkad239</doi><orcidid>https://orcid.org/0009-0005-0984-2524</orcidid><orcidid>https://orcid.org/0000-0001-9079-4649</orcidid><orcidid>https://orcid.org/0000-0002-9231-0641</orcidid><orcidid>https://orcid.org/0000-0003-0447-1451</orcidid><orcidid>https://orcid.org/0000-0003-1673-9910</orcidid><oa>free_for_read</oa></addata></record> |
fulltext | fulltext |
identifier | ISSN: 2160-1836 |
ispartof | G3 : genes - genomes - genetics, 2023-12, Vol.13 (12) |
issn | 2160-1836 2160-1836 |
language | eng |
recordid | cdi_hal_primary_oai_HAL_hal_04669175v1 |
source | MEDLINE; DOAJ Directory of Open Access Journals; Access via Oxford University Press (Open Access Collection); EZB-FREE-00999 freely available EZB journals; PubMed Central |
subjects | Analysis Animals Biochemistry, Molecular Biology Biodiversity Butterflies Butterflies - genetics Demography DNA Transposable Elements - genetics Ecology Endangered species Evolution Genome Size Genomes Genomics Life Sciences Phylogeny Populations and Evolution Transposons Wildlife conservation |
title | Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-25T19%3A33%3A52IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_hal_p&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genomics%20of%20the%20relict%20species%20Baronia%20brevicornis%20sheds%20light%20on%20its%20demographic%20history%20and%20genome%20size%20evolution%20across%20swallowtail%20butterflies&rft.jtitle=G3%20:%20genes%20-%20genomes%20-%20genetics&rft.au=Marino,%20Alba&rft.date=2023-12-06&rft.volume=13&rft.issue=12&rft.issn=2160-1836&rft.eissn=2160-1836&rft_id=info:doi/10.1093/g3journal/jkad239&rft_dat=%3Cgale_hal_p%3EA779138791%3C/gale_hal_p%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2878712877&rft_id=info:pmid/37847748&rft_galeid=A779138791&rft_oup_id=10.1093/g3journal/jkad239&rfr_iscdi=true |