De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes
Supernumerary B chromosomes (Bs) are accessory elements to the regular chromosome set (As) and have been observed in a huge diversity of eukaryotic species. Although extensively investigated, the biological significance of Bs remains enigmatic. Here, we present de novo genome assemblies for the cich...
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| Veröffentlicht in: | Chromosoma 2019-06, Vol.128 (2), p.81-96 |
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| creator | Jehangir, Maryam Ahmad, Syed F. Cardoso, Adauto L. Ramos, Erica Valente, Guilherme T. Martins, Cesar |
| description | Supernumerary B chromosomes (Bs) are accessory elements to the regular chromosome set (As) and have been observed in a huge diversity of eukaryotic species. Although extensively investigated, the biological significance of Bs remains enigmatic. Here, we present de novo genome assemblies for the cichlid fish
Astatotilapia latifasciata
, a well-known model to study Bs. High coverage data with Illumina sequencing was obtained for males and females with 0B (B−), 1B, and 2B (B+) chromosomes to provide information regarding the diversity among these genomes
.
The draft assemblies comprised 771 Mb for the B− genome and 781 Mb for the B+ genome. Comparative analysis of the B+ and B− assemblies reveals syntenic discontinuity, duplicated blocks and several insertions, deletions, and inversions indicative of rearrangements in the B+ genome. Hundreds of transposable elements and 1546 protein coding sequences were annotated in the duplicated B+ regions. Our work contributes a list of thousands of genes harbored on the B chromosome, with functions in several biological processes, including the cell cycle. |
| doi_str_mv | 10.1007/s00412-019-00707-7 |
| format | Article |
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Astatotilapia latifasciata
, a well-known model to study Bs. High coverage data with Illumina sequencing was obtained for males and females with 0B (B−), 1B, and 2B (B+) chromosomes to provide information regarding the diversity among these genomes
.
The draft assemblies comprised 771 Mb for the B− genome and 781 Mb for the B+ genome. Comparative analysis of the B+ and B− assemblies reveals syntenic discontinuity, duplicated blocks and several insertions, deletions, and inversions indicative of rearrangements in the B+ genome. Hundreds of transposable elements and 1546 protein coding sequences were annotated in the duplicated B+ regions. Our work contributes a list of thousands of genes harbored on the B chromosome, with functions in several biological processes, including the cell cycle.</description><identifier>ISSN: 0009-5915</identifier><identifier>EISSN: 1432-0886</identifier><identifier>DOI: 10.1007/s00412-019-00707-7</identifier><identifier>PMID: 31115663</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Animal Genetics and Genomics ; Animals ; Astatotilapia ; B chromosome ; Biochemistry ; Biomedical and Life Sciences ; Cell Biology ; Cell cycle ; Chromosome Mapping ; Chromosomes ; Chromosomes - genetics ; Cichlids - genetics ; Comparative analysis ; Developmental Biology ; DNA Transposable Elements ; Eukaryotic Microbiology ; Evolution, Molecular ; Female ; Gene polymorphism ; Genome ; Genomes ; Genomics ; Human Genetics ; Life Sciences ; Male ; Original Article ; Polymorphism, Genetic ; Supernumerary ; Synteny</subject><ispartof>Chromosoma, 2019-06, Vol.128 (2), p.81-96</ispartof><rights>Springer-Verlag GmbH Germany, part of Springer Nature 2019</rights><rights>Chromosoma is a copyright of Springer, (2019). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c441t-abc31192d8e6b3f922ed52ed244ff31715305f8a41380afe717760ad5c75ebc63</citedby><cites>FETCH-LOGICAL-c441t-abc31192d8e6b3f922ed52ed244ff31715305f8a41380afe717760ad5c75ebc63</cites><orcidid>0000-0003-3534-974X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00412-019-00707-7$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00412-019-00707-7$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31115663$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Jehangir, Maryam</creatorcontrib><creatorcontrib>Ahmad, Syed F.</creatorcontrib><creatorcontrib>Cardoso, Adauto L.</creatorcontrib><creatorcontrib>Ramos, Erica</creatorcontrib><creatorcontrib>Valente, Guilherme T.</creatorcontrib><creatorcontrib>Martins, Cesar</creatorcontrib><title>De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes</title><title>Chromosoma</title><addtitle>Chromosoma</addtitle><addtitle>Chromosoma</addtitle><description>Supernumerary B chromosomes (Bs) are accessory elements to the regular chromosome set (As) and have been observed in a huge diversity of eukaryotic species. Although extensively investigated, the biological significance of Bs remains enigmatic. Here, we present de novo genome assemblies for the cichlid fish
Astatotilapia latifasciata
, a well-known model to study Bs. High coverage data with Illumina sequencing was obtained for males and females with 0B (B−), 1B, and 2B (B+) chromosomes to provide information regarding the diversity among these genomes
.
The draft assemblies comprised 771 Mb for the B− genome and 781 Mb for the B+ genome. Comparative analysis of the B+ and B− assemblies reveals syntenic discontinuity, duplicated blocks and several insertions, deletions, and inversions indicative of rearrangements in the B+ genome. Hundreds of transposable elements and 1546 protein coding sequences were annotated in the duplicated B+ regions. Our work contributes a list of thousands of genes harbored on the B chromosome, with functions in several biological processes, including the cell cycle.</description><subject>Animal Genetics and Genomics</subject><subject>Animals</subject><subject>Astatotilapia</subject><subject>B chromosome</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Cell Biology</subject><subject>Cell cycle</subject><subject>Chromosome Mapping</subject><subject>Chromosomes</subject><subject>Chromosomes - genetics</subject><subject>Cichlids - genetics</subject><subject>Comparative analysis</subject><subject>Developmental Biology</subject><subject>DNA Transposable Elements</subject><subject>Eukaryotic Microbiology</subject><subject>Evolution, Molecular</subject><subject>Female</subject><subject>Gene polymorphism</subject><subject>Genome</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Human Genetics</subject><subject>Life Sciences</subject><subject>Male</subject><subject>Original Article</subject><subject>Polymorphism, Genetic</subject><subject>Supernumerary</subject><subject>Synteny</subject><issn>0009-5915</issn><issn>1432-0886</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kc9u1DAQxi0EokvhBTggS1y4BPwniZNjaaFFqsSlPVuOM964cuLg8VbaN-Fx6-0WkDj0YFkz830_j_UR8p6zz5wx9QUZq7moGO-rUjJVqRdkw2tZWl3XviQbxlhfNT1vTsgbxLtDKVr2mpxIznnTtnJDfl8AXeJ9pFtY4gzUIMI8hD2NjuYJqPV2Cn6kzuNEzzCbHLMPZvWGBpO9M2i9yYYmuAcTkBo6-e0EiYbSCAfKI9hbusawn2NaJ48zNct4GAAWY-HASHOkX6mdUpwjlkXwLXnlChDePd2n5Pb7t5vzq-r65-WP87PrytY1z5UZbPlML8YO2kG6XggYm3JEXTsnueKNZI3rTM1lx4wDxZVqmRkbqxoYbCtPyacjd03x1w4w69mjhRDMAnGHWggpWMdVz4v043_Su7hLS9muqERXsuAtKypxVNkUERM4vSY_m7TXnOlDbvqYmy656cfctCqmD0_o3TDD-NfyJ6gikEcBltGyhfTv7WewDwOvpMA</recordid><startdate>20190601</startdate><enddate>20190601</enddate><creator>Jehangir, Maryam</creator><creator>Ahmad, Syed F.</creator><creator>Cardoso, Adauto L.</creator><creator>Ramos, Erica</creator><creator>Valente, Guilherme T.</creator><creator>Martins, Cesar</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><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>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-3534-974X</orcidid></search><sort><creationdate>20190601</creationdate><title>De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes</title><author>Jehangir, Maryam ; Ahmad, Syed F. ; Cardoso, Adauto L. ; Ramos, Erica ; Valente, Guilherme T. ; Martins, Cesar</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c441t-abc31192d8e6b3f922ed52ed244ff31715305f8a41380afe717760ad5c75ebc63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Animal Genetics and Genomics</topic><topic>Animals</topic><topic>Astatotilapia</topic><topic>B chromosome</topic><topic>Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>Cell Biology</topic><topic>Cell cycle</topic><topic>Chromosome Mapping</topic><topic>Chromosomes</topic><topic>Chromosomes - genetics</topic><topic>Cichlids - genetics</topic><topic>Comparative analysis</topic><topic>Developmental Biology</topic><topic>DNA Transposable Elements</topic><topic>Eukaryotic Microbiology</topic><topic>Evolution, Molecular</topic><topic>Female</topic><topic>Gene polymorphism</topic><topic>Genome</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Human Genetics</topic><topic>Life Sciences</topic><topic>Male</topic><topic>Original Article</topic><topic>Polymorphism, Genetic</topic><topic>Supernumerary</topic><topic>Synteny</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Jehangir, Maryam</creatorcontrib><creatorcontrib>Ahmad, Syed F.</creatorcontrib><creatorcontrib>Cardoso, Adauto L.</creatorcontrib><creatorcontrib>Ramos, Erica</creatorcontrib><creatorcontrib>Valente, Guilherme T.</creatorcontrib><creatorcontrib>Martins, Cesar</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Chromosoma</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Jehangir, Maryam</au><au>Ahmad, Syed F.</au><au>Cardoso, Adauto L.</au><au>Ramos, Erica</au><au>Valente, Guilherme T.</au><au>Martins, Cesar</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes</atitle><jtitle>Chromosoma</jtitle><stitle>Chromosoma</stitle><addtitle>Chromosoma</addtitle><date>2019-06-01</date><risdate>2019</risdate><volume>128</volume><issue>2</issue><spage>81</spage><epage>96</epage><pages>81-96</pages><issn>0009-5915</issn><eissn>1432-0886</eissn><abstract>Supernumerary B chromosomes (Bs) are accessory elements to the regular chromosome set (As) and have been observed in a huge diversity of eukaryotic species. Although extensively investigated, the biological significance of Bs remains enigmatic. Here, we present de novo genome assemblies for the cichlid fish
Astatotilapia latifasciata
, a well-known model to study Bs. High coverage data with Illumina sequencing was obtained for males and females with 0B (B−), 1B, and 2B (B+) chromosomes to provide information regarding the diversity among these genomes
.
The draft assemblies comprised 771 Mb for the B− genome and 781 Mb for the B+ genome. Comparative analysis of the B+ and B− assemblies reveals syntenic discontinuity, duplicated blocks and several insertions, deletions, and inversions indicative of rearrangements in the B+ genome. Hundreds of transposable elements and 1546 protein coding sequences were annotated in the duplicated B+ regions. Our work contributes a list of thousands of genes harbored on the B chromosome, with functions in several biological processes, including the cell cycle.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>31115663</pmid><doi>10.1007/s00412-019-00707-7</doi><tpages>16</tpages><orcidid>https://orcid.org/0000-0003-3534-974X</orcidid></addata></record> |
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| subjects | Animal Genetics and Genomics Animals Astatotilapia B chromosome Biochemistry Biomedical and Life Sciences Cell Biology Cell cycle Chromosome Mapping Chromosomes Chromosomes - genetics Cichlids - genetics Comparative analysis Developmental Biology DNA Transposable Elements Eukaryotic Microbiology Evolution, Molecular Female Gene polymorphism Genome Genomes Genomics Human Genetics Life Sciences Male Original Article Polymorphism, Genetic Supernumerary Synteny |
| title | De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes |
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