Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae
Abstract Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity a...
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| Veröffentlicht in: | G3 : genes - genomes - genetics 2024-09, Vol.14 (9) |
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| creator | Low, Eng-Ti Leslie Chan, Kuang-Lim Zaki, Noorhariza Mohd Taranenko, Elizaveta Ordway, Jared M Wischmeyer, Corey Buntjer, Jaap Halim, Mohd Amin Ab Sanusi, Nik Shazana Nik Mohd Nagappan, Jayanthi Rosli, Rozana Bondar, Eugeniya Amiruddin, Nadzirah Sarpan, Norashikin Ting, Ngoot-Chin Chan, Pek-Lan Ong-Abdullah, Meilina Marjuni, Marhalil Mustaffa, Suzana Abdullah, Norziha Azizi, Norazah Bacher, Blaire Lakey, Nathan Tatarinova, Tatiana V Manaf, Mohamad Arif Abd Sambanthamurti, Ravigadevi Singh, Rajinder |
| description | Abstract
Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes. |
| doi_str_mv | 10.1093/g3journal/jkae135 |
| format | Article |
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Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.</description><identifier>ISSN: 2160-1836</identifier><identifier>EISSN: 2160-1836</identifier><identifier>DOI: 10.1093/g3journal/jkae135</identifier><identifier>PMID: 38918881</identifier><language>eng</language><publisher>US: Oxford University Press</publisher><subject>Arecaceae - genetics ; Chromosome Mapping ; Chromosomes, Plant - genetics ; Genome Report ; Genome, Plant ; Genomics - methods ; Molecular Sequence Annotation ; Repetitive Sequences, Nucleic Acid</subject><ispartof>G3 : genes - genomes - genetics, 2024-09, Vol.14 (9)</ispartof><rights>The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. 2024</rights><rights>The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c319t-7d8dba313f8917a8d48563cdd1a68cdf67dfa32e9da520f656c06c78818972793</cites><orcidid>0000-0003-1787-1112 ; 0000-0002-3349-4225 ; 0000-0003-3414-8401 ; 0000-0002-8419-0432</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373658/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373658/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38918881$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Low, Eng-Ti Leslie</creatorcontrib><creatorcontrib>Chan, Kuang-Lim</creatorcontrib><creatorcontrib>Zaki, Noorhariza Mohd</creatorcontrib><creatorcontrib>Taranenko, Elizaveta</creatorcontrib><creatorcontrib>Ordway, Jared M</creatorcontrib><creatorcontrib>Wischmeyer, Corey</creatorcontrib><creatorcontrib>Buntjer, Jaap</creatorcontrib><creatorcontrib>Halim, Mohd Amin Ab</creatorcontrib><creatorcontrib>Sanusi, Nik Shazana Nik Mohd</creatorcontrib><creatorcontrib>Nagappan, Jayanthi</creatorcontrib><creatorcontrib>Rosli, Rozana</creatorcontrib><creatorcontrib>Bondar, Eugeniya</creatorcontrib><creatorcontrib>Amiruddin, Nadzirah</creatorcontrib><creatorcontrib>Sarpan, Norashikin</creatorcontrib><creatorcontrib>Ting, Ngoot-Chin</creatorcontrib><creatorcontrib>Chan, Pek-Lan</creatorcontrib><creatorcontrib>Ong-Abdullah, Meilina</creatorcontrib><creatorcontrib>Marjuni, Marhalil</creatorcontrib><creatorcontrib>Mustaffa, Suzana</creatorcontrib><creatorcontrib>Abdullah, Norziha</creatorcontrib><creatorcontrib>Azizi, Norazah</creatorcontrib><creatorcontrib>Bacher, Blaire</creatorcontrib><creatorcontrib>Lakey, Nathan</creatorcontrib><creatorcontrib>Tatarinova, Tatiana V</creatorcontrib><creatorcontrib>Manaf, Mohamad Arif Abd</creatorcontrib><creatorcontrib>Sambanthamurti, Ravigadevi</creatorcontrib><creatorcontrib>Singh, Rajinder</creatorcontrib><title>Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae</title><title>G3 : genes - genomes - genetics</title><addtitle>G3 (Bethesda)</addtitle><description>Abstract
Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.</description><subject>Arecaceae - genetics</subject><subject>Chromosome Mapping</subject><subject>Chromosomes, Plant - genetics</subject><subject>Genome Report</subject><subject>Genome, Plant</subject><subject>Genomics - methods</subject><subject>Molecular Sequence Annotation</subject><subject>Repetitive Sequences, Nucleic Acid</subject><issn>2160-1836</issn><issn>2160-1836</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqNUcFu2zAMFYYWa9H2A3YZdNyhbi0rluVehiJIuwEFdtnOAiPRiTLJckW7QP9-3pIF3W28kADfe3zEY-yDKG9E2crbjdylKfcQbnc_AYWs37HzSqiyEFqqkzfzGbsi2pVz1bVSC_WenUndCq21OGe03OYUE6WIBVkIyFcB0BPfTL5H7GkeoXd8dcNTQN9hBg5EGNfBI91xm-IAGUb_gnyDfYreEk8dTz7wAUL8Q07jFjO_z2jBIuAlO-0gEF4d-gX78bD6vvxSPH17_Lq8fyqsFO1YNE67NUghu9ltA9otdK2kdU6A0tZ1qnEdyApbB3VVdqpWtlS2md_SbVM1rbxgn_e6w7SO6Cz2Y4Zghuwj5FeTwJt_N73fmk16MULIRqpazwqfDgo5PU9Io4meLIYAPaaJjCybqmrlol7MULGH2pyIMnbHO6I0vwMzx8DMIbCZ8_GtwSPjbzwz4HoPSNPwH3q_ABu5pnQ</recordid><startdate>20240904</startdate><enddate>20240904</enddate><creator>Low, Eng-Ti Leslie</creator><creator>Chan, Kuang-Lim</creator><creator>Zaki, Noorhariza Mohd</creator><creator>Taranenko, Elizaveta</creator><creator>Ordway, Jared M</creator><creator>Wischmeyer, Corey</creator><creator>Buntjer, Jaap</creator><creator>Halim, Mohd Amin Ab</creator><creator>Sanusi, Nik Shazana Nik Mohd</creator><creator>Nagappan, Jayanthi</creator><creator>Rosli, Rozana</creator><creator>Bondar, Eugeniya</creator><creator>Amiruddin, Nadzirah</creator><creator>Sarpan, Norashikin</creator><creator>Ting, Ngoot-Chin</creator><creator>Chan, Pek-Lan</creator><creator>Ong-Abdullah, Meilina</creator><creator>Marjuni, Marhalil</creator><creator>Mustaffa, Suzana</creator><creator>Abdullah, Norziha</creator><creator>Azizi, Norazah</creator><creator>Bacher, Blaire</creator><creator>Lakey, Nathan</creator><creator>Tatarinova, Tatiana V</creator><creator>Manaf, Mohamad Arif Abd</creator><creator>Sambanthamurti, Ravigadevi</creator><creator>Singh, Rajinder</creator><general>Oxford University Press</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>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-1787-1112</orcidid><orcidid>https://orcid.org/0000-0002-3349-4225</orcidid><orcidid>https://orcid.org/0000-0003-3414-8401</orcidid><orcidid>https://orcid.org/0000-0002-8419-0432</orcidid></search><sort><creationdate>20240904</creationdate><title>Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae</title><author>Low, Eng-Ti Leslie ; Chan, Kuang-Lim ; Zaki, Noorhariza Mohd ; Taranenko, Elizaveta ; Ordway, Jared M ; Wischmeyer, Corey ; Buntjer, Jaap ; Halim, Mohd Amin Ab ; Sanusi, Nik Shazana Nik Mohd ; Nagappan, Jayanthi ; Rosli, Rozana ; Bondar, Eugeniya ; Amiruddin, Nadzirah ; Sarpan, Norashikin ; Ting, Ngoot-Chin ; Chan, Pek-Lan ; Ong-Abdullah, Meilina ; Marjuni, Marhalil ; Mustaffa, Suzana ; Abdullah, Norziha ; Azizi, Norazah ; Bacher, Blaire ; Lakey, Nathan ; Tatarinova, Tatiana V ; Manaf, Mohamad Arif Abd ; Sambanthamurti, Ravigadevi ; Singh, Rajinder</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c319t-7d8dba313f8917a8d48563cdd1a68cdf67dfa32e9da520f656c06c78818972793</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Arecaceae - genetics</topic><topic>Chromosome Mapping</topic><topic>Chromosomes, Plant - genetics</topic><topic>Genome Report</topic><topic>Genome, Plant</topic><topic>Genomics - methods</topic><topic>Molecular Sequence Annotation</topic><topic>Repetitive Sequences, Nucleic Acid</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Low, Eng-Ti Leslie</creatorcontrib><creatorcontrib>Chan, Kuang-Lim</creatorcontrib><creatorcontrib>Zaki, Noorhariza Mohd</creatorcontrib><creatorcontrib>Taranenko, Elizaveta</creatorcontrib><creatorcontrib>Ordway, Jared M</creatorcontrib><creatorcontrib>Wischmeyer, Corey</creatorcontrib><creatorcontrib>Buntjer, Jaap</creatorcontrib><creatorcontrib>Halim, Mohd Amin Ab</creatorcontrib><creatorcontrib>Sanusi, Nik Shazana Nik Mohd</creatorcontrib><creatorcontrib>Nagappan, Jayanthi</creatorcontrib><creatorcontrib>Rosli, Rozana</creatorcontrib><creatorcontrib>Bondar, Eugeniya</creatorcontrib><creatorcontrib>Amiruddin, Nadzirah</creatorcontrib><creatorcontrib>Sarpan, Norashikin</creatorcontrib><creatorcontrib>Ting, Ngoot-Chin</creatorcontrib><creatorcontrib>Chan, Pek-Lan</creatorcontrib><creatorcontrib>Ong-Abdullah, Meilina</creatorcontrib><creatorcontrib>Marjuni, Marhalil</creatorcontrib><creatorcontrib>Mustaffa, Suzana</creatorcontrib><creatorcontrib>Abdullah, Norziha</creatorcontrib><creatorcontrib>Azizi, Norazah</creatorcontrib><creatorcontrib>Bacher, Blaire</creatorcontrib><creatorcontrib>Lakey, Nathan</creatorcontrib><creatorcontrib>Tatarinova, Tatiana V</creatorcontrib><creatorcontrib>Manaf, Mohamad Arif Abd</creatorcontrib><creatorcontrib>Sambanthamurti, Ravigadevi</creatorcontrib><creatorcontrib>Singh, Rajinder</creatorcontrib><collection>Oxford Journals 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>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>G3 : genes - genomes - genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Low, Eng-Ti Leslie</au><au>Chan, Kuang-Lim</au><au>Zaki, Noorhariza Mohd</au><au>Taranenko, Elizaveta</au><au>Ordway, Jared M</au><au>Wischmeyer, Corey</au><au>Buntjer, Jaap</au><au>Halim, Mohd Amin Ab</au><au>Sanusi, Nik Shazana Nik Mohd</au><au>Nagappan, Jayanthi</au><au>Rosli, Rozana</au><au>Bondar, Eugeniya</au><au>Amiruddin, Nadzirah</au><au>Sarpan, Norashikin</au><au>Ting, Ngoot-Chin</au><au>Chan, Pek-Lan</au><au>Ong-Abdullah, Meilina</au><au>Marjuni, Marhalil</au><au>Mustaffa, Suzana</au><au>Abdullah, Norziha</au><au>Azizi, Norazah</au><au>Bacher, Blaire</au><au>Lakey, Nathan</au><au>Tatarinova, Tatiana V</au><au>Manaf, Mohamad Arif Abd</au><au>Sambanthamurti, Ravigadevi</au><au>Singh, Rajinder</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae</atitle><jtitle>G3 : genes - genomes - genetics</jtitle><addtitle>G3 (Bethesda)</addtitle><date>2024-09-04</date><risdate>2024</risdate><volume>14</volume><issue>9</issue><issn>2160-1836</issn><eissn>2160-1836</eissn><abstract>Abstract
Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.</abstract><cop>US</cop><pub>Oxford University Press</pub><pmid>38918881</pmid><doi>10.1093/g3journal/jkae135</doi><orcidid>https://orcid.org/0000-0003-1787-1112</orcidid><orcidid>https://orcid.org/0000-0002-3349-4225</orcidid><orcidid>https://orcid.org/0000-0003-3414-8401</orcidid><orcidid>https://orcid.org/0000-0002-8419-0432</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Oxford Journals Open Access Collection; MEDLINE; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Arecaceae - genetics Chromosome Mapping Chromosomes, Plant - genetics Genome Report Genome, Plant Genomics - methods Molecular Sequence Annotation Repetitive Sequences, Nucleic Acid |
| title | Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae |
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