A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome

Persistent Link:
http://hdl.handle.net/10150/610097
Title:
A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome
Author:
Figueira, Thais Rezende; Okura, Vagner; Rodrigues, da Silva; Jose, da Silva; Kudrna, Dave; Ammiraju, Jetty; Talag, Jayson; Wing, Rod; Arruda, Paulo
Affiliation:
Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil; EMBRAPA Informática na Agricultura, São Paulo, Brazil; Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA; Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
Issue Date:
2012
Publisher:
BioMed Central
Citation:
Figueira et al. BMC Research Notes 2012, 5:185 http://www.biomedcentral.com/1756-0500/5/185
Journal:
BMC Research Notes
Rights:
© 2012 Figueira et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:Sugarcane breeding has significantly progressed in the last 30 years, but achieving additional yield gains has been difficult because of the constraints imposed by the complex ploidy of this crop. Sugarcane cultivars are interspecific hybrids between Saccharum officinarum and Saccharum spontaneum. S. officinarum is an octoploid with 2n=80 chromosomes while S. spontaneum has 2n=40 to 128 chromosomes and ploidy varying from 5 to 16. The hybrid genome is composed of 70-80%S. officinaram and 5-20%S. spontaneum chromosomes and a small proportion of recombinants. Sequencing the genome of this complex crop may help identify useful genes, either per se or through comparative genomics using closely related grasses. The construction and sequencing of a bacterial artificial chromosome (BAC) library of an elite commercial variety of sugarcane could help assembly the sugarcane genome.RESULTS:A BAC library designated SS_SBa was constructed with DNA isolated from the commercial sugarcane variety SP80-3280. The library contains 36,864 clones with an average insert size of 125 Kb, 88% of which has inserts larger than 90 Kb. Based on the estimated genome size of 760-930 Mb, the library exhibits 5-6 times coverage the monoploid sugarcane genome. Bidirectional BAC end sequencing (BESs) from a random sample of 192 BAC clones sampled genes and repetitive elements of the sugarcane genome. Forty-five per cent of the total BES nucleotides represents repetitive elements, 83% of which belonging to LTR retrotransposons. Alignment of BESs corresponding to 42 BACs to the genome sequence of the 10 sorghum chromosomes revealed regions of microsynteny, with expansions and contractions of sorghum genome regions relative to the sugarcane BAC clones. In general, the sampled sorghum genome regions presented an average 29% expansion in relation to the sugarcane syntenic BACs.CONCLUSION:The SS_SBa BAC library represents a new resource for sugarcane genome sequencing. An analysis of insert size, genome coverage and orthologous alignment with the sorghum genome revealed that the library presents whole genome coverage. The comparison of syntenic regions of the sorghum genome to 42 SS_SBa BES pairs revealed that the sorghum genome is expanded in relation to the sugarcane genome.
EISSN:
1756-0500
DOI:
10.1186/1756-0500-5-185
Keywords:
Sugarcane genomics; BAC library; Genome organization; Microsynteny; Sorghum
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1756-0500/5/185

Full metadata record

DC FieldValue Language
dc.contributor.authorFigueira, Thais Rezendeen
dc.contributor.authorOkura, Vagneren
dc.contributor.authorRodrigues, da Silvaen
dc.contributor.authorJose, da Silvaen
dc.contributor.authorKudrna, Daveen
dc.contributor.authorAmmiraju, Jettyen
dc.contributor.authorTalag, Jaysonen
dc.contributor.authorWing, Roden
dc.contributor.authorArruda, Pauloen
dc.date.accessioned2016-05-20T08:58:29Z-
dc.date.available2016-05-20T08:58:29Z-
dc.date.issued2012en
dc.identifier.citationFigueira et al. BMC Research Notes 2012, 5:185 http://www.biomedcentral.com/1756-0500/5/185en
dc.identifier.doi10.1186/1756-0500-5-185en
dc.identifier.urihttp://hdl.handle.net/10150/610097-
dc.description.abstractBACKGROUND:Sugarcane breeding has significantly progressed in the last 30 years, but achieving additional yield gains has been difficult because of the constraints imposed by the complex ploidy of this crop. Sugarcane cultivars are interspecific hybrids between Saccharum officinarum and Saccharum spontaneum. S. officinarum is an octoploid with 2n=80 chromosomes while S. spontaneum has 2n=40 to 128 chromosomes and ploidy varying from 5 to 16. The hybrid genome is composed of 70-80%S. officinaram and 5-20%S. spontaneum chromosomes and a small proportion of recombinants. Sequencing the genome of this complex crop may help identify useful genes, either per se or through comparative genomics using closely related grasses. The construction and sequencing of a bacterial artificial chromosome (BAC) library of an elite commercial variety of sugarcane could help assembly the sugarcane genome.RESULTS:A BAC library designated SS_SBa was constructed with DNA isolated from the commercial sugarcane variety SP80-3280. The library contains 36,864 clones with an average insert size of 125 Kb, 88% of which has inserts larger than 90 Kb. Based on the estimated genome size of 760-930 Mb, the library exhibits 5-6 times coverage the monoploid sugarcane genome. Bidirectional BAC end sequencing (BESs) from a random sample of 192 BAC clones sampled genes and repetitive elements of the sugarcane genome. Forty-five per cent of the total BES nucleotides represents repetitive elements, 83% of which belonging to LTR retrotransposons. Alignment of BESs corresponding to 42 BACs to the genome sequence of the 10 sorghum chromosomes revealed regions of microsynteny, with expansions and contractions of sorghum genome regions relative to the sugarcane BAC clones. In general, the sampled sorghum genome regions presented an average 29% expansion in relation to the sugarcane syntenic BACs.CONCLUSION:The SS_SBa BAC library represents a new resource for sugarcane genome sequencing. An analysis of insert size, genome coverage and orthologous alignment with the sorghum genome revealed that the library presents whole genome coverage. The comparison of syntenic regions of the sorghum genome to 42 SS_SBa BES pairs revealed that the sorghum genome is expanded in relation to the sugarcane genome.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1756-0500/5/185en
dc.rights© 2012 Figueira et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.subjectSugarcane genomicsen
dc.subjectBAC libraryen
dc.subjectGenome organizationen
dc.subjectMicrosyntenyen
dc.subjectSorghumen
dc.titleA BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genomeen
dc.typeArticleen
dc.identifier.eissn1756-0500en
dc.contributor.departmentCentro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazilen
dc.contributor.departmentEMBRAPA Informática na Agricultura, São Paulo, Brazilen
dc.contributor.departmentArizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USAen
dc.contributor.departmentDepartamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazilen
dc.identifier.journalBMC Research Notesen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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