A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome
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 sp...
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ndltd-arizona.edu-oai-arizona.openrepository.com-10150-6100972016-05-22T03:01:44Z A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome Figueira, Thais Rezende Okura, Vagner Rodrigues, da Silva Jose, da Silva Kudrna, Dave Ammiraju, Jetty Talag, Jayson Wing, Rod Arruda, Paulo 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 Sugarcane genomics BAC library Genome organization Microsynteny Sorghum 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. 2012 Article Figueira et al. BMC Research Notes 2012, 5:185 http://www.biomedcentral.com/1756-0500/5/185 10.1186/1756-0500-5-185 http://hdl.handle.net/10150/610097 http://arizona.openrepository.com/arizona/handle/10150/610097 1756-0500 BMC Research Notes en http://www.biomedcentral.com/1756-0500/5/185 © 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) BioMed Central |
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language |
en |
sources |
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topic |
Sugarcane genomics BAC library Genome organization Microsynteny Sorghum |
spellingShingle |
Sugarcane genomics BAC library Genome organization Microsynteny Sorghum Figueira, Thais Rezende Okura, Vagner Rodrigues, da Silva Jose, da Silva Kudrna, Dave Ammiraju, Jetty Talag, Jayson Wing, Rod Arruda, Paulo A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome |
description |
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. |
author2 |
Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil |
author_facet |
Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil Figueira, Thais Rezende Okura, Vagner Rodrigues, da Silva Jose, da Silva Kudrna, Dave Ammiraju, Jetty Talag, Jayson Wing, Rod Arruda, Paulo |
author |
Figueira, Thais Rezende Okura, Vagner Rodrigues, da Silva Jose, da Silva Kudrna, Dave Ammiraju, Jetty Talag, Jayson Wing, Rod Arruda, Paulo |
author_sort |
Figueira, Thais Rezende |
title |
A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome |
title_short |
A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome |
title_full |
A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome |
title_fullStr |
A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome |
title_full_unstemmed |
A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome |
title_sort |
bac library of the sp80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome |
publisher |
BioMed Central |
publishDate |
2012 |
url |
Figueira et al. BMC Research Notes 2012, 5:185 http://www.biomedcentral.com/1756-0500/5/185 http://hdl.handle.net/10150/610097 http://arizona.openrepository.com/arizona/handle/10150/610097 |
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