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

Thais Rezende E Silva Figueira, Vagner Okura, Felipe Rodrigues Da Silva, Marcio Jose Da Silva, David A Kudrna, Jetty S S Ammiraju, Jayson Talag, Rod A Wing, Paulo Arruda

Research output: Contribution to journalArticle

18 Citations (Scopus)

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.

Original languageEnglish (US)
Article number185
JournalBMC Research Notes
Volume5
DOIs
StatePublished - 2012

Fingerprint

Bacterial Artificial Chromosomes
Saccharum
Sorghum
Chromosomes
Genes
Genome
Genome Size
Clone Cells
Ploidies
Libraries
Crops
Chromosomes, Human, Pair 10
Retroelements
Genomic Library

Keywords

  • BAC library
  • Genome organization
  • Microsynteny
  • Sorghum
  • Sugarcane genomics

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Figueira, T. R. E. S., Okura, V., Rodrigues Da Silva, F., Jose Da Silva, M., Kudrna, D. A., Ammiraju, J. S. S., ... Arruda, P. (2012). A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome. BMC Research Notes, 5, [185]. https://doi.org/10.1186/1756-0500-5-185

A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome. / Figueira, Thais Rezende E Silva; Okura, Vagner; Rodrigues Da Silva, Felipe; Jose Da Silva, Marcio; Kudrna, David A; Ammiraju, Jetty S S; Talag, Jayson; Wing, Rod A; Arruda, Paulo.

In: BMC Research Notes, Vol. 5, 185, 2012.

Research output: Contribution to journalArticle

Figueira, Thais Rezende E Silva ; Okura, Vagner ; Rodrigues Da Silva, Felipe ; Jose Da Silva, Marcio ; Kudrna, David A ; Ammiraju, Jetty S S ; Talag, Jayson ; Wing, Rod A ; Arruda, Paulo. / A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome. In: BMC Research Notes. 2012 ; Vol. 5.
@article{512bbbc57d70468296797e095bef6842,
title = "A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome",
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.",
keywords = "BAC library, Genome organization, Microsynteny, Sorghum, Sugarcane genomics",
author = "Figueira, {Thais Rezende E Silva} and Vagner Okura and {Rodrigues Da Silva}, Felipe and {Jose Da Silva}, Marcio and Kudrna, {David A} and Ammiraju, {Jetty S S} and Jayson Talag and Wing, {Rod A} and Paulo Arruda",
year = "2012",
doi = "10.1186/1756-0500-5-185",
language = "English (US)",
volume = "5",
journal = "BMC Research Notes",
issn = "1756-0500",
publisher = "BioMed Central",

}

TY - JOUR

T1 - A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome

AU - Figueira, Thais Rezende E Silva

AU - Okura, Vagner

AU - Rodrigues Da Silva, Felipe

AU - Jose Da Silva, Marcio

AU - Kudrna, David A

AU - Ammiraju, Jetty S S

AU - Talag, Jayson

AU - Wing, Rod A

AU - Arruda, Paulo

PY - 2012

Y1 - 2012

N2 - 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.

AB - 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.

KW - BAC library

KW - Genome organization

KW - Microsynteny

KW - Sorghum

KW - Sugarcane genomics

UR - http://www.scopus.com/inward/record.url?scp=84865238999&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84865238999&partnerID=8YFLogxK

U2 - 10.1186/1756-0500-5-185

DO - 10.1186/1756-0500-5-185

M3 - Article

C2 - 22524198

AN - SCOPUS:84865238999

VL - 5

JO - BMC Research Notes

JF - BMC Research Notes

SN - 1756-0500

M1 - 185

ER -