Comparative analysis of homologous sequences of saccharum officinarum and saccharum spontaneum reveals independent polyploidization events

Anupma Sharma, Jinjin Song, Qingfan Lin, Ratnesh Singh, Ninfa Ramos, Kai Wang, Jisen Zhang, Ray Ming, Qingyi Yu

Research output: Contribution to journalArticle

Abstract

Sugarcane (Saccharum spp. hybrids) is an economically important crop widely grown in tropical and subtropical regions for sugar and ethanol production. However, the large genome size, high ploidy level, interspecific hybridization and aneuploidy make sugarcane one of the most complex genomes and have long hampered genome research in sugarcane. Modern sugarcane cultivars are derived from interspecific hybridization between S. officinarum and S. spontaneum with 80–90% of the genome from S. officinarum and 10–20% of the genome from S. spontaneum. We constructed bacterial artificial chromosome (BAC) libraries of S. officinarum variety LA Purple (2n = 8x = 80) and S. spontaneum haploid clone AP85-441 (2n = 4x = 32), and selected and sequenced 97 BAC clones from the two Saccharum BAC libraries. A total of 5,847,280 bp sequence from S. officinarum and 5,011,570 bp from S. spontaneum were assembled and 749 gene models were annotated in these BACs. A relatively higher gene density and lower repeat content were observed in S. spontaneum BACs than in S. officinarum BACs. Comparative analysis of syntenic regions revealed a high degree of collinearity in genic regions between Saccharum and Sorghum bicolor and between S. officinarum and S. spontaneum. In the syntenic regions, S. spontaneum showed expansion relative to S. officinarum, and both S. officinarum and S. spontaneum showed expansion relative to sorghum. Among the 75 full-length LTR retrotransposons identified in the Saccharum BACs, none of them are older than 2.6 mys and no full-length LTR elements are shared between S. officinarum and S. spontaneum. In addition, divergence time estimated using a LTR junction marker and a syntenic gene shared by 3 S. officinarum and 1 S. spontaneum BACs revealed that the S. spontaneum intergenic region was distant to those from the 3 homologous regions in S. officinarum. Our results suggested that S. officinarum and S. spontaneum experienced at least two rounds of independent polyploidization in each lineage after their divergence from a common ancestor.

Original languageEnglish (US)
Article number1414
JournalFrontiers in Plant Science
Volume9
DOIs
StatePublished - Sep 25 2018

Fingerprint

Saccharum spontaneum
Saccharum officinarum
sequence homology
Saccharum
bacterial artificial chromosomes
sugarcane
genome
interspecific hybridization
clones
genes
retrotransposons
aneuploidy
ethanol production
intergenic DNA
subtropics
Sorghum bicolor
ploidy
Sorghum (Poaceae)
haploidy

Keywords

  • Genetic divergence
  • Polyploidization
  • Retrotransposon
  • Saccharum
  • Sugarcane

ASJC Scopus subject areas

  • Plant Science

Cite this

Comparative analysis of homologous sequences of saccharum officinarum and saccharum spontaneum reveals independent polyploidization events. / Sharma, Anupma; Song, Jinjin; Lin, Qingfan; Singh, Ratnesh; Ramos, Ninfa; Wang, Kai; Zhang, Jisen; Ming, Ray; Yu, Qingyi.

In: Frontiers in Plant Science, Vol. 9, 1414, 25.09.2018.

Research output: Contribution to journalArticle

Sharma, Anupma ; Song, Jinjin ; Lin, Qingfan ; Singh, Ratnesh ; Ramos, Ninfa ; Wang, Kai ; Zhang, Jisen ; Ming, Ray ; Yu, Qingyi. / Comparative analysis of homologous sequences of saccharum officinarum and saccharum spontaneum reveals independent polyploidization events. In: Frontiers in Plant Science. 2018 ; Vol. 9.
@article{6ce88b59f5c2481ab1c73e81db95c1b8,
title = "Comparative analysis of homologous sequences of saccharum officinarum and saccharum spontaneum reveals independent polyploidization events",
abstract = "Sugarcane (Saccharum spp. hybrids) is an economically important crop widely grown in tropical and subtropical regions for sugar and ethanol production. However, the large genome size, high ploidy level, interspecific hybridization and aneuploidy make sugarcane one of the most complex genomes and have long hampered genome research in sugarcane. Modern sugarcane cultivars are derived from interspecific hybridization between S. officinarum and S. spontaneum with 80–90{\%} of the genome from S. officinarum and 10–20{\%} of the genome from S. spontaneum. We constructed bacterial artificial chromosome (BAC) libraries of S. officinarum variety LA Purple (2n = 8x = 80) and S. spontaneum haploid clone AP85-441 (2n = 4x = 32), and selected and sequenced 97 BAC clones from the two Saccharum BAC libraries. A total of 5,847,280 bp sequence from S. officinarum and 5,011,570 bp from S. spontaneum were assembled and 749 gene models were annotated in these BACs. A relatively higher gene density and lower repeat content were observed in S. spontaneum BACs than in S. officinarum BACs. Comparative analysis of syntenic regions revealed a high degree of collinearity in genic regions between Saccharum and Sorghum bicolor and between S. officinarum and S. spontaneum. In the syntenic regions, S. spontaneum showed expansion relative to S. officinarum, and both S. officinarum and S. spontaneum showed expansion relative to sorghum. Among the 75 full-length LTR retrotransposons identified in the Saccharum BACs, none of them are older than 2.6 mys and no full-length LTR elements are shared between S. officinarum and S. spontaneum. In addition, divergence time estimated using a LTR junction marker and a syntenic gene shared by 3 S. officinarum and 1 S. spontaneum BACs revealed that the S. spontaneum intergenic region was distant to those from the 3 homologous regions in S. officinarum. Our results suggested that S. officinarum and S. spontaneum experienced at least two rounds of independent polyploidization in each lineage after their divergence from a common ancestor.",
keywords = "Genetic divergence, Polyploidization, Retrotransposon, Saccharum, Sugarcane",
author = "Anupma Sharma and Jinjin Song and Qingfan Lin and Ratnesh Singh and Ninfa Ramos and Kai Wang and Jisen Zhang and Ray Ming and Qingyi Yu",
year = "2018",
month = "9",
day = "25",
doi = "10.3389/fpls.2018.01414",
language = "English (US)",
volume = "9",
journal = "Frontiers in Plant Science",
issn = "1664-462X",
publisher = "Frontiers Media S. A.",

}

TY - JOUR

T1 - Comparative analysis of homologous sequences of saccharum officinarum and saccharum spontaneum reveals independent polyploidization events

AU - Sharma, Anupma

AU - Song, Jinjin

AU - Lin, Qingfan

AU - Singh, Ratnesh

AU - Ramos, Ninfa

AU - Wang, Kai

AU - Zhang, Jisen

AU - Ming, Ray

AU - Yu, Qingyi

PY - 2018/9/25

Y1 - 2018/9/25

N2 - Sugarcane (Saccharum spp. hybrids) is an economically important crop widely grown in tropical and subtropical regions for sugar and ethanol production. However, the large genome size, high ploidy level, interspecific hybridization and aneuploidy make sugarcane one of the most complex genomes and have long hampered genome research in sugarcane. Modern sugarcane cultivars are derived from interspecific hybridization between S. officinarum and S. spontaneum with 80–90% of the genome from S. officinarum and 10–20% of the genome from S. spontaneum. We constructed bacterial artificial chromosome (BAC) libraries of S. officinarum variety LA Purple (2n = 8x = 80) and S. spontaneum haploid clone AP85-441 (2n = 4x = 32), and selected and sequenced 97 BAC clones from the two Saccharum BAC libraries. A total of 5,847,280 bp sequence from S. officinarum and 5,011,570 bp from S. spontaneum were assembled and 749 gene models were annotated in these BACs. A relatively higher gene density and lower repeat content were observed in S. spontaneum BACs than in S. officinarum BACs. Comparative analysis of syntenic regions revealed a high degree of collinearity in genic regions between Saccharum and Sorghum bicolor and between S. officinarum and S. spontaneum. In the syntenic regions, S. spontaneum showed expansion relative to S. officinarum, and both S. officinarum and S. spontaneum showed expansion relative to sorghum. Among the 75 full-length LTR retrotransposons identified in the Saccharum BACs, none of them are older than 2.6 mys and no full-length LTR elements are shared between S. officinarum and S. spontaneum. In addition, divergence time estimated using a LTR junction marker and a syntenic gene shared by 3 S. officinarum and 1 S. spontaneum BACs revealed that the S. spontaneum intergenic region was distant to those from the 3 homologous regions in S. officinarum. Our results suggested that S. officinarum and S. spontaneum experienced at least two rounds of independent polyploidization in each lineage after their divergence from a common ancestor.

AB - Sugarcane (Saccharum spp. hybrids) is an economically important crop widely grown in tropical and subtropical regions for sugar and ethanol production. However, the large genome size, high ploidy level, interspecific hybridization and aneuploidy make sugarcane one of the most complex genomes and have long hampered genome research in sugarcane. Modern sugarcane cultivars are derived from interspecific hybridization between S. officinarum and S. spontaneum with 80–90% of the genome from S. officinarum and 10–20% of the genome from S. spontaneum. We constructed bacterial artificial chromosome (BAC) libraries of S. officinarum variety LA Purple (2n = 8x = 80) and S. spontaneum haploid clone AP85-441 (2n = 4x = 32), and selected and sequenced 97 BAC clones from the two Saccharum BAC libraries. A total of 5,847,280 bp sequence from S. officinarum and 5,011,570 bp from S. spontaneum were assembled and 749 gene models were annotated in these BACs. A relatively higher gene density and lower repeat content were observed in S. spontaneum BACs than in S. officinarum BACs. Comparative analysis of syntenic regions revealed a high degree of collinearity in genic regions between Saccharum and Sorghum bicolor and between S. officinarum and S. spontaneum. In the syntenic regions, S. spontaneum showed expansion relative to S. officinarum, and both S. officinarum and S. spontaneum showed expansion relative to sorghum. Among the 75 full-length LTR retrotransposons identified in the Saccharum BACs, none of them are older than 2.6 mys and no full-length LTR elements are shared between S. officinarum and S. spontaneum. In addition, divergence time estimated using a LTR junction marker and a syntenic gene shared by 3 S. officinarum and 1 S. spontaneum BACs revealed that the S. spontaneum intergenic region was distant to those from the 3 homologous regions in S. officinarum. Our results suggested that S. officinarum and S. spontaneum experienced at least two rounds of independent polyploidization in each lineage after their divergence from a common ancestor.

KW - Genetic divergence

KW - Polyploidization

KW - Retrotransposon

KW - Saccharum

KW - Sugarcane

UR - http://www.scopus.com/inward/record.url?scp=85054504965&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85054504965&partnerID=8YFLogxK

U2 - 10.3389/fpls.2018.01414

DO - 10.3389/fpls.2018.01414

M3 - Article

AN - SCOPUS:85054504965

VL - 9

JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

M1 - 1414

ER -