Recent polyploidization events in three Saccharum founding species

Zhang, Jisen; Zhang, Qing; Li, Leiting; Tang, Haibao; Zhang, Qiong; Chen, Yang; Arrow, Jie; Zhang, Xingtan; Wang, Aiqin; Miao, Chenyong; Ming, Ray

doi:10.1111/pbi.12962

Title: Recent polyploidization events in three Saccharum founding species

Authors:

^[3]; Tang, Haibao ^[4]; Zhang, Qiong ^[5]; Chen, Yang ^[6]; Arrow, Jie ^[7]; Zhang, Xingtan ^[4]; Wang, Aiqin ^[8]; Miao, Chenyong ^[4];

^[9]

FAFU and UIUC Joint Center for Genomics and Biotechnology Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture Fujian Agriculture and Forestry University Fuzhou Fujian China, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of Genetics Breeding and Multiple Utilization of Corps Ministry of Education Fujian Agriculture and Forestry University Fuzhou Fujian China, College of Life Sciences Fujian Normal University Fuzhou China
FAFU and UIUC Joint Center for Genomics and Biotechnology Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture Fujian Agriculture and Forestry University Fuzhou Fujian China, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of Genetics Breeding and Multiple Utilization of Corps Ministry of Education Fujian Agriculture and Forestry University Fuzhou Fujian China, College of Life Sciences Fujian Agriculture and Forestry University Fuzhou Fujian China
College of Horticulture Nanjing Agricultural University Nanjing China
FAFU and UIUC Joint Center for Genomics and Biotechnology Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture Fujian Agriculture and Forestry University Fuzhou Fujian China, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of Genetics Breeding and Multiple Utilization of Corps Ministry of Education Fujian Agriculture and Forestry University Fuzhou Fujian China
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden Chinese Academy of Sciences Wuhan China
College of Life Sciences Fujian Normal University Fuzhou China
Department of Plant Biology University of Illinois at Urbana‐Champaign Urbana IL USA
State Key Lab for Conservation and Utilization of Subtropical Agro‐biological Resources Guangxi University Nanning China
FAFU and UIUC Joint Center for Genomics and Biotechnology Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture Fujian Agriculture and Forestry University Fuzhou Fujian China, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of Genetics Breeding and Multiple Utilization of Corps Ministry of Education Fujian Agriculture and Forestry University Fuzhou Fujian China, Department of Plant Biology University of Illinois at Urbana‐Champaign Urbana IL USA

Publication Date:: 2018-07-24

Sponsoring Org.:: USDOE

OSTI Identifier:: 1461564

Alternate Identifier(s):: OSTI ID: 1461565

Grant/Contract Number:: DE‐SC0010686

Resource Type:: Published Article

Journal Name:: Plant Biotechnology Journal

Additional Journal Information:: Journal Name: Plant Biotechnology Journal Journal Volume: 17 Journal Issue: 1; Journal ID: ISSN 1467-7644

Publisher:: Wiley-Blackwell

Country of Publication:: United Kingdom

Language:: English

Citation Formats


                    Zhang, Jisen, Zhang, Qing, Li, Leiting, Tang, Haibao, Zhang, Qiong, Chen, Yang, Arrow, Jie, Zhang, Xingtan, Wang, Aiqin, Miao, Chenyong, and Ming, Ray. Recent polyploidization events in three Saccharum founding species.  United Kingdom: N. p., 2018. 
Web.  doi:10.1111/pbi.12962.

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                    Zhang, Jisen, Zhang, Qing, Li, Leiting, Tang, Haibao, Zhang, Qiong, Chen, Yang, Arrow, Jie, Zhang, Xingtan, Wang, Aiqin, Miao, Chenyong, & Ming, Ray. Recent polyploidization events in three Saccharum founding species.  United Kingdom.  https://doi.org/10.1111/pbi.12962

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                    Zhang, Jisen, Zhang, Qing, Li, Leiting, Tang, Haibao, Zhang, Qiong, Chen, Yang, Arrow, Jie, Zhang, Xingtan, Wang, Aiqin, Miao, Chenyong, and Ming, Ray. Tue .  
"Recent polyploidization events in three Saccharum founding species".  United Kingdom.  https://doi.org/10.1111/pbi.12962.

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@article{osti_1461564,

  title        = {Recent polyploidization events in three Saccharum founding species},

  author       = {Zhang, Jisen and Zhang, Qing and Li, Leiting and Tang, Haibao and Zhang, Qiong and Chen, Yang and Arrow, Jie and Zhang, Xingtan and Wang, Aiqin and Miao, Chenyong and Ming, Ray},

  abstractNote = {},

  doi          = {10.1111/pbi.12962},

  journal      = {Plant Biotechnology Journal},

  number       = 1,

  volume       = 17,

  place        = {United Kingdom},

  year         = {2018},

  month        = {7}

}

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Similar Records

Title: Recent polyploidization events in three Saccharum founding species

Citation Formats

Adaptive seeds tame genomic sequence comparison journal, January 2011

Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics journal, March 1996

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato journal, May 2013

Sequence polymorphism from EST data in sugarcane: a fine analysis of 6-phosphogluconate dehydrogenase genes journal, December 2001

Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates journal, June 2014

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments journal, July 2006

Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum journal, June 2016

Analysis of clonal germplasm from five Saccharum species: S. barberi, S. robustum, S. officinarum, S. sinense and S. spontaneum. A study of inter- and intra species relationships using microsatellite markers journal, March 2007

Clustal W and Clustal X version 2.0 journal, September 2007

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences journal, May 2006

Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid journal, March 1997

Studies in Saccharum spontaneum Distribution and Geographical Association of Chromosome Numbers journal, January 1960

Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing journal, May 2009

Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize journal, December 1997

Linkage illuminates a complex genome journal, August 2011

Detailed Alignment of Saccharum and Sorghum Chromosomes: Comparative Organization of Closely Related Diploid and Polyploid Genomes journal, December 1998

Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. journal, September 1996

Haplotype analysis of sucrose synthase gene family in three Saccharum species journal, January 2013

SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids journal, December 2013

A comprehensive genetic map of sugarcane that provides enhanced map coverage and integrates high-throughput Diversity Array Technology (DArT) markers journal, January 2014

Genetic Diversity and Relationships in Native Hawaiian Saccharum officinarum Sugarcane journal, July 2004

Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs journal, May 2004

Characterisation of single nucleotide polymorphisms in sugarcane ESTs journal, May 2006

RFLP linkage map and genome analysis of Saccharum spontaneum journal, August 1993

Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes journal, April 1998

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses journal, March 2011

Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome: Genomic stability in the highly polyploid sugarcane journal, April 2007

CAP3: A DNA Sequence Assembly Program journal, September 1999

Saccharum species as horticultural classes journal, February 1999

EMBOSS: The European Molecular Biology Open Software Suite journal, June 2000

PAML 4: Phylogenetic Analysis by Maximum Likelihood journal, April 2007

Problems in breeding and cytology of sugar cane journal, March 1961

Coexpression of Neighboring Genes in the Genome of Arabidopsis thaliana journal, May 2004

The detection and estimation of linkage in polyploids using single-dose restriction fragments journal, January 1992

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes journal, January 2010

High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane journal, October 2010

ESTs as a source for sequence polymorphism discovery in sugarcane: example of the Adh genes journal, January 2003

Unraveling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana journal, January 2005

Adaptive seeds tame genomic sequence comparison
journal, January 2011

Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics
journal, March 1996

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato
journal, May 2013

Sequence polymorphism from EST data in sugarcane: a fine analysis of 6-phosphogluconate dehydrogenase genes
journal, December 2001

Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates
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PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
journal, July 2006

Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum
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Analysis of clonal germplasm from five Saccharum species: S. barberi, S. robustum, S. officinarum, S. sinense and S. spontaneum. A study of inter- and intra species relationships using microsatellite markers
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Clustal W and Clustal X version 2.0
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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
journal, May 2006

Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid
journal, March 1997

Studies in Saccharum spontaneum Distribution and Geographical Association of Chromosome Numbers
journal, January 1960

Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing
journal, May 2009

Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize
journal, December 1997

Linkage illuminates a complex genome
journal, August 2011

Detailed Alignment of Saccharum and Sorghum Chromosomes: Comparative Organization of Closely Related Diploid and Polyploid Genomes
journal, December 1998

Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.
journal, September 1996

Haplotype analysis of sucrose synthase gene family in three Saccharum species
journal, January 2013

SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids
journal, December 2013

A comprehensive genetic map of sugarcane that provides enhanced map coverage and integrates high-throughput Diversity Array Technology (DArT) markers
journal, January 2014

Genetic Diversity and Relationships in Native Hawaiian Saccharum officinarum Sugarcane
journal, July 2004

Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
journal, May 2004

Characterisation of single nucleotide polymorphisms in sugarcane ESTs
journal, May 2006

RFLP linkage map and genome analysis of Saccharum spontaneum
journal, August 1993

Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes
journal, April 1998

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses
journal, March 2011

Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome: Genomic stability in the highly polyploid sugarcane
journal, April 2007

CAP3: A DNA Sequence Assembly Program
journal, September 1999

Saccharum species as horticultural classes
journal, February 1999

EMBOSS: The European Molecular Biology Open Software Suite
journal, June 2000

PAML 4: Phylogenetic Analysis by Maximum Likelihood
journal, April 2007

Problems in breeding and cytology of sugar cane
journal, March 1961

Coexpression of Neighboring Genes in the Genome of Arabidopsis thaliana
journal, May 2004

The detection and estimation of linkage in polyploids using single-dose restriction fragments
journal, January 1992

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes
journal, January 2010

High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane
journal, October 2010

ESTs as a source for sequence polymorphism discovery in sugarcane: example of the Adh genes
journal, January 2003

Unraveling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana
journal, January 2005