Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

Christopher Saski, Seung Bum Lee, Siri Fjellheim, Chittibabu Guda, Robert K. Jansen, Hong Luo, Jeffrey Tomkins, Odd Arne Rognli, Henry Daniell, Jihong Liu Clarke

Research output: Contribution to journalArticle

120 Citations (Scopus)

Abstract

Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5′ end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19-37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16-21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C-U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae.

Original languageEnglish (US)
Pages (from-to)571-590
Number of pages20
JournalTheoretical and Applied Genetics
Volume115
Issue number4
DOIs
StatePublished - Aug 2007

Fingerprint

Agrostis
Chloroplast Genome
Agrostis stolonifera
Sorghum
Hordeum
Poaceae
Sorghum bicolor
Hordeum vulgare
Triticum
Genome
grasses
intergenic DNA
genome
Intergenic DNA
microsatellite repeats
Saccharum officinarum
genes
Oryza
Microsatellite Repeats
phylogeny

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Genetics

Cite this

Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. / Saski, Christopher; Lee, Seung Bum; Fjellheim, Siri; Guda, Chittibabu; Jansen, Robert K.; Luo, Hong; Tomkins, Jeffrey; Rognli, Odd Arne; Daniell, Henry; Clarke, Jihong Liu.

In: Theoretical and Applied Genetics, Vol. 115, No. 4, 08.2007, p. 571-590.

Research output: Contribution to journalArticle

Saski, Christopher ; Lee, Seung Bum ; Fjellheim, Siri ; Guda, Chittibabu ; Jansen, Robert K. ; Luo, Hong ; Tomkins, Jeffrey ; Rognli, Odd Arne ; Daniell, Henry ; Clarke, Jihong Liu. / Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. In: Theoretical and Applied Genetics. 2007 ; Vol. 115, No. 4. pp. 571-590.
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AU - Saski, Christopher

AU - Lee, Seung Bum

AU - Fjellheim, Siri

AU - Guda, Chittibabu

AU - Jansen, Robert K.

AU - Luo, Hong

AU - Tomkins, Jeffrey

AU - Rognli, Odd Arne

AU - Daniell, Henry

AU - Clarke, Jihong Liu

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AB - Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5′ end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19-37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16-21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C-U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae.

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