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

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.

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

“…The absence of trnM-CAU and the new annotation of trnT-GGU and trnK-UUU were supported by the tRNAscan-SE program (http://lowelab.ucsc.edu/ tRNAscan-SE/; Lowe and Eddy, 1997). Gene content and gene order of the barley chloroplast genome were found to be identical to those of rice (Oryza sativa; Saski et al, 2007). According to experimental data, 17 polycistronic and 22 monocistronic transcripts were detected in rice (Kanno and Hirai, 1993).…”

“…Of these, 76 (green) and 91% (white) were at least twofold enriched in our (+) versus (2) libraries. In both green and white plastids, we identified more TSSs than one might expect for a genome comprising 113 genes (Saski et al, 2007;see Methods), many of which clustered in polycistronic transcription units (Kanno and Hirai, 1993). The initiating nucleotide was a purine in 91 (green) and 84% (white) of the TSSs.…”

“…There are 113 unique genes on the barley chloroplast genome, 78 of which are protein coding and 37 of which code for tRNAs or rRNAs (Saski et al, 2007). Maturation of rps12 mRNA involves trans-splicing of 59-rps12 and 39-rps12 (Hildebrand et al, 1988), and the respective genes were therefore considered as two separate genes.…”

Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)

“…However, complete chloroplast genome sequence of only six species of crop plants were determined until 2004. Therefore, complete plastid genome sequences of several major crop species including fiber crops , tubers (Daniell et al, , 2008, cereals (Saski et al, 2007), trees (Steane, 2005;Bausher et al, 2006;Ravi et al, 2006;Samson et al, 2007), vegetables (Ruhlman et al, 2006), fruits Daniell et al, 2006) and legumes (Saski et al, 2005;Guo et al, 2007) have been determined recently. Plastid genetic engineering offers a number of unique advantages including high level of transgene expression (DeCosa et al, 2001), multi-gene engineering in a single transformation event (Quesda-Vargas et al, 2005), transgene containment via maternal inheritance (Daniell, 2002;Daniell, 2007) or cytoplasmic male sterility .…”

A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

“…Clones were tagged as neighbor or plate-wide contaminated and excluded from further analysis if the overall fragment identity of two clones at neighboring positions within one plate or at an identical position in subsequent plates of the library was higher than 50%. Chloroplast DNA contamination was determined by comparing the fingerprint profiles with a BAC clone containing the chloroplast genome (Saski et al, 2007) of barley (Hordeum vulgare) cv Morex. Clones sharing more than 50% of their fragments with this BAC were excluded from further analysis.…”