Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes

Abstract

Despite the agricultural importance of both potato and tomato, very little is known about their chloroplast genomes. Analysis of the complete sequences of tomato, potato, tobacco, and Atropa chloroplast genomes reveals significant insertions and deletions within certain coding regions or regulatory sequences (e.g., deletion of repeated sequences within 16S rRNA, ycf2 or ribosomal binding sites in ycf2). RNA, photosynthesis, and atp synthase genes are the least divergent and the most divergent genes are clpP, cemA, ccsA, and matK. Repeat analyses identified 33-45 direct and inverted repeats >or=30 bp with a sequence identity of at least 90%; all but five of the repeats shared by all four Solanaceae genomes are located in the same genes or intergenic regions, suggesting a functional role. A comprehensive genome-wide analysis of all coding sequences and intergenic spacer regions was done for the first time in chloroplast genomes. Only four spacer regions are fully conserved (100% sequence identity) among all genomes; deletions or insertions within some intergenic spacer regions result in less than 25% sequence identity, underscoring the importance of choosing appropriate intergenic spacers for plastid transformation and providing valuable new information for phylogenetic utility of the chloroplast intergenic spacer regions. Comparison of coding sequences with expressed sequence tags showed considerable amount of variation, resulting in amino acid changes; none of the C-to-U conversions observed in potato and tomato were conserved in tobacco and Atropa. It is possible that there has been a loss of conserved editing sites in potato and tomato.

The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron

“…Bacterial artificial chromosome-related resources for this public library (BAC library ME_TBa) can be obtained from the Clemson University Genomics Institute BAC/EST Resource Center (http://www.genome.clemson.edu). Bacterial artificial chromosome clone screening, selection and sequencing followed Daniell et al (2006). Chloroplast genome inserts were identified with a soybean chloroplast DNA probe and the first 96 positive clones were pulled from the library, arrayed in a 96-well microtitre plate, copied, and archived.…”

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 .…”

Conservation of Plastid Sequences in the Plant Nuclear Genome for Millions of Years Facilitates Endosymbiotic Evolution

“…The origins of the nupts were determined by phylogenetic analyses, and their ages were estimated by comparing each nupt with the related chloroplastic sequences from the native plastome and six other plastomes from other Solanaceae species (Shinozaki et al, 1986;Schmitz-Linneweber et al, 2002;Chung et al, 2006;Daniell et al, 2006;Kahlau et al, 2006;Yukawa et al, 2006). The evolutionary forces acting on the potential protein-coding and noncoding nupt sequences were also analyzed.…”