Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA

Ogihara, Yasunari; Isono, Kazuriho; Kojima, Toshio; Endo, Akira; Hanaoka, Mitsumasa; Shiina, Takashi; Terachi, Toru; Utsugi, Shigeko; Murata, Minoru; Mori, Naoki; Takumi, Shigeo; Ikeo, Kazuho; Gojobori, Takashi; Murai, Rika; Murai, Koji; Matsuoka, Yoshihiro; Ohnishi, Yusuke; Tajiri, H.; Tsunewaki, Koichiro

doi:10.1007/s00438-001-0606-9

Cited by 145 publications

(63 citation statements)

References 21 publications

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“…The small inversion regions correspond to the stem-loop-forming regions located downstream of the genes involved in stabilizing mRNA molecules. Large inversion mutations have been frequently noted in several widely diverse vascular plants [24], [25], [26], [27], [28]. In contrast, the short inversions have been recently reported in just a few cp genomes [29], [30], [31], [32].…”

Section: Resultsmentioning

confidence: 99%

Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L

Kim

2012

PLoS ONE

138

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Sesamum indicum is an important crop plant species for yielding oil. The complete chloroplast (cp) genome of S. indicum (GenBank acc no. JN637766) is 153,324 bp in length, and has a pair of inverted repeat (IR) regions consisting of 25,141 bp each. The lengths of the large single copy (LSC) and the small single copy (SSC) regions are 85,170 bp and 17,872 bp, respectively. Comparative cp DNA sequence analyses of S. indicum with other cp genomes reveal that the genome structure, gene order, gene and intron contents, AT contents, codon usage, and transcription units are similar to the typical angiosperm cp genomes. Nucleotide diversity of the IR region between Sesamum and three other cp genomes is much lower than that of the LSC and SSC regions in both the coding region and noncoding region. As a summary, the regional constraints strongly affect the sequence evolution of the cp genomes, while the functional constraints weakly affect the sequence evolution of cp genomes. Five short inversions associated with short palindromic sequences that form step-loop structures were observed in the chloroplast genome of S. indicum. Twenty-eight different simple sequence repeat loci have been detected in the chloroplast genome of S. indicum. Almost all of the SSR loci were composed of A or T, so this may also contribute to the A-T richness of the cp genome of S. indicum. Seven large repeated loci in the chloroplast genome of S. indicum were also identified and these loci are useful to developing S. indicum-specific cp genome vectors. The complete cp DNA sequences of S. indicum reported in this paper are prerequisite to modifying this important oilseed crop by cp genetic engineering techniques.

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Section: Resultsmentioning

confidence: 99%

Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L

Kim

2012

PLoS ONE

138

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“…The composition of chloroplasts from the Poaceae family is very similar between species and consists of a large single copy region (LSC), which is approximately 80 kb, and a small single copy region (SSC) of approximately 13 kb in length, located between the two inverted repeat sequences of approximately 20 kb [28], [29].…”

Section: Introductionmentioning

confidence: 99%

Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe

et al. 2014

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Using Roche/454 technology, we sequenced the chloroplast genomes of 12 Triticeae species, including bread wheat, barley and rye, as well as the diploid progenitors and relatives of bread wheat Triticum urartu, Aegilops speltoides and Ae. tauschii. Two wild tetraploid taxa, Ae. cylindrica and Ae. geniculata, were also included. Additionally, we incorporated wild Einkorn wheat Triticum boeoticum and its domesticated form T. monococcum and two Hordeum spontaneum (wild barley) genotypes. Chloroplast genomes were used for overall sequence comparison, phylogenetic analysis and dating of divergence times. We estimate that barley diverged from rye and wheat approximately 8–9 million years ago (MYA). The genome donors of hexaploid wheat diverged between 2.1–2.9 MYA, while rye diverged from Triticum aestivum approximately 3–4 MYA, more recently than previously estimated. Interestingly, the A genome taxa T. boeoticum and T. urartu were estimated to have diverged approximately 570,000 years ago. As these two have a reproductive barrier, the divergence time estimate also provides an upper limit for the time required for the formation of a species boundary between the two. Furthermore, we conclusively show that the chloroplast genome of hexaploid wheat was contributed by the B genome donor and that this unknown species diverged from Ae. speltoides about 980,000 years ago. Additionally, sequence alignments identified a translocation of a chloroplast segment to the nuclear genome which is specific to the rye/wheat lineage. We propose the presented phylogeny and divergence time estimates as a reference framework for future studies on Triticeae.

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“…The mtDNA region is the site of the active mt- trnC gene of chloroplast origin, 14) while the ctDNA region is the site of the native ct- trnC gene. 15) This suggests that the no. 3 mtDNA segment was derived by transfer of the no.…”

Section: Resultsmentioning

confidence: 99%

“…no. NC_007579) 15,14) as the subject and query sequences, respectively. To screen other genomes for homologies to the 52 wheat mtDNA sequences that had homology to ctDNA segments, the subject sequence was always the wheat mtDNA sequence and the query sequence was one of the following: the complete mt genome sequence of rice ( Oryza sativa ssp.…”

Section: Materials and Data Analysismentioning

confidence: 99%

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Interorganellar DNA transfer in wheat: dynamics and phylogenetic origin

Tsunewaki

2011

Proceedings of the Japan Academy. Ser. B: Physical and Biologic

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A homology search of wheat chloroplast (ct) and mitochondrial (mt) genomes identified 54 ctDNA segments that have homology with 66 mtDNA segments. The mtDNA segments were classified according to their origin: orthologs (prokaryotic origin), xenologs (interorganellar DNA transfer origin) and paralogs (intraorganellar DNA amplification origin). The 66 mtDNA sequences with homology to ctDNA segments included 14 paralogs, 18 orthologs and 34 xenologs. Analysis of the xenologs indicated that the DNA transfer occurred unidirectionally from the ct genome to the mt genome. The evolutionary timing of each interorganellar DNA transfer that generated a xenolog was estimated. This analysis showed that 2 xenologs originated early in green plant evolution, 4 in angiosperm evolution, 3 in monocotyledon evolution, 9 during cereal diversification and 8 in the evolution of wheat. Six other xenologs showed recurrent transfer from the ct to mt genomes in more than one taxon. The two remaining xenologs were uninformative on the evolutionary timing of their transfer. The wheat mt nad9 gene was found to be chimeric, consisting of the cereal nad9 gene and its 291 bp 5′-flanking region that included a 58 bp xenolog of the ct-ndhC origin.

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Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA

Cited by 145 publications

References 21 publications

Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L

Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L

Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe

Interorganellar DNA transfer in wheat: dynamics and phylogenetic origin

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