Sequence of the Tomato Chloroplast DNA and Evolutionary Comparison of Solanaceous Plastid Genomes

Kahlau, Sabine; Aspinall, Sue; Gray, John C.; Bock, Ralph

doi:10.1007/s00239-005-0254-5

Cited by 145 publications

(112 citation statements)

References 71 publications

Supporting

Mentioning

102

Contrasting

Unclassified

Order By: Relevance

“…These editing sites occurred on 14 genes, with ndhB containing nine. ndhB transcripts were also found to be highly edited in other plants such as maize, sugarcane, rice, barley, tomato, tobacco, and Arabidopsis (Freyer et al, 1995;Kahlau et al, 2006;Chateigner-Boutin and Small, 2007). The genes ndhA and rpoB were predicted to have four editing sites; ropC2 and ndhF, three; ycf3, two; and one each in atpA, ccsA, matK, ndhD, rpl2, rpl20, rps8, and rps14.…”

Section: Predicted Rna Editing Sites In the Z Latifolia Chloroplast mentioning

confidence: 99%

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Gao

Zhang

et al. 2016

Front. Ecol. Evol.

View full text Add to dashboard Cite

Zizania latifolia (Griseb.) Turcz. ex Stapf was once utilized as an important grain in ancient China and has been cultivated as an aquatic vegetable. Here, we report the complete Z. latifolia chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads generated by directly purified chloroplast (cp) DNA genome sequencing. The Z. latifolia cp genome is 136,501 bp in length, comprising a pair of 20,878-bp inverted repeat regions (IR) separated by small and large single copy regions (SSC and LSC) of 12,590 and 82,155 bp, respectively. The Z. latifolia cp genome encodes 110 unique genes (77 protein-coding genes, 29 tRNA genes, and 4 rRNA genes), of which 15 encompass introns. Sequence analysis identified a total of 39 direct/inverted repeats and 63 simple sequence repeats (SSR) with an average rate of 0.46 SSRs/kb. Our results revealed that the Z. latifolia cp genome is AT-rich (61.02%) and gene codon usage may be largely affected by a low GC content and codon usage bias for A, T-ending codons. We predicted 33 RNA editing sites in the chloroplast of Z. latifolia, all for C-to-U transitions. Comparative analyses with other available Oryzeae plastid genomes showed that the coding and IR sequences were more conserved than the single-copy and non-coding regions, suggesting that the indels should be cautiously employed in phylogenetic studies. Phylogenetic analysis of 52 complete grass chloroplast genomes including the reported Z. latifolia cp genome in this study yielded an identical tree topology as previous plastid-based trees, providing strong support for a sister relationship between Bambusoideae+Pooideae and Ehrhartoideae in the BEP (Bambusoideae, Ehrhartoideae, Pooideae) clade of the grass family.

show abstract

Section: Predicted Rna Editing Sites In the Z Latifolia Chloroplast mentioning

confidence: 99%

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Gao

Zhang

et al. 2016

Front. Ecol. Evol.

View full text Add to dashboard Cite

show abstract

“…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.…”

mentioning

confidence: 99%

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

2011

View full text Add to dashboard Cite

The nuclear genome of eukaryotes contains large amounts of cytoplasmic organelle DNA (nuclear integrants of organelle DNA [norgs]). The recent sequencing of many mitochondrial and chloroplast genomes has enabled investigation of the potential role of norgs in endosymbiotic evolution. In this article, we describe a new polymerase chain reaction-based method that allows the identification and evolutionary study of recent and older norgs in a range of eukaryotes. We tested this method in the genus Nicotiana and obtained sequences from seven nuclear integrants of plastid DNA (nupts) totaling 25 kb in length. These nupts were estimated to have been transferred 0.033 to 5.81 million years ago. The spectrum of mutations present in the potential protein-coding sequences compared with the noncoding sequences of each nupt revealed that nupts evolve in a nuclear-specific manner and are under neutral evolution. Indels were more frequent in noncoding regions than in potential coding sequences of former chloroplastic DNA, most probably due to the presence of a higher number of homopolymeric sequences. Unexpectedly, some potential protein-coding sequences within the nupts still contained intact open reading frames for up to 5.81 million years. These results suggest that chloroplast genes transferred to the nucleus have in some cases several millions of years to acquire nuclear regulatory elements and become functional. The different factors influencing this time frame and the potential role of nupts in endosymbiotic gene transfer are discussed.More than a billion years ago, the ancestors of mitochondria and plastids were free-living eubacteria that were sequentially engulfed by a precursor of the nucleated cell (Timmis et al., 2004). Since these two separate endosymbiotic events, organelle DNA has been continuously transferred and integrated into the nucleus. Insertions of organelle DNA are referred to as numts (nuclear integrants of mitochondrial DNA; Lopez et al., 1994) and nupts (nuclear integrants of plastid DNA; Timmis et al., 2004) or collectively as norgs (nuclear integrants of organelle DNA; Leister, 2005). Transfer of mitochondrial and plastid DNA to the nucleus has been shown to occur at a very high frequency ( Thorsness and Fox, 1990;Huang et al., 2003;Stegemann et al., 2003;Sheppard et al., 2008). Several molecular mechanisms involved in the integration of mitochondrial DNA into the nucleus have been suggested and are likely to be similar for nupts.These include the degradation and lysis of mitochondria, the encapsulation of mitochondrial DNA inside the nucleus, the direct physical association between the mitochondria and nucleus with membrane fusions, or the entry and incorporation of mitochondrial DNA into nuclear chromosomes (for review, see Hazkani-Covo et al., 2010). During evolution, this DNA transfer and integration into the nucleus have resulted in the functional relocation of many organelle genes in the nucleus, leading to a massive reduction in the size of organelle genomes compared with those of their fr...

show abstract

“…Currently, 12 chromosomes have been split between 10 countries as follows: Korea (chromosome 2), China (3), UK (4), India (5), The Netherlands (6), France (7), Japan (8), Spain (9), Italy (12) and USA (1, 10, 11). In addition, chloroplast genome sequence is available (Kahlau et al 2006) and mitochondrial genome sequence is to be sequenced by Argentina.…”

Section: Tomato Genome Sequencing Strategymentioning

confidence: 99%

Solanaceae genomics: Current status of tomato (<i>Solanum lycopersicum</i>) genome sequencing and its application to pepper (<i>Capsicum</i> spp.) genome research

Lee¹,

Jo²,

Choi

2007

Plant Biotechnology

View full text Add to dashboard Cite

Sequence of the Tomato Chloroplast DNA and Evolutionary Comparison of Solanaceous Plastid Genomes

Cited by 145 publications

References 71 publications

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

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

Solanaceae genomics: Current status of tomato (<i>Solanum lycopersicum</i>) genome sequencing and its application to pepper (<i>Capsicum</i> spp.) genome research

Contact Info

Product

Resources

About