Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus

Raubeson, Linda A.; Peery, Rhiannon; Chumley, Timothy W.; Dziubek, Chris; Fourcade, H. Matthew; Boore, Jeffrey L.; Jansen, Robert K.

doi:10.1186/1471-2164-8-174

Cited by 378 publications

(358 citation statements)

References 79 publications

Supporting

Mentioning

318

Contrasting

Unclassified

Order By: Relevance

“…Three genes, rps16, infA, and ycf4, found in most angiosperm plastid genomes, including representatives of the early-branching lineages (Goremykin et al, 2003;Hansen et al, 2007;Raubeson et al, 2007) are not present in the chickpea plastid genome. In ndhB, there is an internal stop codon, similar to other legume plastid genomes.…”

Section: Size Gene Content Order and Organization Of Chickpea Plasmentioning

confidence: 98%

“…The genomes usually include 120-130 genes and range in size from 120 to 170 kilobases (kb). Gene content and gene order are conserved throughout angiosperms with the ancestral configuration depicted by the earliest-branching angiosperm clades Amborella and Nymphaeales (Goremykin et al, 2003;Raubeson et al, 2007;Jansen et al, 2007). In a typical angiosperm chloroplast genome, there are 18 genes containing introns, six in tRNA genes and the remaining twelve in protein-coding genes.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Jansen

Wojciechowski

Elumalai

et al. 2008

Molecular Phylogenetics and Evolution

188

200

View full text Add to dashboard Cite

Chickpea (Cicer arietinum, Leguminosae), an important grain legume, is widely used for food and fodder throughout the world. We sequenced the complete plastid genome of chickpea, which is 125,319 bp in size, and contains only one copy of the inverted repeat (IR). The genome encodes 108 genes, including 4 rRNAs, 29 tRNAs, and 75 proteins. The genes rps16, infA, and ycf4 are absent in the chickpea plastid genome, and ndhB has an internal stop codon in the 5′exon, similar to other legumes. Two genes have lost their introns, one in the 3′exon of the transpliced gene rps12, and the one between exons 1 and 2 of clpP; this represents the first documented case of the loss of introns from both of these genes in the same plastid genome. An extensive phylogenetic survey of these intron losses was performed on 302 taxa across legumes and the related family Polygalaceae. The clpP intron has been lost exclusively in taxa from the temperate "IR-lacking clade" (IRLC), whereas the rps12 intron has been lost in most members of the IRLC (with the exception of Wisteria, Callerya, Afgekia, and certain species of Millettia, which represent the earliest diverging lineages of this clade), and in the tribe Desmodieae, which is closely related to the tribes Phaseoleae and Psoraleeae. Data provided here suggest that the loss of the rps12 intron occurred after the loss of the IR. The two new genomic changes identified in the present study provide additional support of the monophyly of the IR-loss clade, and resolution of the pattern of the earliest-branching lineages in this clade. The availability of the complete chickpea plastid genome sequence also provides valuable information on intergenic spacer regions among legumes and endogenous regulatory sequences for plastid genetic engineering.

show abstract

Section: Size Gene Content Order and Organization Of Chickpea Plasmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

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

Jansen

Wojciechowski

Elumalai

et al. 2008

Molecular Phylogenetics and Evolution

188

200

View full text Add to dashboard Cite

show abstract

“…According to this, it is an important source of genetic markers for phylogenetic analysis, population-level studies, genotyping, and mapping, which can be used for genomic characterization and inter-specific comparison (Raubeson et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

“…Many studies have identified chloroplast SSRs (cpSSRs) within plastomes (Rajendrakumar et al, 2007;Raubeson et al, 2007), and these markers are sufficiently variable for phylogeographic studies within a species (Dick and Heuertz, 2008). Lack of recombination reduces homoplasy, which in turn increases the precision of phylogenetic inference in such studies (Marshall et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

Characterization of chloroplast DNA microsatellites from Saccharum spp and related species

Melotto-Passarin¹,

Tambarussi²,

Dressano³

et al. 2011

Genet. Mol. Res.

View full text Add to dashboard Cite

ABSTRACT. Microsatellites, or simple sequence repeats (SSRs), and their flanking regions in chloroplast genomes (plastomes) of some species of the family Poaceae were analyzed in silico to look for DNA sequence variations. Comparison of the complete chloroplast DNA sequences (cpDNAs) of sugarcane (Saccharum hybrid cv. SP-80-3280 and S. officinarum cv. NCo310) and related species, Agrostis stolonifera, Brachypodium distachyon, Hordeum vulgare subsp vulgare, Lolium perenne, Oryza nivara, O. sativa subsp indica, O. sativa subsp japonica, Sorghum bicolor, Triticum aestivum, Zea mays, and Z. mays cv. B73, allowed us to examine the organization of chloroplast SSRs (cpSSRs) in genic and intergenic regions. We identified 204 cpSSRs in the sugarcane cpDNA; 22.5% were in genic regions. The ndh, rps, trn, and rpl gene clusters of the chloroplasts had the most repeats. Mononucleotide repeats were the most abundant cpSSRs in these species; however, di-, tri-, tetra-, penta-, and hexanucleotide repeats were also identified. Chloroplast SSRs in Poaceae variability possible; repeat motifs are not uniformly distributed across the Poaceae plastomes, but are mostly confined to intergenic regions. Phylogeny was determined by maximum parsimony and neighborjoining inference methods. The cpSSRs of these species were found to be polymorphic. It appears that individual cpSSRs in the Poaceae are stable, at least over short periods of evolutionary time. We conclude that the plastome database can be exploited for phylogenetic analysis and biotechnological development.

show abstract

“…The genome consists of 134,821 bp containing a pair of inverted repeats (IRs) of 20,819 bp, which was separated by a large single-copy region and a small single-copy region of 80,853 bp and 12,330 bp, respectively. The high plant cp genomes are AT-rich (Raubeson et al 2007;Gao et al 2009;Yang et al 2010), and the O. eichingeri cp genome has alike characteristic, AT content is 61%.…”

mentioning

confidence: 99%

The complete chloroplast genome sequence of Oryza eichingeri (Poaceae)

Liu

Zhao

Luo

et al. 2017

Mitochondrial DNA Part B

View full text Add to dashboard Cite

The complete chloroplast genome sequence of Oryza eichingeri (GenBank accession number: KX085496) was generated by de novo assembly with low-coverage whole-genome sequence data. The chloroplast genome is 134,821 bp in length and showed conserved typical chloroplast structure. The cpDNA contained four rRNA, 39 tRNA, and 79 unique protein-coding genes. Seventeen genes contain one intron, only ycf3 contains two introns; rps12 is trans-spliced, one of its exons is in the LSC region (5′_end) and the two reside in the IR regions (3′_end) separated. A pair of gene ndhH, due to the 5′ part of ndhH which overlaps the IR/SSC junctions, was two unique genes. The AT content of O. eichingeri cp genome is 61%. Phylogenomic analysis showed that O. eichingeri is closely related to O. officinalis . The complete cpDNA of O. eichingeri provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for the genus Oryza .

show abstract

Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus

Cited by 378 publications

References 79 publications

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

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

Characterization of chloroplast DNA microsatellites from Saccharum spp and related species

The complete chloroplast genome sequence of Oryza eichingeri (Poaceae)

Contact Info

Product

Resources

About