Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts

Guo, Xianwu; Castillo-Ramírez, Santiago; González, Víctor; Bustos, Patricia; Fernández-Vázquez, José Luís; Santamaría, Rosa I.; Arellano, Jesús; Cevallos, Miguel A.; Dávila, Guillermo

doi:10.1186/1471-2164-8-228

Cited by 91 publications

(85 citation statements)

References 64 publications

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“…Gene order in chickpea is similar to the ancestral angiosperm gene order except for the loss of one copy of the IR and by the presence of a single, large inversion of approximately 50 kb that reverses the order of the genes between rbcL and rps16. The same inversion is present in the four other completely sequenced legume plastid genomes Glycine max (Saski et al, 2005), Lotus japonicus (Kato et al, 2000), Medicago truncatula, and Phaseolus vulgaris (Guo et al, 2007), and is apparently shared by the majority of papilionoid legumes (Doyle et al, 1996). The AT content of the chickpea plastid genome is 66.1%, similar to other legumes including Glycine max (64.63%), Lotus japonicus (64.0%), Phaseolus vulgaris (64.56%), and Medicago truncatula (66.03%).…”

Section: Size Gene Content Order and Organization Of Chickpea Plasmentioning

confidence: 67%

“…MultiPipMaker (Schwartz et al, 2003; http://bio.cse.psu.edu) was used for multiple genome alignment of chickpea with four published legume plastid genomes from the subfamily Papilionoideae; Lotus japonicus (NC_002694, Kato et al, 2000), Medicago truncatula (NC_003119), Glycine max (NC_007942, Saski et al, 2005), and Phaseolus vulgaris (NC_009259, Guo et al, 2007). We generated the alignments of whole genomes using chickpea as the reference genome.…”

Section: Whole Genome Sequence Alignmentmentioning

confidence: 99%

“…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 .…”

Section: Introductionmentioning

confidence: 99%

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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

187

200

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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.

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Section: Size Gene Content Order and Organization Of Chickpea Plasmentioning

confidence: 67%

Section: Whole Genome Sequence Alignmentmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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

187

200

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“…A similar tendency to lose the cp rps16 in selfcompatible plants is observed in these species. The loss of the functional rps16 from the chloroplast genome has been demonstrated in M. truncatula, P. vulgaris, C. arietinum, and V. radiata, and these are all self-compatible plants (Choi et al, 2004;Guo et al, 2007;Khan et al, 2004;Toker et al, 2006). The epistatic model (Wade and Goodnight, 2006) predicts that selfing reproduction maintains cyto-nuclear gene combinations and increases the response to the selection of epistatic combinations, potentially encouraging gene transfer.…”

Section: Discussionmentioning

confidence: 99%

“…Although the number of genes and their order are generally conserved among angiosperm chloroplast genomes, exceptional gene losses have been identified (e.g., rpl33 in Phaseolus vulgaris (Guo et al, 2007) and Vigna radiata (Tangphatsornruang et al, 2010), infA in almost all rosid species (Millen et al, 2001), rpl32 in the Populus genus (Okumura et al, 2006;Steane, 2005), rps16 in Medicago truncatula (Saski et al, 2005), P. vulgaris (Guo et al, 2007), Cicer arietinum (Jansen et al, 2008), V. radiata (Tangphatsornruang et al, 2010), and the Populus genus (Okumura et al, 2006;Steane, 2005)). It is also possible that genes that have been transferred or substituted recently in evolution remain in the chloroplast genome as remnants when gene transfer or substitution has occurred.…”

Section: Introductionmentioning

confidence: 99%

Different status of the gene for ribosomal protein S16 in the chloroplast genome during evolution of the genus Arabidopsis and closely related species

et al. 2010

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The ribosomal protein S16 (RPS16), the product of the rps16, is generally encoded in the chloroplast genomes of flowering plants. However, it has been reported that chloroplast-encoded RPS16 in mono-and dicotyledonous plants has been substituted by the product of nuclear-encoded rps16, which was transferred from the mitochondria to the nucleus before the early divergence of angiosperms. Current databases show that the chloroplast-encoded rps16 has become a pseudogene in four species of the Brassicaceae (Aethionema grandiflorum, Arabis hirsuta, Draba nemorosa, and Lobularia maritima). Further analysis of Arabidopsis thaliana and its close relatives has shown that pseudogenization has also occurred via the loss of its splicing capacity (Arabidopsis thaliana and Olimarabidopsis pumila). In contrast, the spliced product of chloroplast-encoded rps16 is observed in close relatives of Arabidopsis thaliana (Arabidopsis arenosa, Arabidopsis lyrata, and Crucihimalaya lasiocarpa). In this study, we identified the different functional status of rps16 in several chloroplast genomes in the genus Arabidopsis and its close relatives. Our results strongly suggest that nuclear-and chloroplastencoded rps16 genes coexisted for at least 126 million years. We raise the possibility of the widespread pseudogenization of rps16 in the angiosperm chloroplast genomes via the loss of its splicing capacity, even when the rps16 encoded in the chloroplast genome is transcriptionally active.

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Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time

Jeffery,

Mudukuti,

Buell

et al. 2023

The Plant Genome

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Dry beans (Phaseolus vulgaris L.) are a nutritious food, but their lengthy cooking requirements are barriers to consumption. Presoaking is one strategy to reduce cooking time. Soaking allows hydration to occur prior to cooking, and enzymatic changes to pectic polysaccharides also occur during soaking that shorten the cooking time of beans. Little is known about how gene expression during soaking influences cooking times. The objectives of this study were to (1) identify gene expression patterns that are altered by soaking and (2) compare gene expression in fast‐cooking and slow‐cooking bean genotypes. RNA was extracted from four bean genotypes at five soaking time points (0, 3, 6, 12, and 18 h) and expression abundances were detected using Quant‐seq. Differential gene expression analysis and weighted gene coexpression network analysis were used to identify candidate genes within quantitative trait loci for water uptake and cooking time. Genes related to cell wall growth and development as well as hypoxic stress were differentially expressed between the fast‐ and slow‐cooking beans due to soaking. Candidate genes identified in the slow‐cooking beans included enzymes that increase intracellular calcium concentrations and cell wall modification enzymes. The expression of cell wall‐strengthening enzymes in the slow‐cooking beans may increase their cooking time and ability to resist osmotic stress by preventing cell separation and water uptake in the cotyledon.

show abstract

Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts

Cited by 91 publications

References 64 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)

Different status of the gene for ribosomal protein S16 in the chloroplast genome during evolution of the genus Arabidopsis and closely related species

Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time

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