- Chloroplast genome sequence of. - However, our knowledge of the chloroplast genome level of lima beans is limited.. - including 82 protein-coding genes, 34 tRNA genes, and 8 rRNA genes were identified in the P. - A total of 61 long repeats and 290 SSRs were detected in the lima bean Cp genome. - It has a typical 50 kb inversion of the Leguminosae family and an 70 kb inversion to subtribe Phaseolinae. - Conclusions: The characteristics of the lima bean Cp genome was identified for the first time, these results will provide useful insights for species identification, evolutionary studies and molecular biology research.. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - Full list of author information is available at the end of the article. - distributed all over the world, Chongming lima bean, an important characteristic vegetable variety in the Chongming area, has been grown on Chongming Island for more than 100 years [6].. - With the development of high- throughput sequencing technologies, there were more than 2400 plant Cp genomes have been published in the NCBI database [14]. - and loss of the rps12 and clpP introns [8, 26].. - However, the classification and phylogenetic relation- ships of the main branches within the subfamilies are still unclear. - Due to the limited chloroplast genomes of legumes that have been sequenced, phylogenetic chloroplast phyl- ogeny has not been applied to classification of the Leguminosae.. - Currently, there are no published studies of the Cp genome of lima bean. - It is expected that the results will help us to understand of the Cp genome of lima bean and provide markers for phylogenetic and genetic studies.. - Characteristics of the P. - Cp genome. - Although the sizes of the overall genome had differences, the GC content was similar in each region (LSC, SSC and IR) of different species.. - There were 129 genes found in the P. - Among them, 35 genes (13 CDS, 14 tRNAs and 8 rRNAs genes) were duplicated in the IR regions (Fig. - Codon usage frequency of the P. - In the P. - The analysis of long-repeat in the P. - Among them, 46 re- peats were 30–39 bp in length, 8 repeats were 40–49 bp, 7 repeats were more than 50 bp, and the longest repeat was 287 bp in length and was located in the IR region (Fig. - Most repeats were located in the in- tron sequences and intergenic spacer (IGS), and the mi- nority were found in the ycf2, rpl16, ndhA, ycf3, psbL,. - 1 Gene map of the P.lunatus. - Chloroplast genome. - Table 1 Base composition of the P.lunatus. - Chloroplast genome Region A. - truncatula have lost one copy of the IR. - on comparison with Arabi- dopsis, all have a common 50-kb inversion, spanning from rbcL to rps16 gene in the LSC region. - Table 3 The genes present in the P.lunatus. - max and G soja except for the loss of the IRb region.. - The re- sult shows high sequence identity with Phaseolinae Table 4 The lengths of exons and introns in genes with introns in the P. - The boxes above the line represent the gene sequence in the clockwise direction, and the boxes below the line represent gene sequences in the opposite orientation. - The gene names at the bottom indicate the genes located at the boundaries of the boxes in the Cp genome of Arabidopsis. - rpl16, accD, petB, rsp16, clpP, ndhA, ndhF and ycf1 genes in coding regions was found with significant variation, trnk-rbcL, rbcL-atpB, ndhJ-rps4, psbD-rpoB, atpI-atpA, atpA-accD, accD-psbJ, psbE-psbB, rsp11- rsp19, ndhF-ccsA in the intergenic regions were identi- fied with a high degree of divergence. - A comparison of the boundaries of the lima bean Cp genome was performed among the other six Legumino- sae species: P. - At the LSC/IR junction of lima bean, the rps19 and trnN genes are duplicated at the IR/SSC junction completely and included in the IR region. - Compared to other species in the genus, the range of each region showed substantial differences. - The rps19 gene in the P. - radiate Cp genomes was shifted by 564 bp from IR to LSC at the LSC/IR border and 701 bp from IR to LSC in the V.. - The grey arrows above the contrast indicate the direction of the gene translation. - In contrast, the Ka/Ks ratio of the ndhD gene was greater than 1 in four of the ten comparison groups, four of them had no this gene and another two exhibited low Ka/Ks ratios. - 0.5 in the other species.. - 6 Comparison of the borders of the LSC and SSC regions and IRs among seven Leguminosae species. - Extensions of the genes are also indicated above the boxes. - High GC content is conducive to the stability of the genome and maintaining the complexity of the sequence. - The four rRNAs genes have high GC content, which results in a high GC content in the IR re- gion [40]. - lunatus Cp genome, and most of the repeats were distributed within the intergenic spacer regions, intron sequences, and ycf2 genes, which is highly homologous to the sequence in V.radiata [20].. - Two hundred ninety SSRs were found in the lima bean Cp genime. - Leguminosae is an excellent choice for studying the evolution of the Cp genome because legume plastid genomes have undergone multiple genomic rearrange- ments and the loss of genes or introns [50. - lunatus has a common 50 kb inversion in the LSC region, spanning from rbcL to rps16, which has been found in other legumes (Fig. - lunatus as a member of the subtribe Phaseolinae shows the same inversion. - All the results shown in the gene order suggest that consid- erable rearrangements and diversification were occurred in the legume Cp genomes and a valuable resource for phylogenetic analysis is provided.. - polymorphisms of the Cp DNA is very use- ful to study the evolutionary of Lima bean and to pinpoint domestication places in several studies. - The size change of the angiosperm plastid genome is caused by the contraction and expansion of the IR re- gion at the boundary [51, 60]. - The change of the IR/SC junction is a common phenomenon and plays an im- portant role in evolution . - In the seven Legu- minosae species, P. - 1 in most of the genes, indicating that they are under purifying selection in lima bean. - 1 in four of the ten compari- son groups, ycf2 exhibited a ratios >. - 0.5 in the other species. - The Cp genomes have been used for phylogenetic analyses in the genus Quercus, which pro- vide strong support for the deep phylogenetic relation- ship between subfamily tribes [67. - Genome annotation of the cp DNA sequences. - The annotation of the Lima bean Cp genome was per- formed by blast v2.2.2 (parameter: -nproc 20, −bestn 5 [74. - The synonym- ous codon usage, relative synonymous codon usage values (RSCU) and codon usage of the complete plastid genomes were analyzed using MEGA 6.0 PREP suit [78]. - with cut off values of 8.0 was used to predict the RNA editing sites in the plastome.. - MUMmer was used to pair sequence alignment of the chloroplast genome [81]. - The chloroplast genome of P.. - unguiculata (NC_018051) in the Leguminosae tribe by mVISTA with the shuffle-LAGAN. - The number of genes in the P. - The relative synonymous codon usage of the P. - lunatus chloroplast genome.. - Repeated sequences of the P. - Simple sequence repeats (SSRs) in the P.. - The funding bodies did not play a role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.. - in the central valley of Costa Rica. - BaudoinSample size for collecting seeds in germplasm conservation: the case of the Lima bean (Phaseolus lunatus L. - Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae). - Recombination within the inverted repeat sequences of the Chlamydomonas reinhardii chloroplast genome produces two orientation isomers. - Sequence-analysis of the junction of the large single copy region and the large inverted repeat in the petunia chloroplast genome. - Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. - A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny.. - Complete Structure of the Chloroplast Genome of a Legume, Lotus japonicus. - EVOLUTIONARY SIGNIFICANCE OF THE LOSS OF THE CHLOROPLAST-DNA INVERTED REPEAT IN THE LEGUMINOSAE SUBFAMILY PAPILIONOIDEAE. - Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions. - The complete plastid genome sequence of the wild Rice Zizania latifolia and comparative chloroplast genomics of the Rice tribe Oryzeae, Poaceae. - Phylogenetic relationships in the Papilionoideae (family Leguminosae) based on nucleotide sequences of cpDNA (rbcL) and ncDNA (ITS 1 and 2). - Phylogenetic relationships in the genus Leonardoxa (Leguminosae: Caesalpinioideae) inferred from chloroplast trnL intron and trnL-trnF intergenic spacer sequences. - Phylogeny reconstruction in the Caesalpinieae grade (Leguminosae) based on duplicated copies of the sucrose synthase gene and plastid markers. - Comparative chloroplast genome analyses of Streptophyte Green algae uncover major structural alterations in the Klebsormidiophyceae, Coleochaetophyceae and Zygnematophyceae. - Fine structural features of the chloroplast genome:. - comparison of the sequenced chloroplast genomes. - Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera). - A chloroplast DNA inversion as a subtribal character in the Phaseoleae (Leguminosae). - Multiple domestications of the Mesoamerican gene pool of lima bean (Phaseolus lunatus L. - Migration of endpoints of two genes relative to boundaries between regions of the plastid genome in the grass family (POACEAE). - Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. - Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. - Characterization of the complete chloroplast genome of Dalbergia hainanensis (Leguminosae), a vulnerably endangered legume endemic to China
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