The chloroplasts genomic analyses of Rosa laevigata, R. rugosa and R. canina

Yin, Xiao; Liao, Baosheng; Guo, Shuai; Liang, Conglian; Pei, Jin; Xu, Jiang; Chen, Shilin

doi:10.1186/s13020-020-0298-x

Cited by 15 publications

(10 citation statements)

References 70 publications

(69 reference statements)

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“…The length of the LSC, SSC, and IRs varied in the range of 84,046–89,021 bp, 16,914–18,821 bp, and 23,902–25,914 bp, respectively. Chloroplast genome size variation among different species, or even within different individuals of the same species, which has been reported in other species, such as Camptotheca acuminata [ 48 , 49 ], Eucommia ulmoides [ 50 ], Rosa rugosa [ 51 – 53 ] and Calanthe davidii [ 54 ]. This, besides polyploidy of plant material, has been shown to be due to the expansion/contraction of IR [ 55 ].…”

Section: Discussionmentioning

confidence: 84%

Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences

et al. 2022

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Background Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the center of diversity in Africa. Previous studies on species of this genus have not obtained the complete chloroplast genomes, structures and variations. Additionally, the phylogenetic position of the genus in the Orchidaceae is still controversial and uncertain. Therefore, in this study, we sequenced the complete plastomes of six Kenya Polystachya species based on genome skimming, subjected them to comparative genomic analysis, and reconstructed the phylogenetic relationships with other Orchidaceae species. Results The results exhibited that the chloroplast genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The plastomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had an almost similar GC content of 36.9–37.0%. Gene annotation revealed 106–109 single-copy genes. In addition, 19 genes are duplicated in the inverted regions, and 16 genes each possessd one or more introns. Although no large structural variations were observed among the Polystachya plastomes, about 1 kb inversion was found in Polystachya modesta and all 11 ndh genes in the Polystachya plastomes were lost or pseudogenized. Comparative analysis of the overall sequence identity among six complete chloroplast genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR regions among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out SSRs and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis showed that the six Polystachya species formed a monophyletic clade and were more closely related to the tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 chloroplast genome sequences were generally consistent with previous studies and robust. Conclusions Our study is the initial report of the complete chloroplast genomes of the six Polystachya species, elucidates the structural characteristics of the chloroplast genome of Polystachya, and filters out highly variable sequences that can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the phylogenetic results strongly support that the genus of Polystachya is a part of the tribe Vandeae.

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Section: Discussionmentioning

confidence: 84%

Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences

et al. 2022

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“…The length of the LSC, SSC, and IRs varied in the range of 84,046-89,021 bp, 16,914-18,821 bp, and 23,902-25,914 bp, respectively. Chloroplast genome size variation among different species, or even within different individuals of the same species, which has been reported in other species, such as Camptotheca acuminate [48,49], Eucommia ulmoides [50], Rosa rugosa [51][52][53] and Calanthe davidii [54]. This, besides polyploidy of plant material, has been shown to be due to the expansion/contraction of IR [55].…”

Section: Discussionmentioning

confidence: 65%

“…Statistical analysis of the locations of all identi ed SSRs showed that the number of SSRs located in the LSC region, SSC region and IR regions were 44-52, 8-12 and 4-14, respectively. Furthermore, we found that these SSRs were mainly distributed in IGS (38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48)(49)(50)(51)(52)(53)(54), and some in the CDS region (9)(10)(11)(12) and introns (8)(9)(10)(11)(12). A/T (no C/G) is the only mononucleotide SSRs type in the six species (Figures 6A and 7), and the repeat units of the other ve SSRs were also mainly composed of A or T (Figures 6A and 7).…”

Section: Repeat Sequences Analysismentioning

confidence: 97%

Comparative And Phylogenetic Analyses of Six Kenya Polystachya (Orchidaceae) Species Based On The Complete Chloroplast Genome Sequences

Jiang

Tian

Yang

et al. 2021

Preprint

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Background: Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the centre of diversity in Africa. Chloroplast (cp) genomes of plants are highly conserved and can provide much more informative DNA sites and generate much better resolution for plant phylogenies. However, for Polystachya, the whole cp genome including its structure features are yet unknown and its phylogenetic placement of the genus within the Orchidaceae is still unclear.Results: In this study, the complete cp genomes of six Polystachya species were assembled based on genome skimming. We subjected them to comparative genomic analyses and reconstructed their phylogenetic relationships. The results exhibited that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had almost similar GC content of 36.9%-37.0%. Gene annotation revealed 113 unique genes. In additions, 19 genes are duplicated in the inverted regions, and 17 gene possessed intron. Comparative analysis of the overall sequence identity among six complete cp genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR region among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out specific SSR and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis suggested that the six Polystachya species formed a monophyletic clade and had more closely related to tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 cp genome sequences were generally consistent with previous studies and robust. Conclusions: Our study reported the complete cp genomes of the six Polystachya species, and provided detailed structural analysis and comparative analysis results, which can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the present results further demonstrate the phylogenetic position of Polystachya.

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“…Species diagnosis for most of the Kaempferia genus was conducted using the loci of psbA-trnH and petA-psbJ as DNA barcodes (Techaprasan et al, 2010). petA-psbJ can be used as a candidate fragment for DNA barcoding in phylogeny and species identification of other species, including those of the Rosa (Yin et al, 2020), Bupleurum (Xie et al, 2021), and Zingiber (Li et al, 2020c) genera, as well as the Papaveraceae (Liu et al, 2020) and Lauraceae (Jo et al, 2019) families. These hypervariable regions are suitable candidates for species identification and provide evolutionary information about Salix species.…”

Section: Comparative Genomic Analysismentioning

confidence: 99%

The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements

et al. 2022

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Salix floderusii is a rare alpine tree species in the Salix genus. Unfortunately, no extensive germplasm identification, molecular phylogeny, and chloroplast genomics of this plant have been conducted. We sequenced the chloroplast (cp) genome of S. floderusii for the first time using second-generation sequencing technology. The cp genome was 155,540 bp long, including a large single-copy region (LSC, 84,401 bp), a small single-copy region (SSC, 16,221 bp), and inverted repeat regions (IR, 54,918 bp). A total of 131 genes were identified, including 86 protein genes, 37 tRNA genes, and 8 rRNA genes. The S. floderusii cp genome contains 1 complement repeat, 24 forward repeats, 17 palindromic repeats, and 7 reverse repeats. Analysis of the IR borders showed that the IRa and IRb regions of S. floderusii and Salix caprea were shorter than those of Salix cinerea, which may affect plastome evolution. Furthermore, four highly variable regions were found, including the rpl22 coding region, psbM/trnD-GUC non-coding region, petA/psbJ non-coding region, and ycf1 coding region. These high variable regions can be used as candidate molecular markers and as a reference for identifying future Salix species. In addition, phylogenetic analysis indicated that the cp genome of S. floderusii is sister to Salix cupularis and belongs to the Subgenus Vetrix. Genes (Sf-trnI, Sf-PpsbA, aadA, Sf-TpsbA, Sf-trnA) obtained via cloning were inserted into the pBluescript II SK (+) to yield the cp expression vectors, which harbored the selectable marker gene aadA. The results of a spectinomycin resistance test indicated that the cp expression vector had been successfully constructed. Moreover, the aadA gene was efficiently expressed under the regulation of predicted regulatory elements. The present study provides a solid foundation for establishing subsequent S. floderusii cp transformation systems and developing strategies for the genetic improvement of S. floderusii.

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The chloroplasts genomic analyses of Rosa laevigata, R. rugosa and R. canina

Cited by 15 publications

References 70 publications

Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences

Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences

Comparative And Phylogenetic Analyses of Six Kenya Polystachya (Orchidaceae) Species Based On The Complete Chloroplast Genome Sequences

The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements

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