Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

Vu, Huyen-Trang; Tran, Ngan; Nguyen, Thanh-Diem; Vu, Quoc-Luan; Bui, My-Huyen; Le, Minh-Tri; Le, Ly

doi:10.3390/plants9010061

Cited by 25 publications

(22 citation statements)

References 82 publications

(113 reference statements)

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“…With the rise of the high-throughput sequencing and accurate assembly technology, chloroplast genomes are inexpensive and easy to obtain [ 31 ]. Phylogenomic studies using chloroplast genomes shed light on a more innovative and profound view than single or multiple genes in the systematic evolution [ 30 ].…”

Section: Discussionmentioning

confidence: 99%

Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification

Jiang

Miao

Wang

et al. 2020

Plants

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Although the medicinal properties of Coelogyne spp. have been previously studied, there is little genomic information providing a valuable tool for the plant taxonomy, conservation, and utilization of this genus. This study used the next-generation MiSeq sequencing platform to characterize the chloroplast (cp) genomes of Coelogyne fimbriata and Coelogyne ovalis. The Maximum Likelihood (ML) and Bayesian (BI) methods were employed to confirm the phylogenetic position of two Coelogyne species based on the whole chloroplast genome sequences. Additionally, we developed eight new primers based on the two cp genomes’ medium variable regions and evaluated the transferability to another 16 Coelogyne species. We constructed phylogenetic trees including 18 Coelogyne species and four outgroup species using the chloroplast fragments with the ML method. Our results showed that the cp genomes of C. fimbriata and C. ovalis contained a small single-copy region (18,839 and 18,851 bp, respectively) and a large single-copy region (87,606 and 87,759 bp, respectively), separated by two same-length inverted-repeat regions (26,675 bp in C. fimbriata and 26,715 bp C. ovalis, respectively). They all contained 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, revealing strong structure and gene content similarities. The phylogenetic analysis indicated a close relationship between the genera Coelogyne and Pleione. The newly developed primers revealed good transferability among the Coelogyne taxa and provided enough variable sites to distinguish C. fimbriata and C. ovalis. The two complete cp genomes and the eight new primers of Coelogyne provide new genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Coelogyne taxa.

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Section: Discussionmentioning

confidence: 99%

Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification

Jiang

Miao

Wang

et al. 2020

Plants

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“…There are short repeats (the length of the repeat unit often contains one to six nucleotides) and long repeats (the size of the repeat unit generally has 10-100 nucleotides) [41]. SSRs or microsatellites are short tandem repeats.…”

Section: Ssr and Long Repeats Identificationmentioning

confidence: 99%

The Chloroplast Genome of Carya illinoinensis: Genome Structure, Adaptive Evolution, and Phylogenetic Analysis

Lou

Chen

et al. 2020

Forests

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Research Highlights: For the first time, the complete chloroplast (cp) genome of Carya illinoinensis cv. ‘Pawnee’ was de novo assembled. Comprehensive analysis the cp genome of C. illinoinensis revealed potential cpDNA markers for intraspecies identification, genes involved in adaptation, and its phylogenetic position. Background and Objectives: C. illinoinensis is an economically important nut tree in the family Juglandaceae. Cp-derived markers are helpful for genetic research, but they still need to be developed in C. illinoinensis. Additionally, the adaptation and phylogenetic relationships of C. illinoinensis have not been revealed based on the complete cp genome. Materials and Methods: Chloroplast genomic DNA of C. illinoinensis cv. ‘Pawnee’ was extracted and subjected to Illumina sequencing. Results: The cp genome is 160,819 bp in size, exhibiting a typical quadripartite structure with a large single copy (LSC) of 90,022 bp, a small single copy (SSC) of 18,791 bp, and a pair of inverted repeats (IRA and IRB) regions of 26,003 bp each. The genome was predicted to encode 112 unique genes, including 79 protein-coding genes, 29 tRNAs, and four rRNAs, with 19 duplicates in the IR regions. In total, 213 SSRs and 44 long repeats were identified in the cp genome. A comparison of two different C. illinoinensis genotypes, ‘Pawnee’ and 87MX3-2.11, obtained 143 SNPs and 74 indels. The highly variable regions such as atpF, clpP, and ndhA genes, and matK-rps16, trnS-trnG, and trnT-psbD intergenic spacers might be helpful for future intraspecific identification. Positive selection was acting on the ccsA and rps12 cp genes based on the Ka/Ks ratios. Phylogenetic analysis indicated that C. illinoinensis forms a sister clade to Asian Carya species, represented by C. kweichowensis and Annamocarya sinensis. Conclusions: The genome information in our study will have significance for further research on the intraspecies identification and genetic improvement of C. illinoinensis.

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“…The Dracaena draco chloroplast genome (Figure 1) has a typical quadripartite structure that is characteristic and observed in many flowering plants [35,36,57]. It contains a pair of inverted repeat regions (IRa and IRb) that comprise 26,504 bp each.…”

Section: Genome Featuresmentioning

confidence: 99%

“…Chloroplast genome sequences have been successfully used to study the phylogeny of many different plant groups [35,36,40,57]. In this study, we were particularly interested in the position of D. draco within the genus Dracaena.…”

Section: Phylogenetic Inferencementioning

confidence: 99%

“…Next generation sequencing, especially in combination with advanced bioinformatic analysis, offers enormous opportunities and is becoming the new standard in biological research. Comparative analysis of complete chloroplast genomes (cp) not only allows advanced phylogenetic reconstruction [35,36], but also allows them to be used as barcode supercodes to distinguish and identify different taxa. This approach can be very useful especially in the study of closely related or recently divergent species [37].…”

Section: Introductionmentioning

confidence: 99%

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Complete Chloroplast Genome Sequence and Phylogenetic Inference of the Canary Islands Dragon Tree (Dracaena draco L.)

Celiński

Kijak

Wiland-Szymańska

2020

Forests

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Dracaena draco, which belongs to the genus Dracaena, is an endemic succulent of the Canary Islands. Although it is one of the most popular and widely grown ornamental plants in the world, little is known about its genomic variability. Next generation sequencing, especially in combination with advanced bioinformatics analysis, is a new standard in taxonomic and phylogenetic research. Therefore, in this study, the complete D. draco chloroplast genome (cp) was sequenced and analyzed in order to provide new genomic information and to elucidate phylogenetic relationships, particularly within the genus Dracaena. The D. draco chloroplast genome is 155,422 bp, total guanine-cytosine (GC) content is 37.6%, and it has a typical quadripartite plastid genome structure with four separate regions, including one large single copy region of 83,942 bp length and one small single copy region of 18,472 bp length, separated by two inverted repeat regions, each 26,504 bp in length. One hundred and thirty-two genes were identified, 86 of which are protein-coding genes, 38 are transfer RNAs, and eight are ribosomal RNAs. Seventy-seven simple sequence repeats were also detected. Comparative analysis of the sequence data of various members of Asparagales revealed mutational hotspots potentially useful for their genetic identification. Phylogenetic inference based on 16 complete chloroplast genomes of Asparagales strongly suggested that Dracaena species form one monophyletic group, and that close relationships exist between D. draco, D. cochinchinensis and D. cambodiana. This study provides new and valuable data for further taxonomic, evolutionary and phylogenetic studies within the Dracaena genus.

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Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

Cited by 25 publications

References 82 publications

Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification

Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification

The Chloroplast Genome of Carya illinoinensis: Genome Structure, Adaptive Evolution, and Phylogenetic Analysis

Complete Chloroplast Genome Sequence and Phylogenetic Inference of the Canary Islands Dragon Tree (Dracaena draco L.)

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