scholarly journals A comparative analysis of the complete chloroplast genome sequences of four peanut botanical varieties

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5349 ◽  
Author(s):  
Juan Wang ◽  
Chunjuan Li ◽  
Caixia Yan ◽  
Xiaobo Zhao ◽  
Shihua Shan
Keyword(s):  
Comparative Analysis ◽  
High Throughput Sequencing ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Oilseed Crop ◽  
Nucleotide Polymorphisms ◽  
Genome Sequences ◽  
Genome Data ◽  
Cp Genome ◽  
Botanical Varieties

BackgroundArachis hypogaeaL. is an economically important oilseed crop worldwide comprising six botanical varieties. In this work, we characterized the chloroplast (cp) genome sequences of the four widely distributed peanut varieties.MethodsThe cp genome data of these four botanical varieties (var.hypogaea, var.hirsuta, var.fastigiata, and var.vulgaris) were obtained by next-generation sequencing. These high-throughput sequencing reads were then assembled, annotated, and comparatively analyzed.ResultsThe total cp genome lengths of the studiedA. hypogaeavarieties were 156,354 bp (var.hypogaea), 156,878 bp (var.hirsuta), 156,718 bp (var.fastigiata), and 156,399 bp (var.vulgaris). Comparative analysis of theses cp genome sequences revealed that their gene content, gene order, and GC content were highly conserved, with only a total of 46 single nucleotide polymorphisms and 26 insertions/deletions identified. Most of the variations were restricted to non-coding sequences, especially, thetrnI-GAU intron region was detected to be highly variable and will be useful for future evolutionary studies.DiscussionThe four cp genome sequences acquired here will provide valuable genetic resources for distinguishingA. hypogaeabotanical varieties and determining their evolutionary relationship.

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

2021 ◽  
Author(s):  
Hui Jiang ◽  
Jing Tian ◽  
Jiaxin Yang ◽  
Xiang Dong ◽  
Zhixiang Zhong ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Phylogenetic Relationships ◽  
Gene Annotation ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Phylogenetic Position ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Detailed Structural Analysis ◽  
Cp Genome

Abstract 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.

scholarly journals Complete Chloroplast Genome Sequence of Justicia flava: Genome Comparative Analysis and Phylogenetic Relationships among Acanthaceae

2019 ◽  
Vol 2019 ◽  
pp. 1-17 ◽  
Author(s):  
Samaila S. Yaradua ◽  
Dhafer A. Alzahrani ◽  
Enas J. Albokhary ◽  
Abidina Abba ◽  
Abubakar Bello
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Inverted Repeat ◽  
Gc Content ◽  
Single Copy ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Cp Genome

The complete chloroplast genome of J. flava, an endangered medicinal plant in Saudi Arabia, was sequenced and compared with cp genome of three Acanthaceae species to characterize the cp genome, identify SSRs, and also detect variation among the cp genomes of the sampled Acanthaceae. NOVOPlasty was used to assemble the complete chloroplast genome from the whole genome data. The cp genome of J. flava was 150, 888bp in length with GC content of 38.2%, and has a quadripartite structure; the genome harbors one pair of inverted repeat (IRa and IRb 25, 500bp each) separated by large single copy (LSC, 82, 995 bp) and small single copy (SSC, 16, 893 bp). There are 132 genes in the genome, which includes 80 protein coding genes, 30 tRNA, and 4 rRNA; 113 are unique while the remaining 19 are duplicated in IR regions. The repeat analysis indicates that the genome contained all types of repeats with palindromic occurring more frequently; the analysis also identified total number of 98 simple sequence repeats (SSR) of which majority are mononucleotides A/T and are found in the intergenic spacer. The comparative analysis with other cp genomes sampled indicated that the inverted repeat regions are conserved than the single copy regions and the noncoding regions show high rate of variation than the coding region. All the genomes have ndhF and ycf1 genes in the border junction of IRb and SSC. Sequence divergence analysis of the protein coding genes showed that seven genes (petB, atpF, psaI, rpl32, rpl16, ycf1, and clpP) are under positive selection. The phylogenetic analysis revealed that Justiceae is sister to Ruellieae. This study reported the first cp genome of the largest genus in Acanthaceae and provided resources for studying genetic diversity of J. flava as well as resolving phylogenetic relationships within the core Acanthaceae.

scholarly journals Construction of complete chloroplast genome of the endemic species Paphiopedilum delenatii Guillaumin (1924) of Vietnam

2020 ◽  
Vol 18 (1) ◽  
pp. 87-102
Author(s):  
Nguyen Thanh Diem ◽  
Le Thi Ly ◽  
Nguyen Huu Thuan Anh ◽  
Nguyen Thanh Cong ◽  
Vu Thi Huyen Trang
Keyword(s):  
Chloroplast Genome ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Single Copy ◽  
Complete Chloroplast Genome ◽  
Genome Data ◽  
A Cell ◽  
Chloroplast Genome Sequencing ◽  
Small Single Copy ◽  
Generation Sequencing

Chloroplasts and mitochondria are organelles that have their own genome in a cell. The chloroplast genome provides information on the evolutionary relationship and species identification, valuable markers for transgenic plants, and cloning plants, etc. The application of Next Generation Sequencing has improved the chloroplast genome sequencing. However, the assembly process of chloroplast genome is quite complicated due to the need of different complex bioinformatics tools, high configuration computer and laborous. Here we configured the process of assembling the chloroplast genome of Paphiopedilum delenatii. The assembled chloroplast genome was 160,955 bp in length, including a large and a small single copy region (LSC, SSC) separated by a pair of inverted repeats (IR). Total genes were 130 genes, GC content is 35.6%. Genome data was mapped and registered in GenBank under accession number MK463585. The optimal parameters for genome assembling were recommended. This study not only provided information for conservation of the Vietnam endemic Paphiopedilum delenatii species but also supported the genome assemble researches which could be applied on other subjects.

Characterization of the Complete Chloroplast Genome of Buddleja Lindleyana

2021 ◽  
Author(s):  
Shanshan Liu ◽  
Shiyin Feng ◽  
Yuying Huang ◽  
Wenli An ◽  
Zerui Yang ◽  
...  
Keyword(s):  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Future Research ◽  
Trna Genes ◽  
Similar Species ◽  
Protein Coding ◽  
Genome Data ◽  
Cp Genome ◽  
Genomic Resource

Abstract Background Buddleja lindleyana Fort., which belongs to the Loganiaceae with a distribution throughout the tropics, is widely used as an ornamental plant in China. Buddleja contains several morphologically similar species, which need to be identified by molecular identification. But there is little molecular research on the genus Buddleja. Objective Using molecular biology techniques to sequence and analyze the complete chloroplast (cp) genome of B. lindleyana Methods According to next-generation sequencing to sequence the genome data, a series of bioinformatics software were used to assembly and analysis the molecular structure of cp genome of B. lindleyana. Results The complete cp genome of B. lindleyana is a circular 154,487-bp-long molecule with a GC content of 38.1%. It has a familiar quadripartite structure, including a large single-copy region (LSC; 85,489 bp), a small single-copy region (SSC; 17,898bp) and a pair of inverted repeats (IRs; 25,550 bp). A total of 133 genes were identified in the genome, including 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 2 pseudogenes. Conclusions These results suggested that B. lindelyana cp genome could be used as a potential genomic resource to resolve the phylogenetic positions and relationships of Loganiaceae, and will offer valuable information for future research in the identification of Buddleja species and will conduce to genomic investigations of these species.

scholarly journals A comparative analysis of the complete chloroplast genomes of three Chrysanthemum boreale strains

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9448
Author(s):  
Swati Tyagi ◽  
Jae-A Jung ◽  
Jung Sun Kim ◽  
So Youn Won
Keyword(s):  
Phylogenetic Analysis ◽  
De Novo ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Nucleotide Polymorphisms ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Chrysanthemum Boreale

Background Chrysanthemum boreale Makino (Anthemideae, Asteraceae) is a plant of economic, ornamental and medicinal importance. We characterized and compared the chloroplast genomes of three C. boreale strains. These were collected from different geographic regions of Korea and varied in floral morphology. Methods The chloroplast genomes were obtained by next-generation sequencing techniques, assembled de novo, annotated, and compared with one another. Phylogenetic analysis placed them within the Anthemideae tribe. Results The sizes of the complete chloroplast genomes of the C. boreale strains were 151,012 bp (strain 121002), 151,098 bp (strain IT232531) and 151,010 bp (strain IT301358). Each genome contained 80 unique protein-coding genes, 4 rRNA genes and 29 tRNA genes. Comparative analyses revealed a high degree of conservation in the overall sequence, gene content, gene order and GC content among the strains. We identified 298 single nucleotide polymorphisms (SNPs) and 106 insertions/deletions (indels) in the chloroplast genomes. These variations were more abundant in non-coding regions than in coding regions. Long dispersed repeats and simple sequence repeats were present in both coding and noncoding regions, with greater frequency in the latter. Regardless of their location, these repeats can be used for molecular marker development. Phylogenetic analysis revealed the evolutionary relationship of the species in the Anthemideae tribe. The three complete chloroplast genomes will be valuable genetic resources for studying the population genetics and evolutionary relationships of Asteraceae species.

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