The Complete Chloroplast Genome Sequences of&lt;em&gt; Fritillaria ussuriensis&lt;/em&gt; Maxim. and &lt;em&gt;Fritillaria cirrhosa&lt;/em&gt; D. Don, and Comparative Analysis with Other&lt;em&gt; Fritillaria&lt;/em&gt; Species

Park, Inkyu; Kim, Wook-Jin; Yeo, Sang-Min; Choi, Goya; Kang, Young Min; Piao, Renzhe; Moon, Byeong-Cheol

doi:10.20944/preprints201703.0139.v1

2017

DOI: 10.20944/preprints201703.0139.v1

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The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species

Inkyu Park¹,

Wook-Jin Kim²,

Sang-Min Yeo³

et al.

Abstract: Abstract:The genus Fritillaria belongs to the widely distributed family Liliaceae. The bulbs of Fritillaria ussuriensis and Fritillaria cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species is therefore required. Here, we report the complete chloroplast (cp) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria cp genomes were 151,524 and 151,083 bp in le… Show more

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Cited by 19 publications

References 48 publications

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Complete chloroplast genome sequences of Dipterygium glaucum and Cleome chrysantha and other Cleomaceae Species, comparative analysis and phylogenetic relationships

Alzahrani

Albokhari

Yaradua

et al. 2021

Saudi Journal of Biological Sciences

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This current study presents, for the first time, the complete chloroplast genome of two Cleomaceae species: Dipterygium glaucum and Cleome chrysantha in order to evaluate the evolutionary relationship. The cp genome is 158,576 bp in length with 35.74% GC content in D. glaucum and 158,111 bp with 35.96% GC in C. chrysantha . Inverted repeats IR 26,209 bp, 26,251 bp each, LSC of 87,738 bp, 87,184 bp and SSC of 18,420 bp, 18,425 bp respectively. There are 136 genes in the genome, which includes 80 protein coding genes, 31 tRNA genes and four rRNA genes were observed in both chloroplast genomes. 117 genes are unique while the remaining 19 genes are duplicated in IR regions. The analysis of repeats shows that the cp genome includes all types of repeats with more frequent occurrences of palindromic; Also, this analysis indicates that the total number of simple sequence repeats (SSR) were 323 in D. glaucum , and 313 in C. chrysantha , of which the majority of the SSRs in these plastid genomes were mononucleotide repeats A/T which are located in the intergenic spacer. Moreover, the comparative analysis of the four cp sequences revealed four hotspot genes ( atpF, rpoC2, rps19 , and ycf1 ), these variable regions could be used as molecular makers for the species authentication as well as resources for inferring phylogenetic relationships of the species. All the relationships in the phylogenetic tree are with high support, this indicate that the complete chloroplast genome is a useful data for inferring phylogenetic relationship within the Cleomaceae and other families. The simple sequence repeats identified will be useful for identification, genetic diversity, and other evolutionary studies of the species. This study reported the first cp genome of the genus Dipterygium and Cleome . The finding of this study will be beneficial for biological disciplines such as evolutionary and genetic diversity studies of the species within the core Cleomaceae.

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Complete chloroplast genome sequences of Dipterygium glaucum and Cleome chrysantha and other Cleomaceae Species, comparative analysis and phylogenetic relationships

Alzahrani

Albokhari

Yaradua

et al. 2021

Saudi Journal of Biological Sciences

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Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae

et al. 2020

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Background: The plastome of medicinal and endangered species in Kingdom of Saudi Arabia, Barleria prionitis was sequenced. The plastome was compared with that of seven Acanthoideae species in order to describe the plastome, spot the microsatellite, assess the dissimilarities within the sampled plastomes and to infer their phylogenetic relationships. Results: The plastome of B. prionitis was 152,217 bp in length with Guanine-Cytosine and Adenine-Thymine content of 38.3 and 61.7% respectively. It is circular and quadripartite in structure and constitute of a large single copy (LSC, 83, 772 bp), small single copy (SSC, 17, 803 bp) and a pair of inverted repeat (IRa and IRb 25, 321 bp each). 131 genes were identified in the plastome out of which 113 are unique and 18 were repeated in IR region. The genome consists of 4 rRNA, 30 tRNA and 80 protein-coding genes. The analysis of long repeat showed all types of repeats were present in the plastome and palindromic has the highest frequency. A total number of 98 SSR were also identified of which mostly were mononucleotide Adenine-Thymine and are located at the non coding regions. Comparative genomic analysis among the plastomes revealed that the pair of the inverted repeat is more conserved than the single copy region. In addition high variation is observed in the intergenic spacer region than the coding region. The genes, ycf1and ndhF and are located at the border junction of the small single copy region and IRb region of all the plastome. The analysis of sequence divergence in the protein coding genes indicates that the following genes undergo positive selection (atpF, petD, psbZ, rpl20, petB, rpl16, rps16, rpoC, rps7, rpl32 and ycf3). Phylogenetic analysis indicated sister relationship between Ruellieae and Justcieae. In addition, Barleria, Justicia and Ruellia are paraphyletic, suggesting that Justiceae, Ruellieae, Andrographideae and Barlerieae should be treated as tribes. Conclusions: This study sequenced and assembled the first plastome of the taxon Barleria and reported the basics resources for evolutionary studies of B. prionitis and tools for phylogenetic relationship studies within the core Acanthaceae.

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Chloroplast Genome of Salvia Sect. Drymosphace: Comparative and Phylogenetic Analysis

Geng

Xiang

et al. 2022

Diversity

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Sect. Drymosphace is one of eight sections of Salvia subg. Glutinaria and includes 13 species and one dubious species that hold great economic value. Although the section is well supported, interspecific relationships remain unresolved. Moreover, most of this section’s plastome information remains unknown. In this study, we sequenced and assembled eight sect. Drymosphace plastomes and conducted comparative analyses within this section. The length of plastid genome sequences ranged from 151,330 bp to 151,614 bp, with 80 protein-coding, 30 tRNA, and four rRNA genes being annotated. The plastomes were found to be as conservative as other Lamiaceae species, showing high consistency and similarity in terms of gene content, order, and structure. Within the sect. Drymosphace, single-copy regions were more variable than IR regions, and the intergenic regions were more variable than the coding regions; nine hypervariable regions were detected, and some of them may be useful for the phylogenetic analysis of Salvia. The topologies inferred from all of the data sets indicated that sect. Drymosphace was monophyletic and that S. honania was sister to S. meiliensis. Compared to previous studies involving more sect. Drymosphace species, phylogenomic analyses can improve the phylogenetic resolution considerably.

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The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

Cited by 19 publications

References 48 publications

Complete chloroplast genome sequences of Dipterygium glaucum and Cleome chrysantha and other Cleomaceae Species, comparative analysis and phylogenetic relationships

Complete chloroplast genome sequences of Dipterygium glaucum and Cleome chrysantha and other Cleomaceae Species, comparative analysis and phylogenetic relationships

Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae

Chloroplast Genome of Salvia Sect. Drymosphace: Comparative and Phylogenetic Analysis

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