Cp Genome Research Articles

Complete chloroplast genome of a semi-mangrove plant Hibiscus tiliaceus (Malvaceae)

Hibiscus tiliaceus is a semi-mangrove species that is widely distributed in tropical and subtropical coastal areas around the world. Here, the complete chloroplast (cp) genome sequence of H. tiliaceus was assembled and characterized. The cp genome was 161,748 bp in length, consisting of a large single copy (LSC) region of 89,190 bp and a small single copy (SSC) region of 19,616 bp, which were separated by a pair of 26,471 bp inverted repeat (IR) regions. The overall GC content was 36.88%. A total of 131 genes, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes were identified. Phylogenetic tree reconstructed by 15 complete cp genomes revealed that H. tiliaceus was sister to the congeneric species H. cannabinus.

Complete chloroplast genome characterization and phylogenetic analysis of Anredera cordifolia (Tenore) Steenis (Basellaceae)

Madeira vine (Anredera cordifolia (Tenore) Steenis) is a widely distributed liana that is also used as a medicinal plant. In this study, the complete chloroplast (cp) genome of this species was sequenced and annotated. The complete cp genome sequence of A. cordifolia is 156,662 base pairs in length, and the GC content is 36.84%. The genome contains 123 functional genes, including 83 protein-coding genes, 36 tRNA genes, and four rRNA genes. The phylogenetic tree showed that A. cordifolia was closely related to Cistanthe longiscapa, the species of family Montiaceae in Caryophyllales. This study provides genetic information for future studies on phylogenetic evaluation and utilization of A. cordifolia.

Characterization of the complete chloroplast genome of Corydalis bungeana Turcz

Corydalis bungeana Turcz. is a perennial herb belonging to the family Papaveraceae. Its chloroplast genome was sequenced and characterized. The cp genome of C. bungeana is 167,629 bp long with a GC content of 36.52%. A total of 144 genes were identified in this cp genome, including 79 protein-coding genes, 31 tRNAs and four rRNAs. A phylogenetic tree based on the complete nucleic acid sequence indicated that C. bungeana was classified into Corydaleae and had a close relationship with Lamprocapnos spectabilis.

The complete chloroplast genome of Vicia cracca L

Vicia cracca L. is a widespread perennial herb in the Northern Hemisphere. It has purple flowers and leave tendrils for climbing on neighboring vegetation. For knowing the chloroplast genome, a sample’s genomic was extracted, sequenced, assembled and annotated. The chloroplast genome of this plant is a circular form of 126,272bp in length with IR loss. After annotation, a total of 108 genes were predicted, of which, 75 encode proteins, 3 rRNA, 30 tRNA. The evolutionary history, inferred using Maximum Likelihood method, indicates that V. cracca was grouped within Vicia in Fabaceae. The complete cp genome will be helpful for further studies on molecular biology, evolution, population genetics, taxonomy or resources protection.

Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement.

Acanthochlamys P.C. Kao is a Chinese endemic monotypic genus, whereas Xerophyta Juss. is a genus endemic to Africa mainland, Arabian Peninsula and Madagascar with ca.70 species. In this recent study, the complete chloroplast genome of Acanthochlamys bracteata was sequenced and its genome structure compared with two African Xerophyta species (Xerophyta spekei and Xerophyta viscosa) present in the NCBI database. The genomes showed a quadripartite structure with their sizes ranging from 153,843 bp to 155,498 bp, having large single-copy (LSC) and small single-copy (SSC) regions divided by a pair of inverted repeats (IR regions). The total number of genes found in A. bracteata, X. spekei and X. viscosa cp genomes are 129, 130, and 132, respectively. About 50, 29, 28 palindromic, forward and reverse repeats and 90, 59, 53 simple sequence repeats (SSRs) were found in the A. bracteata, X. spekei, and X. viscosa cp genome, respectively. Nucleotide diversity analysis in all species was 0.03501, Ka/Ks ratio average score was calculated to be 0.26, and intergeneric K2P value within the Order Pandanales was averaged to be 0.0831. Genomic characterization was undertaken by comparing the genomes of the three species of Velloziaceae and it revealed that the coding regions were more conserved than the non-coding regions. However, key variations were noted mostly at the junctions of IRs/SSC regions. Phylogenetic analysis suggests that A. bracteata species has a closer genetic relationship to the genus Xerophyta. The present study reveals the complete chloroplast genome of A. bracteata and gives a genomic comparative analysis with the African species of Xerophyta. Thus, can be useful in developing DNA markers for use in the study of genetic variabilities and evolutionary studies in Velloziaceae.

The complete chloroplast genome sequence of Machilus robusta W. W. Smith (Lauraceae) from Jiangxi Province, China

Machilus robusta W. W. Smith is an evergreen plant distributed in the Yangtze River Basin and the south regions of China. Here we analyzed the complete chloroplast (cp) genome sequence of M. robusta to determine its structure and evolutionary relationship to other Lauraceae. The cp genome is 152,737 bp in length and has an overall GC content of 39.2% The genome includes a large single-copy (LSC) region of 93,706 bp and a small single-copy (SSC) region of 18,885 bp, and these are separated by a pair of inverted repeats (IRs) of 20,073 bp. The cp genome contains 128 genes, including 83 protein-coding, 37 tRNAs, and 8 rRNAs. Phylogenetic analysis based on complete cp genome sequences fully resolved M. robusta in a clade with M. balansae. This work provides new molecular data for evolutionary studies of the Lauraceae.

The complete chloroplast genome of Phoebe minutiflora (Lauraceae)

Phoebe minutiflora H. W. Li, is a member of the Lauraceae family, while its generic relationship has been long-term controversial. The complete chloroplast (cp) genome of P. minutiflora was first reported in this paper. The cp genome was 152,654 bp in length with four typical quadripartite structures, which was consisted of a large single-copy (LSC) region of 93,697 bp, a small single-copy (SSC) region of 18,809 bp, and two inverted repeats (IRs) of 20,074 bp. In addition, there were a total of 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes. The phylogenetic analysis indicated that P. minutiflora should be placed into Machilus.

The complete chloroplast genome sequence of Ficus formosana Maxim (Moraceae) from Guangzhou, China

Ficus formosana Maxim is an economically valuable plant that is traditionally used in Chinese medicine. Here, we assembled the complete chloroplast (cp) genome of F. formosana using Illumina high-throughput sequencing technology. The cp genome size is 160,606 bp, with 35.90% GC content, including a large single copy region (LSC) of 88,668 bp, a small single copy region (SSC) of 20,140 bp and a pair of inverted repeat regions (IRs) of 25,899 bp. It encodes 86 protein-coding, 37 tRNA and 8 rRNA genes. Phylogenetic analysis fully resolved F. formosana on a branch with Ficus erecta within the genus Ficus. The complete cp genome sequence of F. formosana will provide valuable information for species identification and phylogenetic evolution.

The first complete chloroplast genome of Haymondia wallichii (Fabaceae) and its phylogenetic analysis

Haymondia wallichii DC. was a scandent shrub. In this study, we sequenced the complete chloroplast (cp) genome of H. wallichii to investigate its phylogenetic relationship in Fabaceae. The total length of the cp genome was 153,668 bp, consisted of a large single copy (LSC) region of 84,310 bp, a small single copy (SSC) region of 17,918 bp, and a pair of inverted repeat regions (IRs) of 25,720 bp. The genome contained 132 genes, namely 37 tRNA genes, 87 protein-coding genes, and 8 rRNA genes. The overall GC content was 35.4%. The phylogenetic analysis indicated H. wallichii was closely related to Pueraria montana var. thomsonii and Pueraria montana var. lobata.

The complete chloroplast genome of Mucuna sempervirens (Fabaceae: Papilionoideae)

The complete chloroplast genome of Mucuna sempervirens reported herein was a circular DNA molecule of 154,542 bp in length. The genome had a typical quadripartite structure, consisting of a pair of inverted repeats (IRa and IRb: 24,836 bp) separated by a large single-copy region (LSC: 67,996 bp) and a small single-copy region (SSC: 18,363 bp). The overall GC content of the genome was 35.1%. The cp genome encoded a set of 128 genes, containing 82 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that M. sempervirens was sister to M. macrocarpa. These findings may provide useful information to the phylogeny of the genus Mucuna.

The complete chloroplast genome sequence of Potentilla glabra Lodd

Potentilla glabra Lodd is an important traditional Chinese medicine, which is widely distributed in many areas of China. It has a variety of pharmacological activities and has been drunk as a tea for a long time. Therefore, it has great economic, research, and social value. However, no plastid genome has been reported to date. Here, we report species of this genus complete chloroplast genome of Potentilla glabra Lodd. The chloroplast genome of Potentilla glabra Lodd is found to be 152,900 bp in length with 37.24% GC contents. The cp genome sequences contained 130 genes, including 84 mRNA genes, 37 tRNA, eight rRNA genes, and one pseudogenes, respectively. A phylogenetic tree reconstructed by 42 chloroplast genomes reveals that Potentilla glabra Lodd is most related with Potentilla parvifolia. The complete chloroplast genome of these plants will be benefit for studies on the general characteristics and evolution of the Potentilla family genome.

Phylogenomic Analyses of Hepatica Species and Comparative Analyses Within Tribe Anemoneae (Ranunculaceae).

Hepatica is a small genus of Ranunculaceae with medicinal and horticultural value. We characterized nine complete chloroplast (cp) genomes of Hepatica, which ranged from 159,549 to 161,081 bp in length and had a typical quadripartite structure with a large single-copy region (LSC; 80,270–81,249 bp), a small single-copy region (SSC; 17,029–17,838 bp), and two copies of inverted repeat (IR; 31,008–31,100 bp). The cp genomes of Hepatica possess 76 protein-coding genes (PCGs), 29 tRNAs, and four rRNA genes. Comparative analyses revealed a conserved ca. 5-kb IR expansion in Hepatica and other Anemoneae; moreover, multiple inversion events occurred in Hepatica and its relatives. Analyses of selection pressure (dN/dS) showed that most of the PCGs are highly conserved except for rpl20 and rpl22 in Hepatica falconeri, Hepatica americana, and Hepatica acutiloba. Two genes (rps16 and infA) were identified as pseudogenes in Hepatica. In contrast, rpl32 gene was completely lost. The phylogenetic analyses based on 76 PCGs resolved the phylogeny of Hepatica and its related genera. Non-monophyly of Anemone s.l. indicates that Hepatica should be reclassified as an independent genus. In addition, Hepatica nobilis var. japonica is not closely related to H. nobilis.

The complete chloroplast genome of a purple Ethiopian rape (Brassica carinata: Brassicaceae) from Guizhou Province, China and its phylogenetic analysis

Brassica carinata A. Braun (Ethiopian rape), which was derived from the interspecific hybridization between B. nigra and B. oleracea, is used as both an oilseed and a leafy vegetable. The complete chloroplast (cp) genome of a purple B. carinata was obtained. This cp genome has a typical quadripartite structure and is 153,641 bp in length. The GC content of the cp genome is 36.39%. A total of 113 genes were predicted on this cp genome, including 79 protein coding, 4 rRNA, and 30 tRNA genes. Among these genes, 18 genes were duplicated (7 tRNAs, 4 rRNAs, and 7 protein coding genes). Sixty-eight SSR loci, including 11 compound SSRs, were identified in this cp genome by MISA. The phylogenetic tree analysis fully resolved B. carinata in a clade with B. nigra. This study provides important information for future evolution, genetic and molecular biology studies of B. carinata.

The complete chloroplast genome sequence of Duranta erecta (Verbenaceae)

In this study, the complete chloroplast (cp) genome of Duranta erecta was assembled using Illumina sequencing data. The complete cp genome is 149,869 bp in length, including a pair of invert repeats (IRA and IRB) regions of 22,839 bp, large single-copy (LSC) region of 86,201 bp, and small single-copy (SSC) region of 17,990 bp. The G + C content of this cp genome was 38.26%. A total of 128 genes were predicted in the genome, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis confirmed the phylogenetic relationship between D. erecta and other representative species of Verbenaceae.

The complete chloroplast genome of Chimonobambusa hejiangensis

Chimonobambusa hejiangensis is of the unique edible bamboo specie of high quality in China. We studied the complete chloroplast(cp) genome of C. purpurea in this study. The cp genome of C. hejiangensis (GenBank accession: MW186792) was 138,911 bp in length, including a large single-copy (LSC) region of 82,498 bp, a small single-copy (SSC) region of 12,743 bp and a pair of inverted repeated (IR) regions of 21,835 bp. The genome contained 133 genes, including 86 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Based on 39 cp genomes, we used the phylogenetic analysis to build phylogenetic tree, indicating that C. hejiangensis is closely related to C. tumidissinoda. Also, the phylogenetic relationship of lineages might be (Hsuehochloa + (((Shibataea clade + Arundinaria clade) + Indocalamus wilsonii) + ((Bergbambos + Indocalamus) + (((African alpine bamboos + Gaoligongshania) + (Chimonocalamus + Kuruna))+(Thamnocalamus + Phyllostachys clade))))). It could be devoted to phylogenetic analysis of Arundinarieae.

The complete chloroplast genome sequence of Crassocephalum crepidioides (Benth.) S. Moore. (Asteraceae)

The complete chloroplast (cp) genome of Crassocephalum crepidioides was sequenced and assembled for the first time. In this study, the total genome size is 150,596 bp in length and demonstrates a typical quadripartite structure containing a large single copy (LSC, 82,575 bp) and a small single copy (SSC, 18,293 bp), separated by a pair of inverted repeats (IRa, IRb) of 24,864 bp. The G + C content of this cp genome was 37.21%. Gene annotation analysis identified 130 genes including 85 protein-coding genes, 37 transfer RNA, and 8 ribosomal RNA genes. The maximum-likelihood phylogenetic analysis result showed that C. crepidioides was closely related to Nannoglottis ravida in the phylogenetic relationship.

Complete chloroplast genome of novel Adinandra megaphylla Hu species: molecular structure, comparative and phylogenetic analysis

Adinandra megaphylla Hu is a medicinal plant belonging to the Adinandra genus, which is well-known for its potential health benefits due to its bioactive compounds. This study aimed to assemble and annotate the chloroplast genome of A. megaphylla as well as compare it with previously published cp genomes within the Adinandra genus. The chloroplast genome was reconstructed using de novo and reference-based assembly of paired-end reads generated by long-read sequencing of total genomic DNA. The size of the chloroplast genome was 156,298 bp, comprised a large single-copy (LSC) region of 85,688 bp, a small single-copy (SSC) region of 18,424 bp, and a pair of inverted repeats (IRa and IRb) of 26,093 bp each; and a total of 51 SSRs and 48 repeat structures were detected. The chloroplast genome includes a total of 131 functional genes, containing 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The A. megaphylla chloroplast genome indicated that gene content and structure are highly conserved. The phylogenetic reconstruction using complete cp sequences, matK and trnL genes from Pentaphylacaceae species exhibited a genetic relationship. Among them, matK sequence is a better candidate for phylogenetic resolution. This study is the first report for the chloroplast genome of the A. megaphylla.

The complete chloroplast genome of ‘Yulinglong’ (Narcissus tazetta var. chinensis) with double-petaled in southeast of China

In this study, the complete chloroplast (cp) genome of Narcissus tazetta var. chinensis cv ‘Yulinglong’ was sequenced and assembled by next-generation sequencing. The complete cp genome is 159,376 in length and contained 137 genes, consisting of 91 protein-coding genes, eight ribosomal RNA genes, and 38 transfer RNA genes. Phylogenetic analyses based on chloroplast genomes highly supported that ‘Yulinglong’ was evolutionarily close to Narcissus tazetta subsp.chinensis, which may provide more desirable information for the phylogenetic relationship between Narcissus tazetta var. chinensis and its relative species.

English

Due to outstanding characteristics such as stress resistance and high biomass production, Elymus sibiricus (StH genomes) and E. nutans (StHY genomes) are regarded as ecologically important perennial bunchgrass species belonging to Elymus genus of tribe Triticeae (Poaceae), which were widely used to promote the restoration of degraded grassland in the eastern Tibetan Plateau. In this study, the complete chloroplast (cp) genome of E. sibiricus and E. nutans were sequenced and annotated with de novo analysis, to clarify their inter-species variation and their evolutionary relationships with relative species. The result showed that both two whole cp genomes shared a typical quadripartite structure, the cp genome length of E. sibiricus and E. nutans were 135,075 bp and 135,060 bp, respectively. Three genes tRNA-CGA, tRNA-CGU, and tRNA-CGU were unique in E. sibiricus while the gene ycf1 (hypothetical chloroplast reading frame no. 1) was only found in E. nutans. The identification of hotspot regions (tRNA-GUC~psbM, tRNA-UAA~ndhJ, rbcL~psaI, rpl33~rps18) between the two cp genomes would be pertinent to the development of barcode marker of these two Elymus species. Comparative cp genome analysis and phylogenetic relationships further confirmed that Pseudoroegneria were putative matrilineal donors of St genome of Elymus species at plastome level. Whole cp genomes could be used as an effective barcode for species identification or for developing specific markers, which is essential useful for the evolutionary history and conservation of Elymus species. © 2021 Friends Science Publishers

English

Due to outstanding characteristics such as stress resistance and high biomass production, Elymus sibiricus (StH genomes) and E. nutans (StHY genomes) are regarded as ecologically important perennial bunchgrass species belonging to Elymus genus of tribe Triticeae (Poaceae), which were widely used to promote the restoration of degraded grassland in the eastern Tibetan Plateau. In this study, the complete chloroplast (cp) genome of E. sibiricus and E. nutans were sequenced and annotated with de novo analysis, to clarify their inter-species variation and their evolutionary relationships with relative species. The result showed that both two whole cp genomes shared a typical quadripartite structure, the cp genome length of E. sibiricus and E. nutans were 135,075 bp and 135,060 bp, respectively. Three genes tRNA-CGA, tRNA-CGU, and tRNA-CGU were unique in E. sibiricus while the gene ycf1 (hypothetical chloroplast reading frame no. 1) was only found in E. nutans. The identification of hotspot regions (tRNA-GUC~psbM, tRNA-UAA~ndhJ, rbcL~psaI, rpl33~rps18) between the two cp genomes would be pertinent to the development of barcode marker of these two Elymus species. Comparative cp genome analysis and phylogenetic relationships further confirmed that Pseudoroegneria were putative matrilineal donors of St genome of Elymus species at plastome level. Whole cp genomes could be used as an effective barcode for species identification or for developing specific markers, which is essential useful for the evolutionary history and conservation of Elymus species. © 2021 Friends Science Publishers