Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus

We sequenced and analyzed the complete chloroplast genome of Aster tataricus (family Asteraceae), a Chinese herb used medicinally to relieve coughs and reduce sputum. The A. tataricus chloroplast genome was 152,992 bp in size, and harbored a pair of inverted repeat regions (IRa and IRb, each 24,850 bp) divided into a large single-copy (LSC, 84,698 bp) and a small single-copy (SSC, 18,250 bp) region. Our annotation revealed that the A. tataricus chloroplast genome contained 115 genes, including 81 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. In addition, 70 simple sequence repeats (SSRs) were detected in the A. tataricus chloroplast genome, including mononucleotides (36), dinucleotides (1), trinucleotides (23), tetranucleotides (1), pentanucleotides (8), and hexanucleotides (1). Comparative chloroplast genome analysis of three Aster species indicated that a higher similarity was preserved in the IR regions than in the LSC and SSC regions, and that the differences in the degree of preservation were slighter between A. tataricus and A. altaicus than between A. tataricus and A. spathulifolius. Phylogenetic analysis revealed that A. tataricus was more closely related to A. altaicus than to A. spathulifolius. Our findings offer valuable information for future research on Aster species identification and selective breeding.

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Complete chloroplast genome sequence of a vegetative Bermudagrass cultivar Tifeagle (Cynodon dactylon × Cynodon transvaalensis)

Bangladesh Journal of Botany ◽

10.3329/bjb.v48i4.49056 ◽

2019 ◽

Vol 48 (4) ◽

pp. 1083-1089

Author(s):

Yancai Shi ◽

Shaofeng Jiang ◽

Shilian Huang

Keyword(s):

Chloroplast Genome ◽

Cynodon Dactylon ◽

Single Copy ◽

Rrna Genes ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Chloroplast Genome Sequence ◽

Common Bermudagrass ◽

Trampling Tolerance ◽

Small Single Copy

Hybrid (Cynodonn dactylon × C. transvaalensis) is a widely distributed turfgrass and shows a great value of environment, horticulture and economic. Though, the chloroplast genome of C. dactylon has been reported, it might be helpful finding reasons that triploid bermudagrass shows a better drought and trampling tolerance than common bermudagrass through comparing chloroplast genome analysis. The present results showed the complete chloroplast genome of the C. dactylon × C. transvaalensis is 134655 bp in length. The tetramerous genome contained a large single copy (LSC) region (79,998 bp), a small single copy (SSC) region (12,517 bp), and a pair of inverted repeat (IR) regions (42,140 bp). In the chloroplast genome, 116 genes were predicted, including 83 protein-coding, 29 tRNA and 4 rRNA genes. Furthermore, a total of 80 repeat sequences were identified. Only 0.23% intergenicnon-collinear sequences were found between the chloroplast genome of Cynodon dactylon × C. transvaalensis and Cynodon dactylon.

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The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae - Caesalpinioideae): comparative analysis with related Mimosoid species

Scientific Reports ◽

10.1038/s41598-019-50620-3 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Ueric José Borges de Souza ◽

Rhewter Nunes ◽

Cíntia Pelegrineti Targueta ◽

José Alexandre Felizola Diniz-Filho ◽

Mariana Pires de Campos Telles

Keyword(s):

Chloroplast Genome ◽

De Novo ◽

Phylogenetic Reconstruction ◽

Single Copy ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Coding Regions ◽

Phylogenetic Studies ◽

Rna Genes ◽

Small Single Copy

Abstract Stryphnodendron adstringens is a medicinal plant belonging to the Leguminosae family, and it is commonly found in the southeastern savannas, endemic to the Cerrado biome. The goal of this study was to assemble and annotate the chloroplast genome of S. adstringens and to compare it with previously known genomes of the mimosoid clade within Leguminosae. The chloroplast genome was reconstructed using de novo and referenced-based assembly of paired-end reads generated by shotgun sequencing of total genomic DNA. The size of the S. adstringens chloroplast genome was 162,169 bp. This genome included a large single-copy (LSC) region of 91,045 bp, a small single-copy (SSC) region of 19,014 bp and a pair of inverted repeats (IRa and IRb) of 26,055 bp each. The S. adstringens chloroplast genome contains a total of 111 functional genes, including 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. A total of 137 SSRs and 42 repeat structures were identified in S. adstringens chloroplast genome, with the highest proportion in the LSC region. A comparison of the S. adstringens chloroplast genome with those from other mimosoid species indicated that gene content and synteny are highly conserved in the clade. The phylogenetic reconstruction using 73 conserved coding-protein genes from 19 Leguminosae species was supported to be paraphyletic. Furthermore, the noncoding and coding regions with high nucleotide diversity may supply valuable markers for molecular evolutionary and phylogenetic studies at different taxonomic levels in this group.

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Complete Chloroplast Genome Sequence and Comparative and Phylogenetic Analyses of the Cultivated Cyperus esculentus

Diversity ◽

10.3390/d13090405 ◽

2021 ◽

Vol 13 (9) ◽

pp. 405

Author(s):

Wei Ren ◽

Dongquan Guo ◽

Guojie Xing ◽

Chunming Yang ◽

Yuanyu Zhang ◽

...

Keyword(s):

Chloroplast Genome ◽

Genome Sequence ◽

Inverted Repeat ◽

Single Copy ◽

Cyperus Esculentus ◽

Crop Species ◽

Complete Chloroplast Genome ◽

Chloroplast Genome Sequence ◽

Rna Genes ◽

Small Single Copy

Cyperus esculentus produces large amounts of oil as one of the main oil storage reserves in underground tubers, making this crop species not only a promising resource for edible oil and biofuel in food and chemical industry, but also a model system for studying oil accumulation in non-seed tissues. In this study, we determined the chloroplast genome sequence of the cultivated C. esculentus (var. sativus Boeckeler). The results showed that the complete chloroplast genome of C. esculentus was 186,255 bp in size, and possessed a typical quadripartite structure containing one large single copy (100,940 bp) region, one small single copy (10,439 bp) region, and a pair of inverted repeat regions of 37,438 bp in size. Sequence analyses indicated that the chloroplast genome encodes 141 genes, including 93 protein-coding genes, 40 transfer RNA genes, and 8 ribosomal RNA genes. We also identified 396 simple-sequence repeats and 49 long repeats, including 15 forward repeats and 34 palindromes within the chloroplast genome of C. esculentus. Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with those of the other four Cyperus species indicated that both the large single copy and inverted repeat regions were more divergent than the small single copy region, with the highest variation found in the inverted repeat regions. In the phylogenetic trees based on the complete chloroplast genomes of 13 species, all five Cyperus species within the Cyperaceae formed a clade, and C. esculentus was evolutionarily more related to C. rotundus than to the other three Cyperus species. In summary, the chloroplast genome sequence of the cultivated C. esculentus provides a valuable genomic resource for species identification, evolution, and comparative genomic research on this crop species and other Cyperus species in the Cyperaceae family.

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The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

Agronomy ◽

10.3390/agronomy10091405 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1405

Author(s):

Gurusamy Raman ◽

SeonJoo Park

Keyword(s):

Chloroplast Genome ◽

Genome Sequence ◽

Gene Evolution ◽

Single Copy ◽

Specific Marker ◽

Evolutionary Analysis ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Protein Coding Genes ◽

Chloroplast Genome Sequence

The plant “False Lily of the Valley”, Speirantha gardenii is restricted to south-east China and considered as an endemic plant. Due to its limited availability, this plant was less studied. Hence, this study is focused on its molecular studies, where we have sequenced the complete chloroplast genome of S. gardenii and this is the first report on the chloroplast genome sequence of Speirantha. The complete S. gardenii chloroplast genome is of 156,869 bp in length with 37.6% GC, which included a pair of inverted repeats (IRs) each of 26,437 bp that separated a large single-copy (LSC) region of 85,368 bp and a small single-copy (SSC) region of 18,627 bp. The chloroplast genome comprises 81 protein-coding genes, 30 tRNA and four rRNA unique genes. Furthermore, a total of 699 repeats and 805 simple-sequence repeats (SSRs) markers are identified in the genome. Additionally, KA/KS nucleotide substitution analysis showed that seven protein-coding genes have highly diverged and identified nine amino acid sites under potentially positive selection in these genes. Phylogenetic analyses suggest that S. gardenii species has a closer genetic relationship to the Reineckea, Rohdea and Convallaria genera. The present study will provide insights into developing a lineage-specific marker for genetic diversity and gene evolution studies in the Nolinoideae taxa.

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Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium ‘Summit’

PeerJ ◽

10.7717/peerj.8210 ◽

2019 ◽

Vol 7 ◽

pp. e8210

Author(s):

Xueqing Zhao ◽

Ming Yan ◽

Yu Ding ◽

Yan Huo ◽

Zhaohe Yuan

Keyword(s):

Chloroplast Genome ◽

Phylogenetic Relationships ◽

High Throughput Sequencing ◽

Sweet Cherry ◽

Prunus Avium ◽

Single Copy ◽

Future Research ◽

Sequencing Data ◽

Complete Chloroplast Genome ◽

Rna Genes

Background Sweet cherry (Prunus avium) is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among Prunus based on chloroplast genome data were unclear. Methods In this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium ‘Summit’ from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively. Results The complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other Prunus species showed that P. avium ‘Summit’ was quite conserved in gene content and structure. The non-coding regions, ndhc-trnV, rps12-trnV and rpl32-trnL were the most variable sequences between wild Mazzard cherry and ‘Summit’ cherry. A total of 73 simple sequence repeats (SSRs) were identified in ‘Summit’ cherry and most of them were mononucleotide repeats. ML phylogenetic tree within Prunus species revealed four clades: Amygdalus, Cerasus, Padus, and Prunus. The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and Prunus species.

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Characterization of the complete chloroplast genome sequence of Vitis vinifera ‘Guifeimeigui’

Scientific Journal of Genetics and Gene Therapy ◽

10.17352/sjggt.000019 ◽

2021 ◽

pp. 001-003

Author(s):

Liu Li ◽

Yang Yang ◽

Li Xiujie ◽

Li Bo

Keyword(s):

Vitis Vinifera ◽

Gc Content ◽

Single Copy ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Chloroplast Genome Sequence ◽

Cp Genome ◽

Eurasian Species ◽

Rna Genes

Vitis vinifera ‘Guifeimeigui’ is a diploid table grape, a Eurasian species. This research first reported the complete chloroplast (cp) genome of Vitis vinifera ‘Guifeimeigui’. The size of the complete cp genome is 160,928 bp and its GC content is 37.38%, including a pair of inverted repeats (26,353 bp each) separated by large (89,150 bp) and small (19,072 bp) single-copy regions. It encodes 85 genes, including 40 protein coding genes, 37 transfer RNA genes (tRNA), and 8 ribosomal RNA genes (rRNA). The Maximum Likelihood (ML) phylogenetic tree demonstrated that Vitis vinifera ‘Guifeimeigui’ is close to Vitis vinifera.

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Comparative Chloroplast Genomics and Phylogenetic Analysis of Zygophyllum (Zygophyllaceae) of China

Frontiers in Plant Science ◽

10.3389/fpls.2021.723622 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ling Zhang ◽

Shu Wang ◽

Chun Su ◽

AJ Harris ◽

Liang Zhao ◽

...

Keyword(s):

Single Copy ◽

Rrna Genes ◽

Future Research ◽

Protein Coding ◽

Intergenic Spacers ◽

Morphological Studies ◽

Arid And Semiarid Areas ◽

Rna Genes ◽

Small Single Copy ◽

Simple Sequence

The genus Zygophyllum comprises over 150 species within the plant family Zygophyllaceae. These species predominantly grow in arid and semiarid areas, and about 20 occur in northwestern China. In this study, we sampled 24 individuals of Zygophyllum representing 15 species and sequenced their complete chloroplast (cp) genomes. For comparison, we also sequenced cp genomes of two species of Peganum from China representing the closely allied family, Nitrariaceae. The 24 cp genomes of Zygophyllum were smaller and ranged in size from 104,221 to 106,286 bp, each containing a large single-copy (LSC) region (79,245–80,439 bp), a small single-copy (SSC) region (16,285–17,146 bp), and a pair of inverted repeat (IR) regions (3,792–4,466 bp). These cp genomes contained 111–112 genes each, including 74–75 protein-coding genes (PCGs), four ribosomal RNA genes, and 33 transfer RNA genes, and all cp genomes showed similar gene order, content, and structure. The cp genomes of Zygophyllum appeared to lose some genes such as ndh genes and rRNA genes, of which four rRNA genes were in the SSC region, not in the IR regions. However, the SC and IR regions had greater similarity within Zygophyllum than between the genus and Peganum. We detected nine highly variable intergenic spacers: matK-trnQ, psaC-rps15, psbZ-trnG, rps7-trnL, rps15-trnN, trnE-trnT, trnL-rpl32, trnQ-psbK, and trnS-trnG. Additionally, we identified 156 simple sequence repeat (cpSSR) markers shared among the genomes of the 24 Zygophyllum samples and seven cpSSRs that were unique to the species of Zygophyllum. These markers may be useful in future studies on genetic diversity and relationships of Zygophyllum and closely related taxa. Using the sequenced cp genomes, we reconstructed a phylogeny that strongly supported the division of Chinese Zygophyllum into herbaceous and shrubby clades. We utilized our phylogenetic results along with prior morphological studies to address several remaining taxonomic questions within Zygophyllum. Specifically, we found that Zygophyllum kaschgaricum is included within Zygophyllum xanthoxylon supporting the present treatment of the former genus Sarcozygium as a subgenus within Zygophyllum. Our results provide a foundation for future research on the genetic resources of Zygophyllum.

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Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance

BioMed Research International ◽

10.1155/2020/9014873 ◽

2020 ◽

Vol 2020 ◽

pp. 1-13 ◽

Cited By ~ 3

Author(s):

Lu Wang ◽

Na He ◽

Yao Li ◽

Yanming Fang ◽

Feilong Zhang

Keyword(s):

Phylogenetic Analyses ◽

Single Copy ◽

Evolutionary Patterns ◽

Closely Related Species ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Chloroplast Genome Sequence ◽

Cp Genome ◽

Rna Genes ◽

Toxicodendron Vernicifluum

Chinese lacquer tree (Toxicodendron vernicifluum) is an important commercial arbor species widely cultivated in East Asia for producing highly durable lacquer. Here, we sequenced and analyzed the complete chloroplast (cp) genome of T. vernicifluum and reconstructed the phylogeny of Sapindales based on 52 cp genomes of six families. The plastome of T. vernicifluum is 159,571 bp in length, including a pair of inverted repeats (IRs) of 26,511 bp, separated by a large single-copy (LSC) region of 87,475 bp and a small single-copy (SSC) region of 19,074 bp. A total of 126 genes were identified, of which 81 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Forty-nine mononucleotide microsatellites, one dinucleotide microsatellite, two complex microsatellites, and 49 long repeats were determined. Structural differences such as inversion variation in LSC and gene loss in IR were detected across cp genomes of the six genera in Anacardiaceae. Phylogenetic analyses revealed that the genus Toxicodendron is closely related to Pistacia and Rhus. The phylogenetic relationships of the six families in Sapindales were well resolved. Overall, this study providing complete cp genome resources will be beneficial for determining potential molecular markers and evolutionary patterns of T. vernicifluum and its closely related species.

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The complete chloroplast genome sequence of Korean Neolitsea sericea (Lauraceae)

Korean Journal of Plant Taxonomy ◽

10.11110/kjpt.2021.51.3.332 ◽

2021 ◽

Vol 51 (3) ◽

pp. 332-336

Author(s):

Yoo-Jung PARK ◽

Kyeong-Sik CHEON

Keyword(s):

Genome Sequence ◽

Single Copy ◽

Likelihood Method ◽

Single Nucleotide ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Transfer Rnas ◽

Chloroplast Genome Sequence ◽

Cp Genome ◽

Small Single Copy

The complete chloroplast (cp) genome sequence of Neolitsea sericea was determined by Illumina sequencing. The complete cp genome was 152,446bp in length, containing a large single-copy region of 93,796 bp and a small single-copy region of 18,506bp, which were separated by a pair of 20,072bp inverted repeats. A total of 112 unique genes were annotated, including 78 protein-coding genes (PCGs), 30 transfer RNAs, and four ribosomal RNAs. Among the PCGs, 18 genes contained one or two introns. A very low level of sequence variation between two cp genomes of N. sericea was found with seven insertions or deletions and only one single nucleotide polymorphism. An analysis using the maximum likelihood method showed that N. sericea was closely related to Actinodaphne trichocarpa.

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

Scientific Reports ◽

10.1038/s41598-021-91071-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Huu Quan Nguyen ◽

Thi Ngoc Lan Nguyen ◽

Thi Nhung Doan ◽

Thi Thu Nga Nguyen ◽

Mai Huong Phạm ◽

...

Keyword(s):

Chloroplast Genome ◽

De Novo ◽

Phylogenetic Reconstruction ◽

Single Copy ◽

Potential Health ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Long Read ◽

Phylogenetic Resolution ◽

Rna Genes

AbstractAdrinandra megaphylla Hu is a medicinal plant belonging to the Adrinandra 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 Adrinandra 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.

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