scholarly journals Comparative analysis of chloroplast genomes indicated different origin for Indian Tea (Camellia assamica) cv TV-1 as compared to Chinese tea

2020 ◽  
Author(s):  
Hukam C. Rawal ◽  
Abhishek Mazumder ◽  
Sangeeta Borchetia ◽  
Biswajit Bera ◽  
S. Soundararajan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Morphological Characteristics ◽  
African Countries ◽  
Chloroplast Genomes ◽  
Assam Tea ◽  
Cp Genome ◽  
Indian Tea ◽  
Simple Sequence ◽  
Different Origin

AbstractTea is an important plantation crop of some Asian and African countries. Based upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China joining area, yet specific origin of China and Assam tea are not yet clear. In the present study, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus. Cp genome based phylogenetic analysis indicated that Indian Assam Tea, TV-1 formed a different group from that of China tea, indicating that TV-1 might have undergone different domestication and hence owe different origin. The simple sequence repeats (SSRs) analysis and codon usage distribution pattern also supported the clustering order in the cp genome based phylogenetic tree.

scholarly journals Comparative analysis of chloroplast genomes indicated different origin for Indian tea (Camellia assamica cv TV1) as compared to Chinese tea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hukam C. Rawal ◽  
Sangeeta Borchetia ◽  
Biswajit Bera ◽  
S. Soundararajan ◽  
R. Victor J. Ilango ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Codon Usage ◽  
Simple Sequence Repeats ◽  
Morphological Characteristics ◽  
Distribution Patterns ◽  
Chloroplast Genomes ◽  
Cp Genome ◽  
Different Origins ◽  
Indian Tea ◽  
Simple Sequence

AbstractBased upon the morphological characteristics, tea is classified botanically into 2 main types i.e. Assam and China, which are morphologically very distinct. Further, they are so easily pollinated among themselves, that a third category, Cambod type is also described. Although the general consensus of origin of tea is India, Burma and China adjoining area, yet specific origin of China and Assam type tea are not yet clear. Thus, we made an attempt to understand the origin of Indian tea through the comparative analysis of different chloroplast (cp) genomes under the Camellia genus by performing evolutionary study and comparing simple sequence repeats (SSRs) and codon usage distribution patterns among them. The Cp genome based phylogenetic analysis indicated that Indian Tea, TV1 formed a different group from that of China tea, indicating that TV1 might have undergone different domestications and hence owe different origins. The simple sequence repeats (SSRs) analysis and codon usage distribution patterns also supported the clustering order in the cp genome based phylogenetic tree.

scholarly journals Comparison and Phylogenetic Analysis of Chloroplast Genomes of Three Medicinal and Edible Amomum Species

2019 ◽  
Vol 20 (16) ◽  
pp. 4040 ◽  
Author(s):  
Yingxian Cui ◽  
Xinlian Chen ◽  
Liping Nie ◽  
Wei Sun ◽  
Haoyu Hu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Morphological Characteristics ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Edible Plant ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Cp Genome ◽  
Pharmacologically Active

Amomum villosum is an important medicinal and edible plant with several pharmacologically active volatile oils. However, identifying A. villosum from A. villosum var. xanthioides and A. longiligulare which exhibit similar morphological characteristics to A. villosum, is difficult. The main goal of this study, therefore, is to mine genetic resources and improve molecular methods that could be used to distinguish these species. A total of eight complete chloroplasts (cp) genomes of these Amomum species which were collected from the main producing areas in China were determined to be 163,608–164,069 bp in size. All genomes displayed a typical quadripartite structure with a pair of inverted repeat (IR) regions (29,820–29,959 bp) that separated a large single copy (LSC) region (88,680–88,857 bp) from a small single copy (SSC) region (15,288–15,369 bp). Each genome encodes 113 different genes with 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. More than 150 SSRs were identified in the entire cp genomes of these three species. The Sanger sequencing results based on 32 Amomum samples indicated that five highly divergent regions screened from cp genomes could not be used to distinguish Amomum species. Phylogenetic analysis showed that the cp genomes could not only accurately identify Amomum species, but also provide a solid foundation for the establishment of phylogenetic relationships of Amomum species. The availability of cp genome resources and the comparative analysis is beneficial for species authentication and phylogenetic analysis in Amomum.

scholarly journals The Complete Chloroplast Genome of Critically Endangered Chimonobambusa hirtinoda (Poaceae: Chimonobambusa) and Phylogenetic Analysis

2021 ◽  
Author(s):  
yanjiang liu ◽  
Xiao Zhu ◽  
Mingli Wu ◽  
Xue Xu ◽  
Zhaoxia Dai ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gc Content ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Usage Frequency ◽  
Cp Genome ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Simple Sequence

Abstract Chimonobambusa hirtinoda is a threatened species and only naturally distributed in Doupeng Mountain, Duyun, Guizhou, China. Next-generation sequencing (NGS) is used obtained the complete chloroplast (cp) genome sequence of C. hirtinoda, and then the sequence was assembled and analyze for phylogenetic and evolutionary. We also analyzed comparing the cp genome among Chimonobambusa species with previously published. The complete cp genome of C. hirtinoda has the total length of 139, 561 bp, 38.90% GC content was detected. A total of 130 genes were founded in the cp genome, including 85 protein coding genes, 37 tRNA genes, 8 rRNA. Some genes are missing and the introns occur lost in the cp genome of C. hirtinoda. A total of 48 simple sequence repeat (SSR) were detected and by measuring the codon usage frequency of amino acids, the A/U preference of the third nucleotide in the cp genome of C. hirtinoda was obtained. Furthermore, phylogenetic analysis using complete cp sequences, matk gene exhibited genetic relationship within the Chimonobambusa genus.

scholarly journals Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 296 ◽  
Author(s):  
Jacinta N. Munyao ◽  
Xiang Dong ◽  
Jia-Xin Yang ◽  
Elijah M. Mbandi ◽  
Vincent O. Wanga ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Important Species ◽  
Genomic Resources ◽  
Phylogenetic Studies ◽  
Chloroplast Genomes ◽  
Cp Genome ◽  
High Level

The genus Chlorophytum includes many economically important species well-known for medicinal, ornamental, and horticultural values. However, to date, few molecular genomic resources have been reported for this genus. Therefore, there is limited knowledge of phylogenetic studies, and the available chloroplast (cp) genome of Chlorophytum (C. rhizopendulum) does not provide enough information on this genus. In this study, we present genomic resources for C. comosum and C. gallabatense, which had lengths of 154,248 and 154,154 base pairs (bp), respectively. They had a pair of inverted repeats (IRa and IRb) of 26,114 and 26,254 bp each in size, separating the large single-copy (LSC) region of 84,004 and 83,686 bp from the small single-copy (SSC) region of 18,016 and 17,960 bp in C. comosum and C. gallabatense, respectively. There were 112 distinct genes in each cp genome, which were comprised of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The comparative analysis with five other selected species displayed a generally high level of sequence resemblance in structural organization, gene content, and arrangement. Additionally, the phylogenetic analysis confirmed the previous phylogeny and produced a phylogenetic tree with similar topology. It showed that the Chlorophytum species (C. comosum, C. gallabatense and C. rhizopendulum) were clustered together in the same clade with a closer relationship than other plants to the Anthericum ramosum. This research, therefore, presents valuable records for further molecular evolutionary and phylogenetic studies which help to fill the gap in genomic resources and resolve the taxonomic complexes of the genus.

scholarly journals Complete Chloroplast Genomes of Ampelopsis humulifolia and Ampelopsis japonica: Molecular Structure, Comparative Analysis, and Phylogenetic Analysis

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 410 ◽  
Author(s):  
Xiaolei Yu ◽  
Wei Tan ◽  
Huanyu Zhang ◽  
Han Gao ◽  
Wenxiu Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Z ◽  
Marker Selection ◽  
Chloroplast Genomes ◽  
Potential Marker ◽  
Cp Genome

Ampelopsis humulifolia (A. humulifolia) and Ampelopsis japonica (A. japonica), which belong to the family Vitaceae, are valuably used as medicinal plants. The chloroplast (cp) genomes have been recognized as a convincing data for marker selection and phylogenetic studies. Therefore, in this study we reported the complete cp genome sequences of two Ampelopsis species. Results showed that the cp genomes of A. humulifolia and A. japonica were 161,724 and 161,430 bp in length, respectively, with 37.3% guanine-cytosine (GC) content. A total of 114 unique genes were identified in each cp genome, comprising 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. We determined 95 and 99 small sequence repeats (SSRs) in A. humulifolia and A. japonica, respectively. The location and distribution of long repeats in the two cp genomes were identified. A highly divergent region of psbZ (Photosystem II reaction center protein Z) -trnG (tRNA-Glycine) was found and could be treated as a potential marker for Vitaceae, and then the corresponding primers were designed. Additionally, phylogenetic analysis showed that Vitis was closer to Tetrastigma than Ampelopsis. In general, this study provides valuable genetic resources for DNA barcoding marker identification and phylogenetic analyses of Ampelopsis.

scholarly journals The complete chloroplast genomes of seventeen Aegilops tauschii: genome comparative analysis and phylogenetic inference

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8678 ◽  
Author(s):  
Qing Su ◽  
Luxian Liu ◽  
Mengyu Zhao ◽  
Cancan Zhang ◽  
Dale Zhang ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Bread Wheat ◽  
Yellow River ◽  
Genomic Structure ◽  
Aegilops Tauschii ◽  
Western China ◽  
Chloroplast Genomes ◽  
River Region ◽  
Cp Genome ◽  
Rna Genes

The D genome progenitor of bread wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14), which is naturally distributed in Central Eurasia, ranging from northern Syria and Turkey to western China, is considered a potential genetic resource for improving bread wheat. In this study, the chloroplast (cp) genomes of 17 Ae. tauschii accessions were reconstructed. The cp genome sizes ranged from 135,551 bp to 136,009 bp and contained a typical quadripartite structure of angiosperms. Within these genomes, we identified a total of 124 functional genes, including 82 protein-coding genes, 34 transfer RNA genes and eight ribosomal RNA genes, with 17 duplicated genes in the IRs. Although the comparative analysis revealed that the genomic structure (gene order, gene number and IR/SC boundary regions) is conserved, a few variant loci were detected, predominantly in the non-coding regions (intergenic spacer regions). The phylogenetic relationships determined based on the complete genome sequences were consistent with the hypothesis that Ae. tauschii populations in the Yellow River region of China originated in South Asia not Xinjiang province or Iran, which could contribute to more effective utilization of wild germplasm resources. Furthermore, we confirmed that Ae. tauschii was derived from monophyletic speciation rather than hybrid speciation at the cp genome level. We also identified four variable genomic regions, rpl32-trnL-UAG, ccsA-ndhD, rbcL-psaI and rps18-rpl20, showing high levels of nucleotide polymorphisms, which may accordingly prove useful as cpDNA markers in studying the intraspecific genetic structure and diversity of Ae. tauschii.

scholarly journals Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis

Molecules ◽  
2018 ◽  
Vol 23 (2) ◽  
pp. 437 ◽  
Author(s):  
Jianguo Zhou ◽  
Yingxian Cui ◽  
Xinlian Chen ◽  
Ying Li ◽  
Zhichao Xu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Molecular Structures ◽  
Papaver Rhoeas ◽  
Chloroplast Genomes

scholarly journals Comparative Analysis of Chloroplast Genomes of Thalassiosira Species

2021 ◽  
Vol 8 ◽  
Author(s):  
Kuiyan Liu ◽  
Yang Chen ◽  
Zongmei Cui ◽  
Shuya Liu ◽  
Qing Xu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Primary Productivity ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Negative Impact ◽  
High Specificity ◽  
Evolutionary Analysis ◽  
Chloroplast Genomes ◽  
Genomic Regions

Thalassiosira is a species-rich genus in Bacillariophyta with important ecological contribution to primary productivity but can also pose negative impact on ecology by developing harmful algal blooms (HABs). However, genomic resources of only a few Thalassiosira species are currently available. Here, we constructed complete chloroplast genomes (cpDNAs) of six Thalassiosira strains (representing six Thalassiosira species T. rotula, T. profunda, T. nordenskioeldii, T. tenera, T. weissflogii, and Thalassiosira sp.), and compared them with published cpDNAs of other diatoms. Comparative analysis revealed that Thalassiosira cpDNAs have generally conventional and conserved quadripartite structure with important exceptions. Gene orders of cpDNAs of Thalassiosira sp. (CNS00561) and T. oceanica were different from that of other Thalassiosira species. Additionally, endosymbiotic gene transfers (EGT) were found to occur in the evolution of Thalassiosira cpDNAs. Furthermore, genomic regions of cpDNAs were found to be highly variable, which could be used to construct molecular markers for distinguishing Thalassiosira species with high resolution and high specificity. This study also demonstrated that Thalassiosira species emerged roughly around 51 MYA and diversified 17–28 MYA. Thalassiosira cpDNAs are not only valuable as super-barcode for phylogenetic analysis, but also important for functional and evolutionary analysis of diatoms.

scholarly journals Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea)

Forests ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 861
Author(s):  
Huijuan Zhou ◽  
Xiaoxiao Gao ◽  
Keith Woeste ◽  
Peng Zhao ◽  
Shuoxin Zhang
Keyword(s):  
Comparative Analysis ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Cp Genome ◽  
Species Hybrids ◽  
Rna Genes

Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.

scholarly journals Identification and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Ephedra Herbs Containing Ephedrine

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Xinlian Chen ◽  
Yingxian Cui ◽  
Liping Nie ◽  
Haoyu Hu ◽  
Zhichao Xu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Good Governance ◽  
Herbal Medicines ◽  
Single Copy ◽  
Trna Genes ◽  
Chloroplast Genomes ◽  
Close Phylogenetic Relationship ◽  
Cp Genome ◽  
Original Species ◽  
Parsimony Trees

Ephedrae Herba and Ephedrae Radix et Rhizoma (Mahuang) have been used as Chinese herbal medicines. Ephedra plants mainly live in deserts and have good governance of desertification. Despite their important medicinal and environmental protection value, dietary supplements containing ephedrine from Ephedra species may threaten the health of people. Morphological resemblance amongst species causes difficulty in identifying the original species of Ephedra herbs. Chloroplast (CP) genome shows good prospects in identification and phylogenetic analysis. This study introduced the structures of the CP genomes of three Ephedra species and analysed their phylogenetic relationships. Three complete CP genomes of Ephedra showed four-part annular structures, namely, two single-copy regions and two inverted repeat regions. The entire CP genomes of three Ephedra species in terms of size were 109,550 bp (E. sinica), 109,667 bp (E. intermedia), and 109,558 bp (E. equisetina). Each CP genome of the three Ephedra species encoded 118 genes, including 73 protein-coding genes, 37 tRNA genes and 8 ribosomal RNA genes. Eleven high-variation regions were screened through mVISTA to be potential specific DNA barcodes for identifying Ephedra species. Maximum likelihood and maximum parsimony trees showed that CP genomes could be used to identify Ephedra species. The Ephedra species had a close phylogenetic relationship with Gnetum species and Welwitschia mirabilis. This research provided valuable information for the identification and phylogenetic analysis of gymnosperms and drug safety of Ephedra.

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