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 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 codon usage patterns in chloroplast genomes of six Euphorbiaceae species

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8251 ◽  
Author(s):  
Zhanjun Wang ◽  
Beibei Xu ◽  
Bao Li ◽  
Qingqing Zhou ◽  
Guiyi Wang ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Comparative Analysis ◽  
Codon Usage ◽  
Plant Species ◽  
Populus Trichocarpa ◽  
Model Organisms ◽  
Mutation Pressure ◽  
Chloroplast Genomes ◽  
Usage Patterns ◽  
Exogenous Expression

Euphorbiaceae plants are important as suppliers of biodiesel. In the current study, the codon usage patterns and sources of variance in chloroplast genome sequences of six different Euphorbiaceae plant species have been systematically analyzed. Our results revealed that the chloroplast genomes of six Euphorbiaceae plant species were biased towards A/T bases and A/T-ending codons, followed by detection of 17 identical high-frequency codons including GCT, TGT, GAT, GAA, TTT, GGA, CAT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, TAT and TAA. It was found that mutation pressure was a minor factor affecting the variation of codon usage, however, natural selection played a significant role. Comparative analysis of codon usage frequencies of six Euphorbiaceae plant species with four model organisms reflected that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae should be considered as suitable exogenous expression receptor systems for chloroplast genes of six Euphorbiaceae plant species. Furthermore, it is optimal to choose Saccharomyces cerevisiae as the exogenous expression receptor. The outcome of the present study might provide important reference information for further understanding the codon usage patterns of chloroplast genomes in other plant species.

scholarly journals Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Wen-Hua Qi ◽  
Xue-Mei Jiang ◽  
Chao-Chao Yan ◽  
Wan-Qing Zhang ◽  
Guo-Sheng Xiao ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Distribution Patterns ◽  
Variation Analysis ◽  
Genomic Regions ◽  
Simple Sequence

scholarly journals A Comparative Study of the Chloroplast Genomes of Five Lepidium Medicinal Plants

2021 ◽  
Author(s):  
Qian Zhou ◽  
Yun Chen ◽  
Mingyuan Li ◽  
Weijun Zeng ◽  
Jilian Wang ◽  
...  
Keyword(s):  
Medicinal Plants ◽  
Codon Usage ◽  
Simple Sequence Repeats ◽  
Tandem Repeats ◽  
Species Recognition ◽  
Rrna Genes ◽  
Specific Gene ◽  
Genomic Arrangement ◽  
High Degree ◽  
Simple Sequence

Abstract Background Herb genomics is a rapidly developing field of medicinal plant research and development. Plant genomic studies demonstrate the unique advantage of employing plants in medicinal therapy. The genus Lepidium falls under the Brassicaceae family and it includes crucial medicinal plants. Herein, we sequenced the complete chloroplast (cp) genomes of Lepidium apetalum (LA) and Lepidium perfoliatum (LP) and assessed their genetic profiles against the reported profiles of Lepidium sativum (LS), Lepidium meyenii (LM), and Lepidium virginicum (LV). Results In particular, we examined genomic arrangement, gene number, type, and repeat sequences. Based on our annotation data, both LA and LP possessed 130 distinct genes that included 85 protein-coding, 37 transfer RNA (tRNA), and 8 ribosomal RNA (rRNA) genes. Our repeat analyses revealed that LA harbored 20 forward repeats, 16 palindrome repeats, 30 tandem repeats, and 87 simple sequence repeats, whereas LP had 15 forward repeats, 20 palindrome repeats,4 reverse repeats, 21 tandem repeats, and 98 simple sequence repeats. Using syntenic analysis, we also revealed a high degree of sequence similarity within the coding regions of Lepidium cp genomes and a remarkably high degree of divergence among the intergenic spacers. Pairwise alignment and single-nucleotide polymorphism (SNP) examinations further revealed certain Lepidium-specific gene fragments, particularly in the intergenic regions of the trnK-atpA, trnC-psbC, trnT-rbcL, ndhF-ndhH, ycf1-trnR, accD, ccsA, matK, ndhF, rpoB, rpoC2, and ycf1 genes. Moreover, following codon usage analysis, we observed that codon 14 was the most frequently used codon in the Lepidium CDS. In addition, correlation investigations revealed that the ENC (the effective number of codon) content was strongly associated with GC3, GC3s, and N. Conclusion Based on these data, LA and LP originate from very similar genetic backgrounds. Furthermore, neutrality, ENC, and PR2-plots analyses demonstrated that the CUB (the codon usage bias) of Lepidium cp genome was strongly influenced by mutation and natural selection. Our analysis of the cp genomic sequences of LA and LP will likely enhance breeding, species recognition, phylogenetic evolution, and cp genetic engineering of the Lepidium medicinal plants.

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.

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