scholarly journals Comparative chloroplast genomes and phylogenetic analysis of Aquilegia

2021 ◽  
Author(s):  
Wei Zhang ◽  
Huaying Wang ◽  
Jianhua Dong ◽  
Tengjiao Zhang ◽  
Hongxing Xiao
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genomes

scholarly journals Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

2021 ◽  
Author(s):  
Marcia Gumiel ◽  
Oscar M Rollano-Penaloza ◽  
Carmelo Peralta-Rivero ◽  
Leslie Tejeda ◽  
Valeria D. Palma Encinas ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Theobroma Cacao ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Next Generation ◽  
Center Of Origin ◽  
Chloroplast Genomes ◽  
Geographical Locations ◽  
Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

scholarly journals Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Paeonia Section Moutan Species (Paeoniaceae)

2020 ◽  
Vol 11 ◽  
Author(s):  
Liwei Wu ◽  
Liping Nie ◽  
Zhichao Xu ◽  
Pei Li ◽  
Yu Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genomes

scholarly journals Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 115
Author(s):  
Yuxin Hu ◽  
Weiyue Xing ◽  
Zhengyu Hu ◽  
Guoxiang Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Phylogenetic Relationship ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Substitution Rates ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chloroplast Genomes ◽  
Volvocine Algae

We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.

scholarly journals Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes

2016 ◽  
Vol 33 (1) ◽  
pp. 130-132 ◽  
Author(s):  
Michael R. McKain ◽  
Ryan H. Hartsock ◽  
Molly M. Wohl ◽  
Elizabeth A. Kellogg
Keyword(s):  
Phylogenetic Analysis ◽  
Automated Annotation ◽  
Chloroplast Genomes

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 The complete chloroplast genome of Diarthron linifolium (Thymelaeaceae), a species found on a limestone outcrop in eastern Asia

2021 ◽  
Vol 51 (4) ◽  
pp. 345-352
Author(s):  
Sang-Tae KIM ◽  
Sang-Hun OH ◽  
Jongsun PARK
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Single Copy ◽  
Evolutionary Status ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
Potential Marker ◽  
Anticancer Treatment ◽  
Annual Herb ◽  
Unique Species

Diarthron linifolium Turcz. is an annual herb usually found in sandy soil or limestone areas. Plants in the genus Diarthron are known to have toxic chemicals that may, however, be potentially useful as an anticancer treatment. Diarthron linifolium is a unique species among the species of the genus distributed in Korea. Here, we determine the genetic variation of D. linifolium collected in Korea with a full chloroplast genome and investigate its evolutionary status by means of a phylogenetic analysis. The chloroplast genome of Korean D. linifolium has a total length of 172,644 bp with four subregions; 86,158 bp of large single copy and 2,858 bp of small single copy (SSC) regions are separated by 41,814 bp of inverted repeat (IR) regions. We found that the SSC region of D. linifolium is considerably short but that IRs are relatively long in comparison with other chloroplast genomes. Various simple sequence repeats were identified, and our nucleotide diversity analysis suggested potential marker regions near ndhF. The phylogenetic analysis indicated that D. linifolium from Korea is a sister to the group of Daphne species.

scholarly journals Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

2020 ◽  
Author(s):  
Benwen Liu ◽  
Yu Xin Hu ◽  
Zheng Yu Hu ◽  
Guo Xiang Liu ◽  
Huan Zhu
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Rdna Sequences ◽  
Chloroplast Genomes ◽  
Basal Clade

Abstract Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. Most studies have primarily focused on intergeneric phylogenetic relationships within this order and the phylogenetic relationships with four other Chlorophycean orders (Chaetophorales, Chaetopeltidales and Oedogoniales, and Volvocales). This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales. The taxonomic scheme of Chaetophorales has been inferred primarily through phylogenetic analysis based on rDNA sequences and phylogenetic relationships among families in order Chaetophorales remain unclear. Results In present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales, Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions In conclusion, chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

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.

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