Comparative analyses of the complete chloroplast genomes of nymphoides and menyanthes species (menyanthaceae)

2019 ◽  
Vol 156 ◽  
pp. 73-81 ◽  
Author(s):  
Ann W. Njuguna ◽  
Zhi-Zhong Li ◽  
Josphat K. Saina ◽  
Justus M. Munywoki ◽  
Andrew W. Gichira ◽  
...  
Keyword(s):  
Comparative Analyses ◽  
Chloroplast Genomes

scholarly journals Comparative analyses of 3654 chloroplast genomes unraveled new insights into the evolutionary mechanism of green plants

2019 ◽  
Author(s):  
Ting Yang ◽  
Xuezhu Liao ◽  
Lingxiao Yang ◽  
Yang Liu ◽  
Weixue Mu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Structure ◽  
Strong Support ◽  
Gc Content ◽  
Taxon Sampling ◽  
Data Sets ◽  
Green Plants ◽  
Comparative Analyses ◽  
Chloroplast Genomes ◽  
The Matrix

AbstractBackgroundChloroplast are believed to arise from a cyanobacterium through endosymbiosis and they played vital roles in photosynthesis, oxygen release and metabolites synthesis for the plant. With the advent of next-generation sequencing technologies, until December 2018, about 3,654 complete chloroplast genome sequences have been made available. It is possible to compare the chloroplast genome structure to elucidate the evolutionary history of the green plants.ResultsWe compared the 3654 chloroplast genomes of the green plants and found extreme conservation of gene orders and gene blocks in the green plant such as ATP synthase cluster, Phytosystem, Cytochrome cluster, and Ribosomal cluster. For the chloroplast-based phylogenomics, we used three different data sets to recover the relationships within green plants which accounted for biased GC content and could mitigate the bias in molecular data sets by increasing taxon sampling. The main topology results include: I) Chlorokybales + Mesostigmatales as the earliest-branching lineage and a clade comprising Zygnematales+ Desmidiales formed a grade as the sister group to the land plants, II) Based on matrix AA data, Bryophytes was strongly supported as monophyletic but for matrix nt123 data, hornworts, mosses and liverworts were placed as successive sister lineages of Tracheophytes with strong support, III) Magnoliids were placed in the outside of Monocots using the matrix nt123 data and the matrix AA data, IV) Ceratophyllales + Chloranthales as sister to the Eudicots using matrix nt123 data, but when using matrix nt12 data and AA data, only Ceratophyllales sister to the Eudicots.ConclusionWe present the first of its kind large scale comparative analyses of the chloroplast coding gene constitution for 3654 green plants. Some important genes likely showed co-occurrence and formed gene cluster and gene blocks in Streptophyta. We found a clear expansion of IRs (Inverted Repeats) among seed plants. The comprehensive taxon sampling and different data sets recovered a strong relationship for green plants.

scholarly journals Comparative Analyses of 35 Complete Chloroplast Genomes from the Genus Dalbergia (Fabacaeae) and the Identification of DNA Barcodes for Tracking Illegal Logging and Counterfeit Rosewood

2021 ◽  
Author(s):  
Zhou Hong ◽  
Dan Peng ◽  
Wenchuang He ◽  
Ningnan Zhang ◽  
Zengjiang Yang ◽  
...  
Keyword(s):  
Nucleotide Polymorphisms ◽  
Dna Barcodes ◽  
Variable Regions ◽  
Comparative Analyses ◽  
Illicit Trade ◽  
Traditional Medicines ◽  
Chloroplast Genomes ◽  
In The Wild ◽  
Plastid Markers ◽  
Simple Sequence

Abstract The genus Dalbergia contains more than 120 species several of which are trees that produce traditional medicines and extremely high value timber commonly referred to as rosewood. Due to the rarity of these species in the wild, the high value of the timber, and a growing international illicit trade CITES has listed the entire genus in appendix II and the species D. nigra in appendix I because it is considered threatened with extinction. Given this and the fact that species or even genus level determination is nearly impossible from cut timber alternative molecular methods are needed to identify and track intercepted rosewood. In order to improve molecular identification of rosewood, we sequenced and assembled eight chloroplast genomes including D. nigra as well as conducted comparative analyses with all other available chloroplast genomes in Dalbergia and closely related lineages. From these analyses numerous repeats including simple sequence repeats (SSR) and conserved nucleotide polymorphisms unique to subclades within the genus were detected. From phylogenetic analysis using the CDS of 77 coding genes the groups Siam rosewood and scented rosewood based mainly on wood characteristics were supported as monophyletic. In addition, several instances of paraphyly and polyphyly resulting from mismatch between taxonomic determinations and phylogenetic tree topology were identified. Ultimately, the highly variable regions in the chloroplast genomes will provide useful plastid markers for further studies regarding the identification, phylogeny, and population genetics of Dalbergia species including those frequently intercepted in illegal trade.

Comparative analyses of chloroplast genomes of Theobroma cacao and Theobroma grandiflorum

Biologia ◽  
2019 ◽  
Vol 75 (5) ◽  
pp. 761-771 ◽  
Author(s):  
Abdullah ◽  
Shahid Waseem ◽  
Bushra Mirza ◽  
Ibrar Ahmed ◽  
Mohammad Tahir Waheed
Keyword(s):  
Theobroma Cacao ◽  
Comparative Analyses ◽  
Theobroma Grandiflorum ◽  
Chloroplast Genomes

scholarly journals The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus

DNA Research ◽  
2017 ◽  
Vol 24 (4) ◽  
pp. 343-358 ◽  
Author(s):  
J. Keller ◽  
M. Rousseau-Gueutin ◽  
G.E. Martin ◽  
J. Morice ◽  
J. Boutte ◽  
...  
Keyword(s):  
Comparative Analyses ◽  
Chloroplast Genomes ◽  
Evolutionary Fate

scholarly journals Comparative Analyses and Phylogenetic Relationships between Cryptomeria fortunei and Related Species Based on Complete Chloroplast Genomes

Phyton ◽  
2020 ◽  
Vol 89 (4) ◽  
pp. 957-986
Author(s):  
Yingting Zhang ◽  
Junjie Yang ◽  
Zhenhao Guo ◽  
Jiaxing Mo ◽  
Jiebing Cui ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Relationships ◽  
Comparative Analyses ◽  
Chloroplast Genomes

scholarly journals A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhou Hong ◽  
Xuezhu Liao ◽  
Yuanjun Ye ◽  
Ningnan Zhang ◽  
Zengjiang Yang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Networks ◽  
Complete Mitochondrial Genome ◽  
Genome Structure ◽  
Nuclear Genome ◽  
Trna Genes ◽  
Important Species ◽  
Comparative Analyses ◽  
Chloroplast Genomes ◽  
Dalbergia Odorifera

Abstract Background Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers. Results We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome. Conclusion For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.

scholarly journals Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

2019 ◽  
Author(s):  
Chengcheng Shi ◽  
Kai Han ◽  
Liangwei Li ◽  
Inge Seim ◽  
Simon Ming-Yuen Lee ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Single Copy ◽  
Avicennia Marina ◽  
Terrestrial Plants ◽  
Mangrove Species ◽  
Rhizophora Stylosa ◽  
Comparative Analyses ◽  
Excoecaria Agallocha ◽  
Thespesia Populnea ◽  
Chloroplast Genomes

AbstractMangroves are main components of an ecosystem which connect land and ocean and is of significant ecological importance. They are found around the world and taxonomically distributed in 17 families. Until now there has been no evolutionary phylogenetic analyses on mangroves based on complete plastome sequences. In order to infer the relationship between mangroves and terrestrial plants at the molecular level, we generated chloroplast genomes of 14 mangrove species from eight families, spanning six orders: Fabales (Pongamia pinnata), Lamiales (Avicennia marina), Malpighiales (Excoecaria agallocha, Bruguiera sexangula, Kandelia obovata, Rhizophora stylosa, Ceriops tagal), Malvales (Hibiscus tiliaceus, Heritiera littoralis, Thespesia populnea), Myrtales (Laguncularia racemose, Sonneratia ovata, Pemphis acidula), and Sapindales (Xylocarpus moluccensis). The whole-genome length of these chloroplasts is from 149kb to 168kb. They have a conserved structure, with two Inverted Repeat (IRa and IRb, ~25.8kb), a large single-copy region (LSC, ~89.0kb), a short single-copy (SSC, ~18.9kb) region, as well as ~130 genes (85 protein-coding, 37 tRNA, and 8 rRNA). The number of simple sequence repeats (SSRs) varied between mangrove species. Phylogenetic analysis using complete chloroplast genomes of 71 mangrove and land plants, confirmed the previously reported phylogeny within rosids, including the positioning of obscure families such as Linaceae within Malpighiales. Most mangrove chloroplast genes are conserved and we found six genes subjected to positive or neutral selection. Genomic comparison showed IR regions have lower divergence than other regions. Our study firstly reported several plastid genetic resource for mangroves, and the determined evolutionary locations as well as comparative analyses of these species provid insights into the mangrove genetic and phylogenetic research.

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