scholarly journals Calophyllaceae plastomes, their structure and insights in relationships within the clusioids

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rafaela Jorge Trad ◽  
Fernanda Nunes Cabral ◽  
Volker Bittrich ◽  
Saura Rodrigues da Silva ◽  
Maria do Carmo Estanislau do Amaral
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Gene Trees ◽  
Complete Chloroplast Genome ◽  
Numerous Species ◽  
Evolutionary Studies ◽  
Kielmeyera Coriacea

AbstractA complete chloroplast genome is not yet available for numerous species of plants. Among the groups that lack plastome information is the clusioid clade (Malpighiales), which includes five families: Bonnetiaceae, Calophyllaceae, Clusiaceae, Hypericaceae, and Podostemaceae. With around 2200 species, it has few published plastomes and most of them are from Podostemaceae. Here we assembled and compared six plastomes from members of the clusioids: five from Calophyllaceae (newly sequenced) and one from Clusiaceae. Putative regions for evolutionary studies were identified and the newly assembled chloroplasts were analyzed with other available chloroplasts for the group, focusing on Calophyllaceae. Our results mostly agree with recent studies which found a general conserved structure, except for the two Podostemaceae species that have a large inversion (trnK-UUU–rbcL) and lack one intron from ycf3. Within Calophyllaceae we observed a longer LSC and reduced IRs in Mahurea exstipulata, resulting in some genic rearrangement, and a short inversion (psbJ–psbE) in Kielmeyera coriacea. Phylogenetic analyses recovered the clusioids and the five families as monophyletic and revealed that conflicts in relationships reported in the literature for the group agree with nodes concentrating uninformative or conflicting gene trees. Our study brings new insights about clusioid plastome architecture and its evolution.

Tigridiopalma longmenensis (Melastomataceae), a new species from Guangdong, China

Phytotaxa ◽  
2021 ◽  
Vol 500 (3) ◽  
pp. 241-247
Author(s):  
HUI-FENG WANG ◽  
ZHENG-FENG WANG ◽  
QIAO-MEI QIN ◽  
HONG-LIN CAO ◽  
XIAO-MING GUO
Keyword(s):  
New Species ◽  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Monotypic Genus ◽  
Distribution Map ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
A New Species

Tigridiopalma longmenensis, a new species from Guangdong, China, is described. This species differs from its ally, T. magnifica, by the polychasium consisting of scorpioid cymes, hypanthium with carinas on angles, and longer stamens with a conspicuously white or pink spur at the connective base of anther. A diagnosis and a distribution map of the two species are also provided. The complete chloroplast genome of T. longmenensis was reported here. Phylogenetic analyses based on complete chloroplast genomes from T. longmenensis and other 15 Melastomataceae species indicated that T. longmenensis is sister to T. magnifica. The discovery of T. longmenensis terminates Tigridiopalma as a monotypic genus.

scholarly journals Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6032 ◽  
Author(s):  
Zhenyu Zhao ◽  
Xin Wang ◽  
Yi Yu ◽  
Subo Yuan ◽  
Dan Jiang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Genomic Resources ◽  
Chloroplast Genomes ◽  
The Family ◽  
Small Single Copy

Dioscorea L., the largest genus of the family Dioscoreaceae with over 600 species, is not only an important food but also a medicinal plant. The identification and classification of Dioscorea L. is a rather difficult task. In this study, we sequenced five Dioscorea chloroplast genomes, and analyzed with four other chloroplast genomes of Dioscorea species from GenBank. The Dioscorea chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted repeats separated by a large single-copy region, and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined, and the rapidly evolving chloroplast genome regions (trnK-trnQ, trnS-trnG, trnC-petN, trnE-trnT, petG-trnW-trnP, ndhF, trnL-rpl32, and ycf1) were detected. Phylogenetic relationships of Dioscorea inferred from chloroplast genomes obtained high support even in shortest internodes. Thus, chloroplast genome sequences provide potential molecular markers and genomic resources for phylogeny and species identification.

scholarly journals Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Kadriye Kahraman ◽  
Stuart James Lucas
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Single Copy ◽  
Corylus Avellana ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Complete Chloroplast Genome ◽  
A Genome ◽  
Cp Genome

Abstract Background Several bioinformatics tools have been designed for assembly and annotation of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable to a specific case. The increasing number of plant genomes provide an opportunity to accurately obtain cp genomes from whole genome shotgun (WGS) sequences. Due to the limited genetic information available for European hazelnut (Corylus avellana L.) and as part of a genome sequencing project, we analyzed the complete chloroplast genome of the cultivar ‘Tombul’ with multiple annotation tools. Results Three different annotation strategies were tested, and the complete cp genome of C. avellana cv Tombul was constructed, which was 161,667 bp in length, and had a typical quadripartite structure. A large single copy (LSC) region of 90,198 bp and a small single copy (SSC) region of 18,733 bp were separated by a pair of inverted repeat (IR) regions of 26,368 bp. In total, 125 predicted functional genes were annotated, including 76 protein-coding, 25 tRNA, and 4 rRNA unique genes. Comparative genomics indicated that the cp genome sequences were relatively highly conserved in species belonging to the same order. However, there were still some variations, especially in intergenic regions, that could be used as molecular markers for analyses of phylogeny and plant identification. Simple sequence repeat (SSR) analysis showed that there were 83 SSRs in the cp genome of cv Tombul. Phylogenetic analysis suggested that C. avellana cv Tombul had a close affinity to the sister group of C. fargesii and C. chinensis, and then a closer evolutionary relationship with Betulaceae family than other species of Fagales. Conclusion In this study, the complete cp genome of Corylus avellana cv Tombul, the most widely cultivated variety in Turkey, was obtained and annotated, and additionally phylogenetic relationships were predicted among Fagales species. Our results suggest a very accurate assembly of chloroplast genome from next generation whole genome shotgun (WGS) sequences. Enhancement of taxon sampling in Corylus species provide genomic insights into phylogenetic analyses. The nucleotide sequences of cv Tombul cp genomes can provide comprehensive genetic insight into the evolution of genus Corylus.

scholarly journals The complete chloroplast genome sequence of strawberry (Fragaria × ananassaDuch.) and comparison with related species of Rosaceae

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3919 ◽  
Author(s):  
Hui Cheng ◽  
Jinfeng Li ◽  
Hong Zhang ◽  
Binhua Cai ◽  
Zhihong Gao ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Complete Chloroplast Genome ◽  
Coding Regions ◽  
Chloroplast Genomes

Compared with other members of the family Rosaceae, the chloroplast genomes ofFragariaspecies exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing ofFragariaspecies is needed. In this study, we sequenced the complete chloroplast genome ofF. × ananassa‘Benihoppe’ using the Illumina HiSeq 2500-PE150 platform and then performed a combination ofde novoassembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of theF. × ananassa‘Benihoppe’ chloroplast genome is 155,549 bp, representing the smallestFragariachloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content inFragaria, particularly among three octoploid strawberries which wereF. × ananassa‘Benihoppe’,F.chiloensis(GP33) andF.virginiana(O477). However, when the sequences of the coding and non-coding regions ofF. × ananassa‘Benihoppe’ were compared in detail with those ofF.chiloensis(GP33) andF.virginiana(O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK,trnS-trnG,atpF-atpH,trnC-petN,trnT-psbDandtrnP-psaJ) with a percentage of variable sites greater than 1% and no less than five parsimony-informative sites were identified and may be useful for phylogenetic analysis of the genusFragaria.

scholarly journals Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada

2019 ◽  
Vol 8 (23) ◽  
Author(s):  
Diana Lin ◽  
Lauren Coombe ◽  
Shaun D. Jackman ◽  
Kristina K. Gagalova ◽  
René L. Warren ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Genome Sequence ◽  
Picea Glauca ◽  
Phylogenetic Analyses ◽  
White Spruce ◽  
Eastern Canada ◽  
Ongoing Research ◽  
Complete Chloroplast Genome ◽  
Content Type ◽  
Chloroplast Genome Sequence

Here, we present the complete chloroplast genome sequence of white spruce (Picea glauca, genotype WS77111), a coniferous tree widespread in the boreal forests of North America. This sequence contributes to genomic and phylogenetic analyses of the Picea genus that are part of ongoing research to understand their adaptation to environmental stress.

scholarly journals Complete chloroplast genome sequences of four Allium species: comparative and phylogenetic analyses

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
YuMeng Huo ◽  
LiMin Gao ◽  
BingJiang Liu ◽  
YanYan Yang ◽  
SuPing Kong ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Genome Sequences ◽  
Allium Species ◽  
Complete Chloroplast Genome
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