RETRACTED ARTICLE: Inferring Phylogenetic Relationships of Indian Citron (Citrus medica L.) based on rbcL and matK Sequences of Chloroplast DNA

Uchoi, Ajit; Malik, Sunil; Choudhary, Ravish; Kumar, Susheel; Rohini, M. R.; Pal, Digvender; Erċışlı, Sezai; Chaudhury, Rekha

doi:10.1007/s10528-016-9716-2

Cited by 14 publications

(7 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, in addition to IGS and introns, we identified a number of coding regions that may prove useful for Salvia phylogenetics. The four protein coding genes with highest π values identified by our study (accD, matK, ndhF, and ycf1) have all been used for phylogenetic inference (Zhang and Li 2004;Chang-Li et al 2012;Cruz et al 2013;Qian et al 2013;Luo et al 2014;Patil et al 2015;Srikulnath et al 2015;Uchoi et al 2016;Devi and Chrungoo 2017;Bengtson and Anderberg 2018;Deng et al 2018;Lei et al 2018;Satoh et al 2018;Veranso-Libalah et al 2018), but only matK and ycf1 Sytsma 2011, 2012;Hu et al 2018) have been utilized in sages.…”

Section: Discussionmentioning

confidence: 97%

Chloroplast and nuclear ribosomal cistron phylogenomics in a group of closely related sections in Salvia subg. Calosphace

et al. 2020

View full text Add to dashboard Cite

Sage phylogenies have not resolved many shallow level clades within problematic Salvia subgenus Calosphace, hindered by the difficulty in finding sufficiently variable loci. We assembled fifteen chloroplast genomes and nuclear ribosomal cistrons from non-target reads of a nuclear hybrid enrichment project to assess the phylogenetic utility for a closely related group of mainly Mexican sections. Chloroplast synteny is confirmed with 10 Lamiales chloroplasts, supporting a map to reference assembly. Salvia miltiorrhiza Bunge chloroplast was used as a reference for assemblies, averaging 25,970 reads with mean depth of 20.71 reads; genomes ranged from 141,451 to 150,339 bp. The S. carduacea Benth. nuclear ribosomal cistron (18S, ITS1, 5.8S, ITS2 and 26S) was used as a reference for assembly, averaging 66,387 reads and mean depth of 1508 reads. We evaluated several partitioning schemes for plastid, plastid and nrDNA and reduced sampling, to assess whether these would render the same phylogenetic inferences. Maximum likelihood inferences resulted with high bootstrap support and two main clades with interspersed species from Salvia sect. Scorodoniae: clade A with species from S. sects. Atratae and Mitratae and clade B from S. sects. Sigmoideae and Uricae. Only S. sect. Uricae is monophyletic in every analysis supporting its identity, not merged into S. sect. Scorodoniae; S. sect. Sigmoideae is inferred monophyletic only if the ribosomal DNA sequences are included. Greater resolution and higher branch support are obtained with the entire plastome and nrDNA, rather than subsampling highly variable regions; thus we recommend this approach with expanded taxon sampling, coupled with a morphological review to better solve sectional circumscription in closely related S. subgenus Calosphace species.

show abstract

Section: Discussionmentioning

confidence: 97%

Chloroplast and nuclear ribosomal cistron phylogenomics in a group of closely related sections in Salvia subg. Calosphace

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Nevertheless, both the IGRs and CDSs can serve as useful molecular markers. Some genes (matK, rps16, rbcL, rpl16, ndhA, ndhF, and ycf1) and IGRs (rps16-trnQ, petN-psbM, rps15-ycf1, trnL-trnF) exhibited high nucleotide diversity (Table S2), which have also been used for phylogenetic and phylogeography analyses (Ravi et al, 2007;Chavez et al, 2016;Uchoi et al, 2016;Yang et al, 2016;Khan et al, 2018).…”

Section: Cerasus Cp Genome Features and Genomic Variationmentioning

confidence: 99%

Evolutionary and phylogenetic analyses of 11 Cerasus species based on the complete chloroplast genome

et al. 2023

View full text Add to dashboard Cite

The subgenus Cerasus, one of the most important groups in the genus Prunus sensu lato, comprises over 100 species; however, the taxonomic classification and phylogenetic relationships of Cerasus remain controversial. Therefore, it is necessary to reconstruct the phylogenetic tree for known Cerasus species. Here, we report the chloroplast (cp) genome sequences of 11 Cerasus species to provide insight into evolution of the plastome. The cp genomes of the 11 Cerasus species (157,571–158,830 bp) displayed a typical quadripartite circular structure. The plastomes contain 115 unique genes, including 80 protein-coding genes, four ribosomal RNAs, and 31 transfer RNAs. Twenty genes were found to be duplicated in inverted repeats as well as at the boundary. The conserved non-coding sequences showed significant divergence compared with the coding regions. We found 12 genes and 14 intergenic regions with higher nucleotide diversity and more polymorphic sites, including matK, rps16, rbcL, rps16-trnQ, petN-psbM, and trnL-trnF. During cp plastome evolution, the codon profile has been strongly biased toward the use of A/T at the third base, and leucine and isoleucine codons appear the most frequently. We identified strong purifying selection on the rpoA, cemA, atpA, and petB genes; whereas ccsA, rps19, matK, rpoC2, ycf2 and ndhI showed a signature of possible positive selection during the course of Cerasus evolution. In addition, we further analyzed the phylogenetic relationships of these species with 57 other congenic related species.Through reconstructing the Cerasus phylogeny tree, we found that true cherry is similar to the flora of China forming a distinct group, from which P. mahaleb was separated as an independent subclade. Microcerasus was genetically closer to Amygdalus, Armeniaca, and Prunus (sensu stricto) than to members of true cherry, whereas P. japonica and P. tomentosa were most closely related to P. triloba and P. pedunculata. However, P. tianshanica formed a clade with P. cerasus, P. fruticosa, P. cerasus × P. canescens ‘Gisela 6’, and P. avium as a true cherry group. These results provide new insights into the plastome evolution of Cerasus, along with potential molecular markers and candidate DNA barcodes for further phylogenetic and phylogeographic analyses of Cerasus species.

show abstract

“…These results indicated that multi-region sampling can improve the resolution of the analysis. In addition, two protein-coding genes (rpoB and rbcL), which were considered as having a high level of variability in angiosperms, have been recommended and used for phylogenetic studies (Chase et al 2007;Okoth et al 2016;Uchoi et al 2016;Sha et al 2017;Oyebanji et al 2020). They were also used for understanding the phylogenetic relationships and diversity in subgenus Cerasus (Jung and Oh.…”

Section: Discussionmentioning

confidence: 99%

Comparative chloroplast genomes of Prunus subgenus Cerasus (Rosaceae): insights into sequence variations and phylogenetic relationships

Yan

et al. 2021

Tree Genetics & Genomes

View full text Add to dashboard Cite

Prunus subgenus Cerasus is a large and diverse genus. Its botanical classification has long been controversial and complicated. Molecular markers derived from the chloroplast genome may provide useful tools for phylogenetic resolution and taxonomic study in Prunus species. Thus, we compared chloroplast genomes of 23 Prunus species to identify sequences with high variation levels. The repeated sequences (RSs) and two types of sequence variation, comprising divergent homologous regions and short sequence repeats (SSRs), were identified. The species with the highest number of RSs was P. emarginata (60), whereas P. campanulata contained the highest amount of SSRs (70). In contrast, P. dictyoneura and P. yedoensis contained the lowest number of RSs (37) and SSRs (46), respectively. Out of these homologous SSRs, 11 were shared in the 23 species, and seven of them showed variations. A total of 203 homologous regions were identified. Out of these, 20 regions (19 IGSs and one intron) showed a high variation from 6.75 to 19.31%. The phylogenetic tree which was inferred based on 19 highly variable regions showed a topology similar to the one obtained using the whole chloroplast genome. We conclude that the seven variable SSRs and the 20 highly variable regions may potentially be convenient as molecular markers for phylogenetic and population genetics studies in subgenus Cerasus species. In addition, the molecular phylogenetic position of P. clarofolia was inferred based on the 19 highly variable regions.

show abstract

RETRACTED ARTICLE: Inferring Phylogenetic Relationships of Indian Citron (Citrus medica L.) based on rbcL and matK Sequences of Chloroplast DNA

Cited by 14 publications

References 49 publications

Chloroplast and nuclear ribosomal cistron phylogenomics in a group of closely related sections in Salvia subg. Calosphace

Chloroplast and nuclear ribosomal cistron phylogenomics in a group of closely related sections in Salvia subg. Calosphace

Evolutionary and phylogenetic analyses of 11 Cerasus species based on the complete chloroplast genome

Comparative chloroplast genomes of Prunus subgenus Cerasus (Rosaceae): insights into sequence variations and phylogenetic relationships

Contact Info

Product

Resources

About