Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

Li, Wenwen; Liu, Liqiang; Zhang, Qiu-Ping; Zhou, Weiquan; Fan, Guoquan

doi:10.1038/s41598-021-93050-w

Cited by 7 publications

(7 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Chloroplast genome markers are widely applied to analyzing both phylogeny and population structure (Hu et al., 2019 ; Xie et al., 2018 ). Markers in noncoding regions are commonly utilized for investigating genetic differentiation (Binks et al., 2021 ; Fang et al., 2010 ; Shaw et al., 2007 ), but there are also coding regions that are polymorphic and designed for markers, such as in Saxifraga sinomontana (Li et al., 2018 ), Quercus liaotungensis (Yang et al., 2018 ), and Prunus armeniaca (Li et al., 2021 ). Here, we discovered a polymorphic marker in psa A from sequence alignments, which is infrequently reported in other studies.…”

Section: Discussionmentioning

confidence: 99%

Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes

Xiao,

Wang,

et al. 2023

Ecology and Evolution

View full text Add to dashboard Cite

Toona ciliata is an endangered species due to over‐cutting and low natural regeneration in China. Its genetic conservation is of an increasing concern. However, several varieties are recognized according to the leaf and flower traits, which complicates genetic conservation of T. ciliata. Here, we sequenced the whole chloroplast genome sequences of three samples for each of four varieties (T. ciliata var. ciliata, T. ciliata var. yunnanensis, T. ciliata var. pubescens, and T. ciliata var. henryi) in sympatry and assessed their phylogenetic relationship at a fine spatial scale. The four varieties had genome sizes ranged from 159,546 to 159,617 bp and had small variations in genome structure. Phylogenomic analysis indicated that the four varieties were genetically well‐mixed in branch groups. Genetic diversity from the whole chloroplast genome sequences of 12 samples was low among varieties (average π = 0.0003). Besides, we investigated genetic variation of 58 samples of the four varieties in sympatry using two markers (psaA and trnL‐trnF) and showed that genetic differentiation was generally insignificant among varieties (Фst = 0%–5%). Purifying selection occurred in all protein‐coding genes except for the ycf2 gene that was under weak positive selection. Most amino acid sites in all protein‐coding genes were under purifying selection except for a few sites that were under positive selection. The chloroplast genome‐based phylogeny did not support the morphology‐based classification. The overall results implicated that a conservation strategy based on the T. ciliata complex rather than on intraspecific taxon was more appropriate.

show abstract

Section: Discussionmentioning

confidence: 99%

Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes

Xiao,

Wang,

et al. 2023

Ecology and Evolution

View full text Add to dashboard Cite

show abstract

“…rbcL gene encodes large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco), and ycf1 and ycf2 genes encode unknown function proteins. Both rbcL and ycf1 genes are intensively used for species identification, phylogenetic, phylogeography, germplasm conservation and innovative utilization of many plants [ 55 – 58 ]. Lastly, there is one gene ( ndhA ) encoding subunit of NADH-plastoquinone oxidoreductase, which is found under positive selection with 5 amino acid sites.…”

Section: Discussionmentioning

confidence: 99%

Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

Wang

et al. 2021

BMC Plant Biol

View full text Add to dashboard Cite

Background Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in subfamily Zingiberoideae each possess 50 or more species, including Globba (100), Hedychium (> 80), Kaempferia (50) and Zingiber (150). Despite the agricultural, medicinal and horticultural importance of these species, genomic resources and suitable molecular markers for them are currently sparse. Results Here, we have sequenced, assembled and analyzed ten complete chloroplast genomes from nine species of subfamily Zingiberoideae: Globba lancangensis, Globba marantina, Globba multiflora, Globba schomburgkii, Globba schomburgkii var. angustata, Hedychium coccineum, Hedychium neocarneum, Kaempferia rotunda ‘Red Leaf’, Kaempferia rotunda ‘Silver Diamonds’ and Zingiber recurvatum. These ten chloroplast genomes (size range 162,630–163,968 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 87,172–88,632 bp), a small single copy (SSC, 15,393–15,917 bp) and a pair of inverted repeats (IRs, 29,673–29,833 bp). The genomes contain 111–113 different genes, including 79 protein coding genes, 28–30 tRNAs and 4 rRNA genes. The dynamics of the genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats exhibit similarities, with slight differences observed among the ten genomes. Further comparative analysis of seventeen related Zingiberoideae species, 12 divergent hotspots are identified. Positive selection is observed in 14 protein coding genes, including accD, ccsA, ndhA, ndhB, psbJ, rbcL, rpl20, rpoC1, rpoC2, rps12, rps18, ycf1, ycf2 and ycf4. Phylogenetic analyses, based on the complete chloroplast-derived single-nucleotide polymorphism data, strongly support that Globba, Hedychium, and Curcuma I + “the Kaempferia clade” consisting of Curcuma II, Kaempferia and Zingiber, form a nested evolutionary relationship in subfamily Zingiberoideae. Conclusions Our study provides detailed information on ten complete Zingiberoideae chloroplast genomes, representing a valuable resource for future studies that seek to understand the molecular evolutionary dynamics in family Zingiberaceae. The identified divergent hotspots can be used for development of molecular markers for phylogenetic inference and species identification among closely related species within four genera of Globba, Hedychium, Kaempferia and Zingiber in subfamily Zingiberoideae.

show abstract

“…Higher genetic divergence was observed using the nrDNA (ETS+ITS2) dataset exhibiting four haplotypes in the studied populations. The nrDNA has always shown higher genetic divergence than the cpDNA [ 65 , 66 ]. Indeed, the cpDNA tends to evolve very slowly, with low recombination and mutation rates [ 67 ].…”

Section: Discussionmentioning

confidence: 99%

Multilocus marker-based delimitation of Salicornia persica and its population discrimination assisted by supervised machine learning approach

Jamdade¹,

Al-Shaer²,

Al-Sallani³

et al. 2022

PLoS ONE

View full text Add to dashboard Cite

The Salicornia L. has been considered one of the most taxonomically challenging genera due to high morphological plasticity, intergradation between related species, and lack of diagnostic features in preserved herbarium specimens. In the United Arab Emirates (UAE), only one species of this genus, Salicornia europaea, has been reported, though investigating its identity at the molecular level has not yet been undertaken. Moreover, based on growth form and morphology variation between the Ras-Al-Khaimah (RAK) population and the Umm-Al-Quwain (UAQ) population, we suspect the presence of different species or morphotypes. The present study aimed to initially perform species identification using multilocus DNA barcode markers from chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA), followed by the genetic divergence between two populations (RAK and UAQ) belonging to two different coastal localities in the UAE. The analysis resulted in high-quality multilocus barcode sequences subjected to species discrimination through the unsupervised OTU picking and supervised learning methods. The ETS sequence data from our study sites had high identity with the previously reported sequences of Salicornia persica using NCBI blast and was further confirmed using OTU picking methods viz., TaxonDNAs Species identifier and Assemble Species by Automatic Partitioning (ASAP). Moreover, matK sequence data showed a non-monophyletic relationship, and significant discrimination between the two populations through alignment-based unsupervised OTU picking, alignment-free Co-Phylog, and alignment & alignment-free supervised learning approaches. Other markers viz., rbcL, trnH-psbA, ITS2, and ETS could not distinguish the two populations individually, though their combination with matK (cpDNA & cpDNA+nrDNA) showed enough population discrimination. However, the ITS2+ETS (nrDNA) exhibited much higher genetic divergence, further splitting both the populations into four haplotypes. Based on the observed morphology, genetic divergence, and the number of haplotypes predicted using the matK marker, it can be suggested that two distinct populations (RAK and UAQ) do exist. Further extensive morpho-taxonomic studies are required to determine the inter-population variability of Salicornia in the UAE. Altogether, our results suggest that S. persica is the species that grow in the present study area in UAE, and do not support previous treatments as S. europaea.

show abstract

Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

Cited by 7 publications

References 62 publications

Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes

Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes

Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

Multilocus marker-based delimitation of Salicornia persica and its population discrimination assisted by supervised machine learning approach

Contact Info

Product

Resources

About