Novel insights into Pinus species plastids genome through phylogenetic relationships and repeat sequence analysis

Zeb, Umar; Wang, Xiukang; Fiaz, Sajid; Azizullah, Azizullah; Shah, Asad Ali; Ali, Sajjad; Rahim, Fazli; Ullah, Hafiz; Leghari, S. J.; Wang, Weiqiang; Nawaz, Taufiq

doi:10.1371/journal.pone.0262040

Cited by 3 publications

(2 citation statements)

References 31 publications

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“…In addition, it has relatively high genetic variation; therefore, it is often employed to infer the genetic relationships of species, estimate their differentiation time [12][13][14][15], and sometimes identify germplasm [16]. For example, Zeb et al compared the cp genomes of twenty-four Pinus species and identified a total of thirteen divergent hotspot regions.…”

Section: Introductionmentioning

confidence: 99%

Chloroplast Genomic Variation in Euonymus maackii Rupr. and Its Differentiation Time in Euonymus

Wang

Zhou

Liu

2022

Forests

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Euonymus maackii Rupr. is a small deciduous tree belonging to family Celastraceae. It is an important ornamental tree and a potential medicinal plant resource. Here, we assembled and annotated the chloroplast (cp) genome of E. maackii. By combining this genome with seven available cp genomes from Euonymus species, we performed plastome variation analysis of E. maackii and Euonymus. Furthermore, we reconstructed a phylogenetic tree and estimated the differentiation time of E. maackii. The newly assembled cp genome of E. maackii was 157,551 bp in size and had a typical quadripartite structure, which consisted of one large single-copy (LSC 86,524 bp) region, one small single-copy (SSC 18,337 bp) region, and a pair of inverted repeat regions (26,345 bp). A total of 652 single nucleotide polymorphisms (SNPs) and 65 insertions/deletions (indels) were detected between the two cp genomes of E. maackii, with overall genetic variation of 4.1 SNPs per kb or a π value of 0.00443, reflecting a high level of intraspecific variation. Some coding and noncoding regions with higher variation were identified, including trnV-UAC, petN, ycf1-ndhF, trnM-CAU-atpE, rpl2-rpl23, psbZ-trnG-GCC, trnY-GUA-trnE-UUC, trnW-CCA-trnP-UGG, rps16-trnQ-UUG, and psbC-trnS-UGA. The hypervariable coding and noncoding regions in E. maackii were not the same as those in Euonymus. The phylogenetic tree and divergence time based on the whole cp genomes showed that the seven Euonymus species formed a clade, which was sister to that formed with Catha edulis and Maytenus guangxiensis, and they separated 24.74 million years ago. E. maackii and E. hamiltonianus were most closely related, having separated from each other only approximately 2.68 million years ago. Our study provides important genetic information for further studies of E. maackii, such as studies on its phylogeography, population genetics and molecular ecology, and provides new insights into the evolution of the cp genome in Euonymus.

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Section: Introductionmentioning

confidence: 99%

Chloroplast Genomic Variation in Euonymus maackii Rupr. and Its Differentiation Time in Euonymus

Wang

Zhou

Liu

2022

Forests

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“…The PLOS ONE Editors retract this article [ 1 ] because it was identified as one of a series of submissions for which we have concerns about authorship, competing interests, and peer review. We regret that the issues were not addressed prior to the article’s publication.…”

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confidence: 99%

Retraction: Novel insights into Pinus species plastids genome through phylogenetic relationships and repeat sequence analysis

2023

PLoS ONE

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The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species

Mehmetoğlu,

Kaymaz,

Ateş

et al. 2023

Sci Rep

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The chloroplast (cp) genome is an adequate genomic resource to investigate evolutionary relationships among plant species and it carries marker genes available for species identification. The Cicer reticulatum is one of perennial species as the progenitor of cultivated chickpeas. Although a large part of the land plants has a quadruple chloroplast genome organization, the cp genome of C. reticulatum consists of one LSC (Large Single Copy Region), one SSC (Small Single Copy Region), and one IR (Inverted Repeat) region, which indicates that it has an untypical and unique structure. This type of chloroplast genome belongs to the IR-lacking clade. Chloroplast DNA (cpDNA) was extracted from fresh leaves using a high salt-based protocol and sequencing was performed using DNA Nanoball Sequencing technology. The comparative analysis employed between the species to examine genomic differences and gene homology. The study also included codon usage frequency analysis, hotspot divergence analysis, and phylogenetic analysis using various bioinformatics tools. The cp genome of C. reticulatum was found 125,794 bp in length, with an overall GC content of 33.9%. With a total of 79 protein-coding genes, 34 tRNA genes, and 4 rRNA genes. Comparative genomic analysis revealed 99.93% similarity between C. reticulatum and C. arietinum. Phylogenetic analysis further indicated that the closest evolutionary relative to C. arietinum was C. reticulatum, whereas the previously sequenced wild Cicer species displayed slight distinctions across their entire coding regions. Several genomic regions, such as clpP and ycf1, were found to exhibit high nucleotide diversity, suggesting their potential utility as markers for investigating the evolutionary relationships within the Cicer genus. The first complete cp genome sequence of C. reticulatum will provide novel insights for future genetic research on Cicer crops.

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Novel insights into Pinus species plastids genome through phylogenetic relationships and repeat sequence analysis

Cited by 3 publications

References 31 publications

Chloroplast Genomic Variation in Euonymus maackii Rupr. and Its Differentiation Time in Euonymus

Chloroplast Genomic Variation in Euonymus maackii Rupr. and Its Differentiation Time in Euonymus

Retraction: Novel insights into Pinus species plastids genome through phylogenetic relationships and repeat sequence analysis

The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species

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