Association between Chloroplast and Mitochondrial DNA sequences in Chinese Prunus genotypes (Prunus persica, Prunus domestica, and Prunus avium)

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

Introduction

Prunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome.

Methods

In the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated.

Results and discussion

The P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.

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

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.

The complete plastomes of red fleshed pitaya (Selenicereus monacanthus) and three related Selenicereus species: insights into gene losses, inverted repeat expansions and phylogenomic implications

Selenicereus is a genus of perennial shrub from the family Cactaceae, and some of them play an important role in the food industry, pharmaceuticals, cosmetics and medicine. To date, there are few reports on Selenicereus plastomes, which limits our understanding of this genus. Here, we have reported the complete plastomes of four Selenicereus species (S. monacanthus, S. annthonyanus, S. grandifloras, and S. validus) and carried out a comprehensive comparative analysis. All four Selenicereus plastomes have a typical quartile structure. The plastome size ranged from 133,146 to 134,450 bp, and contained 104 unique genes, including 30 tRNA genes, 4 rRNA genes and 70 protein-coding genes. Comparative analysis showed that there were massive losses of ndh genes in Selenicereus. Besides, we observed the inverted repeat regions had undergone a dramatic expansion and formed a previously unreported small single copy/inverted repeat border in the intron region of the atpF gene. Furthermore, we identified 6 hypervariable regions (trnF-GAA-rbcL, ycf1, accD, clpP-trnS-GCU, clpP-trnT-CGU and rpl22-rps19) that could be used as potential DNA barcodes for the identification of Selenicereus species. Our study enriches the plastome in the family Cactaceae, and provides the basis for the reconstruction of phylogenetic relationships.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01121-z.

ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica

Background

Chloroplast genome sequencing is becoming a valuable process for developing several DNA barcodes. At present, plastid DNA barcode for systematics and evolution in flowering plant rely heavily on the use of non-coding genes. The present study was performed to verify the novelty and suitability of the two hotspot barcode plastid coding gene ycf1 and ndhF, to estimate the rate of molecular evolution in the Prunus genus at low taxonomic levels.

Results

Here, 25 chloroplast genomes of Prunus genus were selected for sequences annotation to search for the highly variable coding DNA barcode regions. Among them, 5 genera were of our own data, including the ornamental, cultivated, and wild haplotype, while 20 genera have been downloaded from the GenBank database. The results indicated that the two hotspot plastid gene ycf1 and ndhF were the most variable regions within the coding genes in Prunus with an average of 3268 to 3416 bp in length, which have been predicted to have the highest nucleotide diversity, with the overall transition/transversion bias (R = 1.06). The ycf1-ndhF structural domains showed a positive trend evident in structure variation among the 25 specimens tested, due to the variant overlap^’s gene annotation and insertion or deletion with a broad trend of the full form of IGS sequence. As a result, the principal component analysis (PCA) and the ML tree data drew an accurate monophyletic annotations cluster in Prunus species, offering unambiguous identification without overlapping groups between peach, almond, and cherry.

Conclusion

To this end, we put forward the domain of the two-locus ycf1-ndhF genes as the most promising coding plastid DNA barcode in P. persica at low taxonomic levels. We believe that the discovering of further variable loci with high evolutionary rates is extremely useful and potential uses as a DNA barcode in P. persica for further phylogeny study and species identification.

The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies

Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. Currently, a 6K SNP array enables genome scans in cherry; however, only a third of these SNPs are informative, with low coverage in many genomic regions. Adding previously detected SNPs to this array could provide a cost-efficient upgrade with increased genomic coverage across the 670 cM/352.9 Mb cherry whole genome sequence. For sweet cherry, new SNPs were chosen following a focal point strategy, grouping six to eight SNPs within 10-kb windows with an average of 0.6 cM (627 kb) between focal points. Additional SNPs were chosen to represent important regions. Sweet cherry, the fruticosa subgenome of sour cherry, and cherry organellar genomes were targeted with 6942, 2020, and 38 new SNPs, respectively. The +9K add-on provided 2128, 1091, and 70 new reliable, polymorphic SNPs for sweet cherry and the avium and the fruticosa subgenomes of sour cherry, respectively. For sweet cherry, 1241 reliable polymorphic SNPs formed 237 informative focal points, with another 2504 SNPs in-between. The +9K SNPs increased genetic resolution and genome coverage of the original cherry SNP array and will help increase understanding of the genetic control of key traits and relationships among individuals in cherry.

Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (HE = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: FST = 0.165***; cpDNA: FST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000-100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex.

Characterization of complete chloroplast genome and phylogenetic analysis of sweet cherry Cerasus avium (L.) Moench (Prunoideae, Rosaceae)

Sweet cherry (Cerasus avium (L.) Moench) belonging to family Rosaceae, is an important economical fruit crop worldwide. In this study, the complete chloroplast (cp) genome of sweet cherry was generated by De novo assembly with low coverage whole-genome sequencing data. The genome size was 157,987 bp in length consisting of a typical quadripartite structure; a large single-copy region (LSC, 85,975 bp), a small single-copy region (SSC, 19,121 bp) and a pair of inverted repeat regions (IRs, 26,445 bp each). A total of 115 genes were predicted including 82 protein-coding genes, 29 tRNA genes and four rRNA genes. Phylogenetic analysis based on 12 reported complete chloroplast genome indicated the monophyly of the genus Creasus including newly sequenced C. avium, which is conform to the traditional classification.

Mathematical Modeling and Optimizing of in Vitro Hormonal Combination for G × N15 Vegetative Rootstock Proliferation Using Artificial Neural Network-Genetic Algorithm (ANN-GA)

The efficiency of a hybrid systems method which combined artificial neural networks (ANNs) as a modeling tool and genetic algorithms (GAs) as an optimizing method for input variables used in ANN modeling was assessed. Hence, as a new technique, it was applied for the prediction and optimization of the plant hormones concentrations and combinations for in vitro proliferation of Garnem (G × N15) rootstock as a case study. Optimizing hormones combination was surveyed by modeling the effects of various concentrations of cytokinin-auxin, i.e., BAP, KIN, TDZ, IBA, and NAA combinations (inputs) on four growth parameters (outputs), i.e., micro-shoots number per explant, length of micro-shoots, developed callus weight (CW) and the quality index (QI) of plantlets. Calculation of statistical values such as R2 (coefficient of determination) related to the accuracy of ANN-GA models showed a considerably higher prediction accuracy for ANN models, i.e., micro-shoots number: R2 = 0.81, length of micro-shoots: R2 = 0.87, CW: R2 = 0.88, QI: R2 = 0.87. According to the results, among the input variables, BAP (19.3), KIN (9.64), and IBA (2.63) showed the highest values of variable sensitivity ratio for proliferation rate. The GA showed that media containing 1.02 mg/l BAP in combination with 0.098 mg/l IBA could lead to the optimal proliferation rate (10.53) for G × N15 rootstock. Another objective of the present study was to compare the performance of predicted and optimized cytokinin-auxin combination with the best optimized obtained concentrations of our other experiments. Considering three growth parameters (length of micro-shoots, micro-shoots number, and proliferation rate), the last treatment was found to be superior to the rest of treatments for G × N15 rootstock in vitro multiplication. Very little difference between the ANN predicted and experimental data confirmed high capability of ANN-GA method in predicting new optimized protocols for plant in vitro propagation.

Characterization and Phylogenetic Analysis of Ancient Italian Landraces of Pear

Pear is one of the oldest fruit tree crops and the third most important temperate fruit species. Its domestication took place independently in the Far East (China) and in the Caucasus region. While the origin of Eastern Asian cultivars is clear, that of European cultivars is still in doubt. Italy has a wealth of local varieties and genetic resources safeguarded by several public and private collections to face the erosion caused by the introduction of improved varieties in specialized orchards. The objectives of the present study were: (i) to characterize the existing germplasm through nuclear (SSR) and (ii) to clarify the genetic divergence between local and cultivated populations through chloroplast DNA (cpDNA) markers in order to provide insights into phylogenetic relationships of Pyrus spp. For this reason, 95 entries from five different germplasm collections, including nine European, Mediterranean and Eastern Asian species, were analyzed, and the intergenic accD-psaI sequences were compared to the worldwide distributed dataset encompassing a total of 298 sequences from 26 different Pyrus species. The nine nuclear SSRs were able to identify a total of 179 alleles, with a loci polymorphism P = 0.89. Most of the variation (97%) was found within groups. Five accessions from different sources were confirmed to be the same. Eight out of 20 accessions of unknown origin were identified, and six synonyms were detected. Locus NH030a was found to be monomorphic in all the cultivated accessions and in reference species interfertile with P. communis, leading to hypothesize selection pressures for adaptation to cultivation. The cpDNA sequences of the 95 accessions were represented by 14 haplotypes, six of which (derived from P. communis, P. cossonii and P. ussuriensis) are recorded here for the first time and may suggest the ancient origin of some local varieties. The network analysis of the 298 cpDNA sequences allowed two different haplogroups, Eastern and Western Eurasia, to be defined, supporting recent views of a clear division between Occidental and Oriental species. By combining the results from nuclear and uniparental markers, it was possible to better define many unknown accessions.