Pollen Morphology in Sorbus L. (Rosaceae) and Its Taxonomic Implications.

The genus Sorbus L. in the Rosaceae family is taxonomically challenging due to its morphological variation, polyploidy, and interspecific hybridization. In this study, we used scanning electron microscopy (SEM) to observe the pollen morphology of eighty species, representing six subgenera, in order to assess the differences within the genus Sorbus and its pollen characteristics. We conducted a cluster analysis on three qualitative and four quantitative characteristics. The results demonstrated that the pollen grains of the studied Sorbus species are isopolar and tricolporate. We identified five types of pollen shapes: suboblate, spheroidal, subprolate, prolate, and perprolate. The pollen ornamentation of the investigated species could be classified into five types: striate-perforate, striate, cerebroid-perforate, cerebroid, and foveolate. Interestingly, within the same subgenera, different species exhibited multiple types of characters. The cluster analysis indicated that all 80 species could be divided into six groups, with group B consisting exclusively of species from the subgenus Sorbus. Although pollen micro-morphologies alone do not provide sufficient evidence to establish the taxonomic relationships of the subgenera within Sorbus, they do offer valuable information for species-level taxonomic treatment.

Comparative analysis of the complete plastid genomes in Prunus subgenus Cerasus (Rosaceae): Molecular structures and phylogenetic relationships.

Prunus subgenus Cerasus (cherry) is an economically important group that distributed in temperate regions of the northern hemisphere. However, shared interspecific morphological traits and variability across taxa of Cerasus are among the impediments to taxonomic efforts to correctly delimit taxa. This is further complicated by a lack of genetic information on these taxa, with no focused genomic or phylogenetic studies being done on Cerasus. In this study, we conducted comparative analysis on the complete plastid genomes (plastomes) of 20 Cerasus species to gain a greater understanding of the attributes of the plastome of these taxa while helping resolve their phylogenetic placement in Prunus sensu lato and interspecific relationships within the subgenus. Our results displayed that (1) the plastomes of the 20 Cerasus species studied exhibited a typical quadripartite structure with conversed genome arrangement, structure, and moderate divergence. (2) The average size of complete plastomes for the Cerasus taxa studied was 157,861 bp, ranging from 157,458 to 158,024 bp. A total of 134 genes were annotated, including 86 protein-coding genes, 40 tRNAs, and 8 rRNAs across all species. In simple sequence repeat analysis, we found Cerasus had a comparable number of dispersed and tandem repeats to those identified in other angiosperm taxa, with only P. pseudocerasus found to contain trinucleotide repeats. Nucleotide diversity analysis revealed that the trnG-GCC gene and rpl32-trnL region had the highest Pi value showing potential as phylogenetic markers. (3) Two phylogenetic trees of the plastomes verified the monophyletic relationship of Cerasus and provided a more resolved species-level phylogeny. Our study provides detailed plastome information for exploring the phylogeny of subg. Cerasus taxa. We identified various types of repeats and nucleotide diversity hotspots, which can be a reference for species identification and reconstruction of phylogenetic relationships.

SWATH-MS based quantitive proteomics reveal regulatory metabolism and networks of androdioecy breeding system in Osmanthus fragrans.

BACKGROUND: The fragrant flower plant Osmanthus fragrans has an extremely rare androdioecious breeding system displaying the occurrence of males and hermaphrodites in a single population, which occupies a crucial intermediate stage in the evolutionary transition between hermaphroditism and dioecy. However, the molecular mechanism of androdioecy plant is very limited and still largely unknown. RESULTS: Here, we used SWATH-MS-based quantitative approach to study the proteome changes between male and hermaphroditic O. fragrans pistils. A total of 428 proteins of diverse functions were determined to show significant abundance changes including 210 up-regulated and 218 down-regulated proteins in male compared to hermaphroditic pistils. Functional categorization revealed that the differentially expressed proteins (DEPs) primarily distributed in the carbohydrate metabolism, secondary metabolism as well as signaling cascades. Further experimental analysis showed the substantial carbohydrates accumulation associated with promoted net photosynthetic rate and water use efficiency were observed in purplish red pedicel of hermaphroditic flower compared with green pedicel of male flower, implicating glucose metabolism serves as nutritional modulator for the differentiation of male and hermaphroditic flower. Meanwhile, the entire upregulation of secondary metabolism including flavonoids, isoprenoids and lignins seem to protect and maintain the male function in male flowers, well explaining important feature of androdioecy that aborted pistil of a male flower still has a male function. Furthermore, nine selected DEPs were validated via gene expression analysis, suggesting an extra layer of post-transcriptional regulation occurs during O. fragrans floral development. CONCLUSION: Taken together, our findings represent the first SWATH-MS-based proteomic report in androdioecy plant O. fragrans, which reveal carbohydrate metabolism, secondary metabolism and post-transcriptional regulation contributing to the androdioecy breeding system and ultimately extend our understanding on genetic basis as well as the industrialization development of O. fragrans.

Characterization of the complete chloroplast genome of Prunus clarofolia C.K. Schneid (Rosaceae).

Prunus clarofolia is an endemic species that widely distributed in subtropical regions of China. Here we present its complete plastome. The plastome of P. clarofolia is successfully assembled from raw reads sequenced by Illumina Hiseq 2500 platform system. The complete chloroplast of this species is 158,053 bp in length with 36.7% overall GC content, including a pair of invert repeat regions (IR) (26,393bp) that is divided by a large single copy region (LSC) (86,088bp) and a small single copy region (SSC) (19,179bp). The plastid genome contained a total of 130 genes, including 85 coding genes, 8 rRNA genes, and 37 tRNA genes. Each of rps16, atpF, rpoC1, clpP, petB, petD, rpl16, rpl2, ndhB, and ndhA contains one intron, rps12 and ycf3 contains two introns. Phylogenetic analysis indicates that P. clarofolia has a closer relationship with P. avium.

The complete plastid genome of cherry plants Prunus sargentii (Rosaceae) and its phylogenetic implication.

Prunus sargentii is an ornamental flowering cherry species, spread in Japan, Korea, Russia, and Northeast China. Little information is available regarding its genomic, with limited phylogenetic relationship study performed on P. sargentii until now. In this research, we reported the complete plastid genome of P. sargentii. The complete chloroplast of this species is 158,138 bp in length, including a pair of invert repeat regions (IR) (26,463bp) that is divided by a large single-copy region (LSC) (85,959bp) and a small single-copy region (SSC) (19,253bp). The plastid genome contained a total of 128 genes, including 84 coding genes, eight rRNA genes, and 36 tRNA genes. Phylogenetic analysis indicates that P. sargentii has a closer relationship with P. kumanoensis.

Complete chloroplast genome of a wild-type Gardenia jasminoides ellis (rubiaceae) adapted to island climate.

Gardenia jasminoides Ellis is a traditional aromatic and medicinal plant in China. Here, the complete chloroplast genome of a wild-type gardenia adapted to island climate was assembled. The assembled genome was 155,247 bp in length, with four typical regions, i.e., a large single-copy (LSC) region (85,414 bp), a small single-copy (SSC) region (18,235 bp) and two inverted repeats (IRs) regions (25,799 bp each). In total, 138 genes were predicted, including 90 protein-coding genes, 40 tRNA genes and eight rRNA genes. The overall GC content of the chloroplast genome was 37.5%. The chloroplast genome would provide more information for the phylogeography and phylogeny study of G. jasminoides.

Phylogeography and the population genetic structure of flowering cherry Cerasus serrulata (Rosaceae) in subtropical and temperate China.

Cerasus serrulata (Rosaceae) is an important flowering cherry resource which is valuable for developing new cultivars of flowering cherries. It is broadly distributed and possesses abundant variations. In this study, phylogeographic analysis was conducted to reveal the evolutionary history to better understand the genetic diversity and genetic structure of C. serrulata so as to provide more accurate molecular insights into better conservation and utilization of the germplasm resources. A total of 327 individuals from 18 wild populations were collected. Three chloroplast DNA (cpDNA) fragments (matK, trnD-E, and trnS-G) and the nuclear internal transcribed spacer (ITS) were utilized. The results showed a high genetic diversity at both species level and population level of C. serrulata. High genetic differentiation and the existence of the phylogeographic structure were detected. No significant expansion events were discovered. Two geographic lineages were inferred. One was confined to the Qinling Mountains and the Taihang Mountains. The other was from the Wuling Mountains to the Jiangnan Hilly Regions and then went northeast to the coast of Asia. In addition, some taxonomic treatments of the C. serrulata complex are discussed and reconsidered. Conservation and utilization strategies of wild C. serrulata germplasm resources were recommended.

The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species.

Cerasus serrulata is a flowering cherry germplasm resource for ornamental purposes. In this work, we present a de novo chromosome-scale genome assembly of C. serrulata by the use of Nanopore and Hi-C sequencing technologies. The assembled C. serrulata genome is 265.40 Mb across 304 contigs and 67 scaffolds, with a contig N50 of 1.56 Mb and a scaffold N50 of 31.12 Mb. It contains 29,094 coding genes, 27,611 (94.90%) of which are annotated in at least one functional database. Synteny analysis indicated that C. serrulata and C. avium have 333 syntenic blocks composed of 14,072 genes. Blocks on chromosome 01 of C. serrulata are distributed on all chromosomes of C. avium, implying that chromosome 01 is the most ancient or active of the chromosomes. The comparative genomic analysis confirmed that C. serrulata has 740 expanded gene families, 1031 contracted gene families, and 228 rapidly evolving gene families. By the use of 656 single-copy orthologs, a phylogenetic tree composed of 10 species was constructed. The present C. serrulata species diverged from Prunus yedoensis ~17.34 million years ago (Mya), while the divergence of C. serrulata and C. avium was estimated to have occurred ∼21.44 Mya. In addition, a total of 148 MADS-box family gene members were identified in C. serrulata, accompanying the loss of the AGL32 subfamily and the expansion of the SVP subfamily. The MYB and WRKY gene families comprising 372 and 66 genes could be divided into seven and eight subfamilies in C. serrulata, respectively, based on clustering analysis. Nine hundred forty-one plant disease-resistance genes (R-genes) were detected by searching C. serrulata within the PRGdb. This research provides high-quality genomic information about C. serrulata as well as insights into the evolutionary history of Cerasus species.

The complete plastid genome of cherry plants Prunus discoidea (Rosaceae) and its phylogenetic implication.

Prunus discoidea is an endemic cherry species with ornamental value, spread in eastern China (Anhui, Jiangxi, Zhejiang provinces). Little information is available regarding its genomic, with limited phylogenetic relationship study performed on P. discoidea until now. The plastid genome was 158,024 bp in length consisting of four regions: large single-copy region (85,953 bp), small single-copy region (19,113 bp), and a pair of inverted repeat regions (26,469 bp each). The plastid genome contained a total of 129 genes, including 84 coding genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis for 20 reported genomes within the Prunus sensu lato showed three main clades of Prunus s.l. with strong supports.

Complete chloroplast genome of the wild Japanese Mountain cherry (Prunus jamasakura, Rosaceae).

Prunus jamasakura is a species of Prunus native to eastern Asia. We determined the first complete chloroplast genome of Prunus jamasakura using genome skimming approach. The cp genome was 157,905 bp long, with a large single-copy region (LSC) of 85,910 bp and a small single-copy region (SSC) of 19,123 bp separated by a pair of inverted repeats (IRs) of 26,436 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Prunus sensu lato using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that P. jamasakura is closely related with Prunus speciosa.

The eIF3a Arg803Lys genetic polymorphism is associated with susceptibility to and chemoradiotherapy efficacy in cervical carcinoma.

We aimed to explore the correlations between eukaryotic translation initiation factor 3, subunit A (eIF3a) polymorphisms and susceptibility to and chemoradiotherapy efficacy in cervical carcinoma. Between August 2007 and August 2011, 176 patients with cervical carcinoma were enrolled as the case group, and 180 healthy individuals were selected as the control group. eIF3a Arg803Lys C>T genotypes were detected by hemi-nested polymerase chain reaction restriction fragment length polymorphism. All patients received chemoradiotherapy and were evaluated for efficacy. Compared with carriers of the CC genotype, carriers of the T genotype of the eIF3a Arg803Lys C>T polymorphism had a higher risk of cervical carcinoma. The eIF3a Arg803Lys C>T polymorphism was associated with tumor size, differentiation degree, Federation of Gynecology and Obstetrics (FIGO) stage, and lymph node metastasis (LNM). The overall response rate of the case group was 69.32% (122/176). The response rate of CC genotype carriers was higher compared to patients with the CT+TT genotypes. Binary-logistic regression analysis showed that tumor size, FIGO stage, LNM, and the eIF3a Arg803Lys C>T polymorphism were influencing factors for chemoradiotherapy efficacy. Univariate analysis revealed that age, eIF3a Arg803Lys C>T polymorphism, differentiation degree, FIGO stage, and LNM were prognostic factors of cervical carcinoma, and multivariate analysis showed that age ≥ 60 years, higher FIGO stage, and LNM, as well as the CT and TT genotypes of the eIF3a Arg803Lys C>T polymorphism, were risk factors related to the prognosis of cervical carcinoma. The eIF3a Arg803Lys C>T polymorphism is connected with a higher susceptibility to cervical carcinoma and may affect chemoradiotherapy efficacy in and prognosis of cervical carcinoma.

Increased expression of miR-15b is associated with clinicopathological features and poor prognosis in cervical carcinoma.

OBJECTIVE: The aims of this study were to explore the expression of microRNA-15b (miR-15b) in cervical carcinoma and to correlate its expression with clinicopathological characteristics and prognosis. METHODS: Quantitative reverse transcriptase polymerase chain reaction analysis was conducted to quantify the expression level of miR-15b in 607 cervical tissues, including 185 cervical carcinoma tissues, 124 CIN I lesions, 148 CIN II-III lesions, and 150 normal cervical tissues. The 5-year overall cumulative survival rates for all patients with cervical carcinoma were calculated using Kaplan-Meier survival analysis, and multivariate survival analysis of these patients was completed using the stepwise Cox proportional hazards regression model. RESULTS: The expression of miR-15b gradually increased from normal cervical tissues to CIN lesions and then to cervical carcinoma tissues (all P < 0.05), and it was strongly correlated with degree of differentiation, clinical stage, tumor diameter, and lymph-node metastases (all P < 0.05). When the median value of miR-15b expression was used as the cut-off point, patients with high miR-15b expression (above the median) had worse 5-year overall cumulative survival rates than those who exhibited low miR-15b expression (below the median; P < 0.05). Multivariate analysis using the Cox regression model identified miR-15b expression, clinical stage, tumor diameter, and lymph-node metastasis as independent risk factors for cervical carcinoma prognosis (all P < 0.05). CONCLUSION: Our results indicate that elevated miRNA-15b expression is a typical feature in cervical carcinoma, which could be a useful clinical predictor for the early diagnosis and evaluation of cervical carcinoma prognosis.