Yazar "Wang, Yunsheng" seçeneğine göre listele
Listeleniyor 1 - 8 / 8
Sayfa Başına Sonuç
Sıralama seçenekleri
Öğe Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome(Springer Heidelberg, 2019) Wang, Yunsheng; Shahid, Muhammad Qasim; Ghouri, Fozia; Ercişli, Sezai; Baloch, Faheem ShehzadTianma (Gastrodia elata Blume) has unique biological characteristics and high medicinal value. The wild resource of G. elata is being overutilized and should be conserved as it is already included in the list of endangered species in China. The population size of cultivated G. elata is small because of domestication bottleneck. Therefore, it is of utmost importance to evolve high-quality varieties and conserve wild resources of G. elata. In this study, we sequenced tuber transcriptomes of three major cultivated sub-species of Gastrodia elata, namely G. elata BI. f. elata, G. elata Bl. f. glauca S. Chow, and G. elata Bl. f. Viridis, and obtained about 7.8G clean data. The assembled high-quality reads of three sub-species were clustered into 56,884 unigenes. Of these, 31,224 (54.89%), 25,733 (45.24%), 22,629 (39.78%), and 11,856 (20.84%) unigenes were annotated by Nr, Swiss-Port, Eukaryotic Ortholog Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Here, a total of 3766 EST-SSRs and 128,921 SNPs were identified from the unigenes. The results not only offer huge number of genes that were responsible for the growth, development, and metabolism of bioactive components, but also a large number of molecular markers were detected for future studies on the conservation genetics and molecular breeding of G. elata.Öğe Evaluation of the geographical pattern of genetic diversity of Glycine soja and Glycine max based on four single copy nuclear gene loci : for conservation of soybean germplasm(Pergamon-Elsevier Science Ltd, 2015) Wang, Yunsheng; Shahid, Muhammad Qasim; Ghouri, Fozia; Baloch, Faheem Shehzad; Wang, YingGenetic diversity and its geographical patterns play a very important role in species conservation and exploitation. Here, nucleotide polymorphism patterns of four single copy nuclear gene loci in wild (Glycine soja) and cultivated soybean (Glycine max) populations from different geographical regions as well as their demographic history were analyzed. The results showed that: (1) Southern subpopulation has the highest, while central subpopulation revealed the lowest genetic diversity among three Chinese G. soja subpopulations. (2) Northern Chinese G. max subpopulation depicted higher genetic diversity than other two Chinese, Korean, Japanese and American G. max subpopulations. (3) Significant genetic differentiation (P < 0.001) was observed among Chinese G. soja subpopulations from three ecological zones. There was also a significant genetic differentiation ( P < 0.01) between three Chinese and Japanese subpopulations of G. max. (4) The demographic dynamics revealed that effective population size of G. soja is expanding, while it was constant in G. max. G. soja is a useful germplasm resource to widen the genetic diversity of G. max. This study suggests that native populations of G. soja from different geo-ecological regions should be protected to conserve the genetic diversity. (C) 2015 Elsevier Ltd. All rights reserved.Öğe The genetic diversity and population structure of wild soybean evaluated by chloroplast and nuclear gene sequences(Pergamon-Elsevier Science Ltd, 2017) Wang, Yunsheng; Ghouri, Fozia; Shahid, Muhammad Qasim; Naeem, Muhammad; Baloch, Faheem ShehzadGlycine sofa, also called wild soybean, is the wild ancestor of domesticated soybean (Glycine max), and one of the world's major cultivated crops. Wild soybean is a valuable resource for the breeding of cultivated soybean and harbors useful genes or agronomic traits. To use and conserve this valuable resource, we conducted a study to evaluate the genetic diversity and population structure of wild soybean using the sequencing data of two nuclear loci (AF105221 and PhyB) and one chloroplast locus (trnQ-rps16) of more than 600 individuals representing 53 populations throughout the natural distribution range. The results showed that most of the variation was found within the populations and groups, but significant genetic differentiation was also detected among different eco-geographical groups. Correlations between genetic and geographical distance at all the loci were consistent with the isolation by distance gene flow model. G. sofa exhibited the highest genetic diversity in middle and downstream of Yangzi River (MDYR) region, followed by North East China (NEC), and was the lowest in North West China (NWC). We concluded that both in situ and ex situ conservation strategies required for wild soybean populations, especially which are native to MDYR and NEC regions. (C) 2017 Elsevier Ltd. All rights reserved.Öğe Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset(Bmc, 2020) Wang, Yunsheng; Nie, Fei; Shahid, Muhammad Qasim; Baloch, Faheem ShehzadBackgroundBoth selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. Vaccinium is species rich genus that comprised of about 450 species, and blueberry is one of the most important species of Vaccinium genus, which is gaining popularity because of high healthful value. In this article, we aimed to decipher the molecular footprints of natural selection on the single copy genes and WGD events occur in the evolutionary history of blueberry species.ResultsWe identified 30,143, 29,922 and 28,891 putative protein coding sequences from 45,535, 42,914 and 43,630 unigenes assembled from the leaves' transcriptome assembly of 19 rabbiteye (T1), 13 southern highbush (T2) and 22 northern highbush (T3) blueberry cultivars. A total of 17, 21 and 27 single copy orthologs were found to undergone positive selection in T1 versus T2, T1 versus T3, and T2 versus T3, respectively, and these orthologs were enriched in metabolic pathways including "Terpenoid backbone biosynthesis", "Valine, leucine and isoleucine biosynthesis", "Butanoate metabolism", "C5-Branched dibasic acid metabolism" "Pantothenate and CoA biosynthesis". We also detected significant molecular footprints of a recent (about 9.04 MYA), medium (about 43.44 MYA) and an ancient (about 116.39 MYA) WGD events that occurred in the evolutionary history of three blueberry species.ConclusionSome important functional genes revealed positive selection effect in blueberry. At least three rounds of WGD events were detected in the evolutionary history of blueberry species. Our work provides insights about the genetic mechanism of adaptive evolution in blueberry and species radiation of Vaccinium in short geological scale time.Öğe De novo assembly and annotation of the juvenile tuber transcriptome of agastrodia elatahybrid by rna sequencing: Detection of ssr markers(Springer/Plenum Publishers, 2020) Wang, Yunsheng; Shahid, Muhammad Qasim; Ghouri, Fozia; Baloch, Faheem ShehzadGastrodia elatais a traditional Chinese herbal medicine with good therapeutic effect on various nervous and cerebrovascular diseases. In the present study, we generated 20,611,556 raw reads from the young tuber transcriptome of aG. elatahybrid (Gastrodia elata BI.f.elata x Gastrodia elata BI.f.pilifera) by using Illumina HiSeq (TM) 4000 sequencing platform. De novo assembly and bioinformatics analysis revealed 20,237,474 clean reads, including 2,529,684,250 bp that assembled into 34,323 unigenes with an average length of 695.19 bp. Among them, 24,698 (71.96%) unigenes were annotated by at least one of the Nr, Swiss-Prot, COG and KEGG databases. A total of 4236 (12.34%) unigenes were identified as candidate transcription factors, and 2007 (5.85%) unigenes were found to contain at least one single sequence repeat (SSR). Of these SSRs, AG/CT repeat motif was the most frequent, with a total of 498 (21.67%). This study will enhance our understanding about the molecular mechanism of physiological metabolism, growth and development ofG. elata, particularly abundant SSR markers will offer plenty of alternative tools for further studies about molecular genetics, molecular breeding and association analysis.Öğe Phylogeographical studies of Glycine Soja: Implicating the refugium during the Quaternary glacial period and large-scale expansion after the Last Glacial Maximum(2016) Wang, Yunsheng; Shahıd, Muhammad Qasim; Baloch, Faheem ShehzadWild soybean (Glycine soja Sieb. & Zucc.), the progenitor of cultivated soybean (Glycine max (L.) Merr.), is widely distributed in the Sino-Japanese Floristic Region (SJFR). Therefore, it is an excellent model organism to study the effect of Quaternary climatic changes on the distribution and migration of plant taxa in the SJFR. To investigate the phylogeography of G. soja, a total of 632 individuals representing 52 populations throughout the species distribution range were genotyped by using the sequencing data of a nuclear locus, AF105221, and a chloroplast locus, trnQ-rps16. We detected a total of 23 haplotypes from two loci, including five common and 18 rare haplotypes. Among them, 17 rare haplotypes were limited to Northeast Asia (Northeast China (NEC) and Korea) and the Yangzi River basin (middle and downstream of the Yangzi River (MDYR) and the eastern end of Southwest China (SWC)). Moreover, two common haplotypes were detected throughout the species distribution wide range. All the haplotypes from Japan and the Korean peninsula were also found in China. The haplotype distribution patterns of the two loci suggested that Northeast Asia (NEC and Korea) and the Yangzi River basin (MDYR and the eastern end of SWC) might have been the refugia for G. soja during the Quaternary glacial period, and G. soja expanded rapidly after the end of the Last Glacial Maximum. There was a land bridge between East China, the Korean peninsula, and Japan that permitted gene flow among populations of these regions in the ice age during the Quaternary.Öğe Phylogeographical studies of Glycine soja: implicating the refugium during the Quaternary glacial period and large-scale expansion after the Last Glacial Maximum(Tubitak Scientific & Technological Research Council Turkey, 2016) Wang, Yunsheng; Shahid, Muhammad Qasim; Baloch, Faheem ShehzadWild soybean (Glycine soja Sieb. & Zucc.), the progenitor of cultivated soybean (Glycine max (L.) Merr.), is widely distributed in the Sino-Japanese Floristic Region (SJFR). Therefore, it is an excellent model organism to study the effect of Quaternary climatic changes on the distribution and migration of plant taxa in the SJFR. To investigate the phylogeography of G. soja, a total of 632 individuals representing 52 populations throughout the species distribution range were genotyped by using the sequencing data of a nuclear locus, AF105221, and a chloroplast locus, trnQ-rps16. We detected a total of 23 haplotypes from two loci, including five common and 18 rare haplotypes. Among them, 17 rare haplotypes were limited to Northeast Asia (Northeast China (NEC) and Korea) and the Yangzi River basin (middle and downstream of the Yangzi River (MDYR) and the eastern end of Southwest China (SWC)). Moreover, two common haplotypes were detected throughout the species distribution wide range. All the haplotypes from Japan and the Korean peninsula were also found in China. The haplotype distribution patterns of the two loci suggested that Northeast Asia (NEC and Korea) and the Yangzi River basin (MDYR and the eastern end of SWC) might have been the refugia for G. soja during the Quaternary glacial period, and G. soja expanded rapidly after the end of the Last Glacial Maximum. There was a land bridge between East China, the Korean peninsula, and Japan that permitted gene flow among populations of these regions in the ice age during the Quaternary.Öğe Transcriptome analysis and annotation: SNPs identified from single copy annotated unigenes of three polyploid blueberry crops(Public Library Science, 2019) Wang, Yunsheng; Shahid, Muhammad Qasim; Ghouri, Fozia; Ercişli, Sezai; Baloch, Faheem Shehzad; Nie, FeiBlueberry is a kind of new rising popular perennial fruit with high healthful quality. It is of utmost importance to develop new blueberry varieties for different climatic zones to satisfy the demand of people in the world. Molecular marker assisted breeding is believed to be an ideal method for the development of new blueberry varieties for its shorter breeding cycle than the conventional breeding. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) markers are widely used molecular tools for marker assisted breeding, which could be detected at large scale by the transcriptome sequencing. Here, we sequenced the leaves transcriptome of 19 rabbiteye (Vaccinium ashei Reade), 13 southern highbush (Vaccinium. corymbosum L x native southern Vaccinium Spp) and 22 cultivars of northern highbush blueberry (Vaccinium corymbosum L) by using next generation sequencing technologies. A total of 80.825 Gb clean data with an average of about 12.525 million reads per cultivar were obtained. We assembled 58,968, 55,973 and 53,887 unigenes by using the clean data from rabbiteye, southern highbush and northern highbush blueberry cultivars, respectively. Among these unigenes, 3599, 3495 and 3513 unigenes were detected as candidate resistance genes in three blueberry crops. Moreover, we identified more than 8756, 9020, and 9198 SSR markers from these unigenes, and 7665, 4861, 13,063 SNPs from the annotated single copy unigenes, respectively. The results will be helpful for the molecular genetics and association analysis of blueberry and the basic molecular information of pest and disease resistance of blueberry, and would also offer huge number of molecular tools for the marker assisted breeding to produce blueberry cultivars with different adaptive characteristics.
