Comparative genome-wide characterization of SSRs leading to marker development for NicotianaXuewen Wang, Shuai Yang, Shumeng Zhang, Qingshi Zhao, Meng Li, Yulong Gao, Long Yang*, Jeffrey L. Bennetzen*.BMC Genomics:2018,doi: 10.1186/s12864-018-4878-4摘要Background
Simple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breeding. In the model plants in Nicotiana genus e.g. N. benthamiana, a comprehensive assessment of SSR content has become possible now because several Nicotiana genomes have been sequenced. We conducted a genome-wide SSR characterization and marker development across seven Nicotiana genomes.
Here, we initially characterized 2,483,032 SSRs (repeat units of 1–10 bp) from seven genomic sequences of Nicotiana and developed SSR markers using the GMATA® software package. Of investigated repeat units, mono-, di- and tri-nucleotide SSRs account for 98% of all SSRs in Nicotiana. More complex SSR motifs, although rare, are highly variable between Nicotiana genomes. A total of 1,224,048 non-redundant Nicotiana (NIX) markers were developed, of which 99.98% are novel. An efficient and uniform genotyping protocol for NIX markers was developed and validated. We created a web-based database of NIX marker information including amplicon sizes of alleles in each genome for downloading and online analysis.
The present work constitutes the first deep characterization of SSRs in seven genomes of Nicotiana, and the development of NIX markers for these SSRs. Our online marker database and an efficient genotyping protocol facilitate the application of these markers. The NIX markers greatly expand Nicotiana marker resources, thus providing a useful tool for future research and breeding. We demonstrate a novel protocol for SSR marker development and utilization at the whole genome scale that can be applied to any lineage of organisms.
QTL mapping combined with comparative analyses identified candidate genes for reduced shattering in Setaria italicaSandra Odonkor, Soyeon Choi, Debkanta Chakraborty, Liliam Martinez-Bello, Xuewen Wang, Bochra A Bahri, Maud I Tenaillon, Olivier Panaud, Katrien M Devos.Frontiers in Plant Science:2018,9,doi: 10.3389/fpls.2018.00918摘要Setaria (L.) P. Beauv is a genus of grasses that belongs to the Poaceae (grass) family, subfamily Panicoideae. Two members of the Setaria genus, S. italica (foxtail millet) and S. viridis (green foxtail), have been studied extensively over the past few years as model species for C4-photosynthesis and to facilitate genome studies in complex Panicoid bioenergy grasses. We exploited the available genetic and genomic resources for S. italica and its wild progenitor, S. viridis, to study the genetic bases of seed shattering. Reduced shattering is a key trait that underwent positive selection during domestication. Phenotyping of F2:3 and recombinant inbred line (RIL) populations generated from a cross between S. italica accession B100 and S. viridis accession A10 identified the presence of additive main effect quantitative trait loci (QTL) on chromosomes V and IX. As expected, enhanced seed shattering was contributed by the wild S. viridis. Comparative analyses pinpointed Sh1 and qSH1, two shattering genes previously identified in sorghum and rice, as potentially underlying the QTL on Setaria chromosomes IX and V, respectively. The Sh1 allele in S. italica was shown to carry a PIF/Harbinger MITE in exon 2, which gave rise to an alternatively spliced transcript that lacked exon 2. This MITE was universally present in S. italica accessions around the world and absent from the S. viridis germplasm tested, strongly suggesting a single origin of foxtail millet domestication. The qSH1 gene carried two MITEs in the 5’UTR. Presence of one or both MITEs was strongly associated with cultivated germplasm. If the MITE insertion(s) in qSH1 played a role in reducing shattering in S. italica accessions, selection for the variants likely occurred after the domestication of foxtail millet.
UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: Finger millet as a case studyPeng Qi, Davis Gimode, Dipnarayan Saha, Stephan Schröder, Debkanta Chakraborty, Xuewen Wang, Mathews M. Dida, Russell L. Malmberg, Katrien M. Devos.BMC Plant Biology:2018,18,doi: 10.1186/s12870-018-1316-3摘要Research on orphan crops is often hindered by a lack of genomic resources. With the advent of affordable sequencing technologies, genotyping an entire genome or, for large-genome species, a representative fraction of the genome has become feasible for any crop. Nevertheless, most genotyping-by-sequencing (GBS) methods are geared towards obtaining large numbers of markers at low sequence depth, which excludes their application in heterozygous individuals. Furthermore, bioinformatics pipelines often lack the flexibility to deal with paired-end reads or to be applied in polyploid species.
UGbS-Flex combines publicly available software with in-house python and perl scripts to efficiently call SNPs from genotyping-by-sequencing reads irrespective of the species’ ploidy level, breeding system and availability of a reference genome. Noteworthy features of the UGbS-Flex pipeline are an ability to use paired-end reads as input, an effective approach to cluster reads across samples with enhanced outputs, and maximization of SNP calling. We demonstrate use of the pipeline for the identification of several thousand high-confidence SNPs with high representation across samples in an F3-derived F2 population in the allotetraploid finger millet. Robust high-density genetic maps were constructed using the time-tested mapping program MAPMAKER which we upgraded to run efficiently and in a semi-automated manner in a Windows Command Prompt Environment. We exploited comparative GBS with one of the diploid ancestors of finger millet to assign linkage groups to subgenomes and demonstrate the presence of chromosomal rearrangements.
The paper combines GBS protocol modifications, a novel flexible GBS analysis pipeline, UGbS-Flex, recommendations to maximize SNP identification, updated genetic mapping software, and the first high-density maps of finger millet. The modules used in the UGbS-Flex pipeline and for genetic mapping were applied to finger millet, an allotetraploid selfing species without a reference genome, as a case study. The UGbS-Flex modules, which can be run independently, are easily transferable to species with other breeding systems or ploidy levels.
Characterization and alternative splicing profiles of lipoxygenase gene family in tea plant (Camellia sinensis)
J Zhu, Xuewen Wang, L Guo, Q Xu, S Zhao, F Li, X Yan, S Liu, C Wei.Plant and Cell Physiology:2018,5,Doi: 10.1093/pcp/pcy091
Dry mycelium of Penicillium chrysogenum activates defense via gene regulation of salicylic acid and jasmonic acid signaling in ArabidopsisZhuang-zhuang Chen, Jian-guang Wang, Yu Li, Yu Zhong, Ju-gou Liao, Shu-gang Lu, Liang Wang, Xuewen Wang, Sui-yun Chena.Physiological and Molecular Plant Pathology:2018,102,10.1016/j.pmpp.2018.04.00摘要The dry mycelium of Penicillium chrysogenum (DMP) induces systemic acquired resistance (SAR), which enhances defenses in plants. To understand the molecular mechanisms involved in DMP-mediated signaling pathways, we examined the mRNA levels in Arabidopsis with jasmonic acid (JA), DMP or salicylic acid (SA) treatment compared with a control. RNA-Seq based transcriptome analysis revealed that the differentially expressed genes (DEGs) after DMP treatment were significantly enriched in three metabolism pathways shared by SA treatment and one additional pathway shared by JA treatment. Key DEGs, including PR1, EIN3 and FRK1, in the SA, JA/ethylene (ET) and pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) pathways for inducing resistance were significantly regulated. Further quantitative real-time PCR (qRT-PCR) analysis revealed that DMP-mediated signaling cross-talked with JA and SA signaling and associated with PAMP-triggered immunity. SA accumulated significantly after DMP treatment. However some known small molecules inducing SA accumulation were not found in DMP. Together, we demonstrated that DMP treatment activated defense in SAR via gene regulation in the JA and SA pathways. These results provide molecular evidence for the mechanisms in the DMP induced SAR and could guide the further identification of the activators.
The Algicidal Fungus Trametes versicolor F21a Eliminating Blue Algae via Genes Encoding Degradation Enzymes and Metabolic Pathways Revealed by Transcriptomic AnalysisWei Dai†, Xiaolin Chen†, Xuewen Wang†, Zimu Xu, Xueyan Gao, Chaosheng Jiang, Ruining Deng and Guomin Han.Front. Microbiol.:2018,2018,https://doi.org/10.3389/fmicb.2018.00826摘要The molecular mechanism underlying the elimination of algal cells by fungal mycelia has not been fully understood. Here, we applied transcriptomic analysis to investigate the gene expression and regulation at time courses of Trametes versicolor F21a during the algicidal process. The obtained results showed that a total of 193, 332, 545, and 742 differentially expressed genes were identified at 0, 6, 12, and 30 h during the algicidal process, respectively. The gene ontology terms were enriched into glucan 1,4-α-glucosidase activity, hydrolase activity, lipase activity, and endopeptidase activity. The KEGG pathways were enriched in degradation and metabolism pathways including Glycolysis/Gluconeogenesis, Pyruvate metabolism, the Biosynthesis of amino acids, etc. The total expression levels of all Carbohydrate-Active enZYmes (CAZyme) genes for the saccharide metabolism were increased by two folds relative to the control. AA5, GH18, GH5, GH79, GH128, and PL8 were the top six significantly up-regulated modules among 43 detected CAZyme modules. Four available homologous decomposition enzymes of other species could partially inhibit the growth of algal cells. The facts suggest that the algicidal mode of T. versicolor F21a might be associated with decomposition enzymes and several metabolic pathways. The obtained results provide a new candidate way to control algal bloom by application of decomposition enzymes in the future.
Comparative transcriptomic analysis identifies genes responsible for fruit count and oil yield in oil tea plant Camellia chekiangoleosaYun Xie, Xuewen Wang.Scientific Reports:2018,Doi: 10.1038/s41598-018-24073-z摘要Fruit yield is an important trait for horticultural crops. However, the limited fruit yield of Camellia chekiangoleosa, a novel promising oil tree, restricts the production of oil. The breeding improvement is little due to its long generation time and lack of available genomic sequence. We identified distinct fruit count phenotypes, high-yield (HY) and low-yield (LY). To understand the underlying genetic basis, we focused on global gene discovery and expression levels in floral buds, which affect fruit count. A total of 140,299 de novo assembled unigenes were obtained using RNA-seq technology, and more genes were expressed in HY than in LY. 2395 differentially expressed genes (DEGs) were identified and enriched in membrane, energy metabolism, secondary metabolism, fatty acid biosynthesis and metabolism, and 18 other metabolic pathways. Of the DEGs, twelve identified transcription factors, including AP2, mostly involve in inflorescence and flower development and in hormone networks. Key DEGs in fatty acid biosynthesis (Fab) FabB, FabF, FabZ, and AccD were highly expressed in floral buds and associated with high oil yield in fruits. We hypothesized that a potential link exists between fruit count and its oil yield. These findings help to elucidate the molecular cues affecting fruit count and oil yield.
Relationships Between Gene Structure and Genome Instability in Flowering PlantsJeffrey L. Bennetzen; Xuewen Wang.Molecular Plant:2018,11,10.1016/j.molp.2018.02.003摘要Flowering plant (angiosperm) genomes are exceptional in their variability with respect to genome size, ploidy, chromosome number, gene content and gene arrangement. Gene movement, although observed in some of the earliest plant genome comparisons, has been relatively under-investigated. We present herein a description of several interesting properties of plant gene and genome structure that are pertinent to the successful movement of a gene to a new location. These considerations lead us to propose a model that can explain the frequent success of plant gene mobility, namely that Small Insulated Genes Move Around (SIGMAR). The SIGMAR model is then compared to known processes for gene mobilization, and predictions of the SIGMAR model are formulated to encourage future experimentation. The overall results indicate that the frequent gene movement in angiosperm genomes is partly an outcome of the unusual properties of angiosperm genes, especially their small size and insulation from epigenetic silencing.
The hardy rubber tree genome provides insights into the evolution of polyisoprene biosynthesisTa-na Wuyun, Lin Wang10, Huimin Liu10, Xuewen Wang10, Liangsheng Zhang10, Jeffrey L. Bennetzen, ..,Fan Liang, Jingjing Hu, Depeng Wang, Ruiwen Gao.Molecular Plant:2017摘要DOI: http://dx.doi.org/10.1016/j.molp.2017.11.014
Eucommia ulmoides is an economically important tree; however, the lack of its genome sequence restricts the theoretical and applied studies. Here we present a high-quality assembly of its ∼1.2 Gb genome (scaffold N50 = 1.88 Mb) with at least 26,723 predicted genes for E. ulmoides, the first sequenced genome of the order Garryales, which we obtained using an integrated strategy combining Illumina sequencing, Pacbio sequencing and Bionano mapping. As a sister taxon to lamiids and campanulids, the E. ulmoides underwent an ancient genome triplication shared by core eudicots but no further whole-genome duplication (WGD) in the last ∼125 million years. E. ulmoides exhibits high expression levels and/or gene number expansion for multiple genes involved in stress responses and biosynthesis of secondary metabolites, which may account for environmental adaptability. In contrast to rubber tree (Hevea brasiliensis), which produces cis-polyisoprene, E. ulmoides has evolved to synthesize long-chain trans-polyisoprene via farnesyl diphosphate synthases (FPSs). Moreover, FPS and rubber elongation factor/small rubber particle protein gene families were expanded independently from the H. brasiliensis lineage. Our results provide new insights into the biology of E. ulmoides and the origin of polyisoprene biosynthesis.
Comparative Analysis of the Response and Gene Regulation in Cold Resistant and Susceptible Tea PlantsQiuyan Ban1#, Xuewen Wang1, 2 #, Cheng Pan1, Yiwei Wang1, Lei Kong1, Huiguang Jiang1, Yiqun Xu1, Wenzhi Wang1, Yuting Pan1, Yeyun Li1&, Changjun Jiang1&.Plos One:2017,2017,doi: 10.1371/journal.pone.0188514摘要Cold environment is the main constraint for tea plants (Camellia sinensis) distribution and tea farming. We identified two tea cultivars, called var. sinensis cv. Shuchazao (SCZ) with a high cold-tolerance and var. assamica cv. Yinghong9 (YH9) with low cold-tolerance. To better understand the response mechanism of tea plants under cold stress for improving breeding, we compared physiological and biochemical responses, and associated genes expression in response to 7-day and 14-day cold acclimation, followed by 7-day de-acclimation in these two tea cultivars. We found that the low EL50, low Fv/Fm, and high sucrose and raffinose accumulation are responsible for higher cold tolerance in SCZ comparing with YH9. We then measured the expression of 14 key homologous genes, known as involved in these responses in other plants, for each stages of treatment in both cultivars using RT-qPCR. Our results suggested that the increased expression of CsCBF1 and CsDHNs coupling with the accumulation of sucrose play key roles in conferring higher cold resistance in SCZ. Our findings have revealed key genes regulation responsible for cold resistance, which help to understand the cold-resistant mechanisms and guide breeding in tea plants.
Whole plastid transcriptomes reveal abundant RNA editing sites and differential editing status in Phalaenopsis aphrodite subsp. formosanaTing‑Chieh Chen, Yu‑Chang Liu, Xuewen Wang, Chi‑Hsuan Wu, Chih‑Hao Huang, Ching‑Chun Chang.Botanical Studies:2017,58:38,doi: 10.1186/s40529-017-0193-7摘要Background
RNA editing is a process of post-transcriptional level of gene regulation by nucleotide modification. Previously, the chloroplast DNA of Taiwan endemic moth orchid, P. aphrodite subsp. formosana was determined, and 44 RNA editing sites were identified from 24 plastid protein-coding transcripts of leaf tissue via RT-PCR and then conventional Sanger sequencing. However, the RNA editing status of whole-plastid transcripts in leaf and other distinct tissue types in moth orchids has not been addressed. To sensitively and extensively examine the plastid RNA editing status of moth orchid, RNA-Seq was used to investigate the editing status of whole-plastid transcripts from leaf and floral tissues by mapping the sequence reads to the corresponding cpDNA template. With the threshold of at least 5% C-to-U or U-to-C conversion events observed in sequence reads considered as RNA editing sites.
In total, 137 edits with 126 C-to-U and 11 U-to-C conversions, including 93 newly discovered edits, were identified in plastid transcripts, representing an average of 0.09% of the nucleotides examined in moth orchid. Overall, 110 and 106 edits were present in leaf and floral tissues, respectively, with 79 edits in common. As well, 79 edits were involved in protein-coding transcripts, and the 58 nucleotide conversions caused the non-synonymous substitution. At least 32 edits showed significant (≧20%) differential editing between leaf and floral tissues. Finally, RNA editing in trnM is required for the formation of a standard clover-leaf structure.
We identified 137 edits in plastid transcripts of moth orchid, the highest number reported so far in monocots. The consequence of RNA editing in protein-coding transcripts mainly cause the amino acid change and tend to increase the hydrophobicity as well as conservation among plant phylogeny. RNA editing occurred in non-protein-coding transcripts such as tRNA, introns and untranslated regulatory regions could affect the formation and stability of secondary structure, which might play an important role in the regulation of gene expression. Furthermore, some unidentified tissue-specific factors might be required for regulating RNA editing in moth orchid.
Integrating transcriptome and microRNA analysis identifies genes and microRNAs for AHO-induced systemic acquired resistance in N. tabacumYongdui Chen, Jiahong Dong, Jeffrey L. Bennetzen, Micai Zhong, Jun Yang, Jie Zhang, Shunlin Li, Xiaojiang Hao, Zhongkai Zhang, Xuewen Wang*.Scientific Reports:2017,7,doi: 10.1038/s41598-017-12249-y摘要3-Acetonyl-3-hydroxyoxindole (AHO) induces systemic acquired resistance (SAR) in Nicotiana. However, the underlying molecular mechanism is not well understood. To understand the molecular regulation during SAR induction, we examined mRNA levels, microRNA (miRNA) expression, and their regulatory mechanisms in control and AHO-treated tobacco leaves. Using RNA-seq analysis, we identified 1,445 significantly differentially expressed genes (DEGs) at least 2 folds with AHO treatment. The DEGs significantly enriched in six metabolism pathways including phenylpropanoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis for protective cuticle and wax. Key DEGs including PALs and PR-10 in salicylic acid pathway involved in SAR were significantly regulated. In addition, we identified 403 miRNAs belonging to 200 miRNA families by miRNA sequencing. In total, AHO treatment led to 17 up- and 6 down-regulated at least 2 folds (Wald test, P < 0.05) miRNAs (DEMs), respectively. Targeting analysis implicated four DEMs regulating three DEGs involved in disease resistance, including miR156, miR172f, miR172g, miR408a, SPL6 and AP2. We concluded that both mRNA and miRNA regulation enhances AHO-induced SAR. These data regarding DEGs, miRNAs, and their regulatory mechanisms provide molecular evidence for the mechanisms involved in tobacco SAR, which are likely to be present in other plants.
Transcriptome and metabolite analysis identifies nitrogen utilization genes in tea plant (Camellia sinensis)Wei Li1, 2, 3†, Fen Xiang1†, Micai Zhong2, Lingyun Zhou1, Hongyan Liu1, Saijun Li1*, and Xuewen Wang2, 4*.Scientific Reports:2017,7,1693摘要Applied nitrogen (N) fertilizer significantly increases the leaf yield. However, most N is not utilized by the plant, negatively impacting the environment. To date, little is known regarding N utilization genes and mechanisms in the leaf production. To understand this, we investigated transcriptomes using RNA-seq and amino acid levels with N treatment in tea (Camellia sinensis), the most popular beverage crop. We identified 196 and 29 common differentially expressed genes in roots and leaves, respectively, in response to ammonium in the roots and leaves of two tea varieties. Among those genes, AMT, NRT and AQP for N uptake and GOGAT and GS for N assimilation were the key genes, validated by RT-qPCR, which expressed in a network manner with tissue specificity. Importantly, only AQP and three novel DEGs associated with stress, manganese binding, and gibberellin-regulated transcription factor were common in N responses across all tissues and varieties. A hypothesized gene regulatory network for N was proposed. A strong statistical correlation between key genes’ expression and amino acid content was revealed. The key genes and regulatory network improve our understanding of the molecular mechanism of N usage and offer gene targets for plant improvement.
GMATA: an integrated software package for genome-scale SSR mining, marker development and viewingXuewen Wang, Le Wang.Frontiers in Plant Science:2016,7,doi 10.3389/fpls.2016.01350摘要Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar.
Using in silico techniques: Isolation and characterization of an insect cuticle-degrading-protease gene from Beauveria bassianaKhan S, Nadir S, Wang X, Khan A, Xu J, Li M, Tao L, Khan S, Karunarathna SC.Microbial Pathogenesis:2016摘要Cuticle-degrading-proteases (CDPs) secreted by Beauveria spp. are pivotal biocontrol substances, possessing commercial potential for developing bio-pesticides. Therefore, a thoughtful and contemplative understanding and assessment of the structural and functional features of these proteases would markedly assist the development of biogenic pesticides. Computational molecular biology is a new facile alternative approach to the tedious experimental molecular biology; therefore, by using bioinformatics tools, we isolated and characterized an insect CDP gene from B. bassiana 70 s.l. genomic DNA.
The CDP gene (1240 bp with GeneBank accession no. KT804651) consisted of three introns and four CDS exons, and shared 74–100% sequence identity to the reference CDP genes. Its phylogenetic tree results showed a unique evolution pattern, and the predicted amino acid peptide (PAAP) consisted of 344 amino acid residues with pI, molecular weight, instability index, grand average hydropathicity value and aliphatic index of 7.2, 35.4 kDa, 24.45, −0.149, and 76.63, respectively. The gene possessed 74–89% amino acid sequence similarity to the 12 reference strains. Three motifs (Peptidase_S8 subtilase family) were detected in the PAAP, and the computed 3D structure possessed 79.09% structural identity to alkaline serine proteases. The PAAP had four (three serine proteases and one Pyridoxal-dependent decarboxylase) conserved domains, a disulfide bridge, two calcium binding sites, MY domain, and three predicted active sites in the serine family domains.
These results will set the groundwork for further exploitation of proteases and understanding the mechanism of disease caused by cuticle-degrading-serine-proteases from entomopathogenic fungi.
Genome-wide microsatellite characterization and marker development for Nicotiana
Xuewen Wang, Meng Li , Yulong Gao , Jeffrey Bennetzen.2016
Characterization of genome-wide variation in Four-row Wax, a waxy maize landrace with a reduced kernel row phenotypeHanmei Liu, Xuewen Wang, Bin Wei, Yongbin Wang, Yinghong Liu, Junjie Zhang, Yufeng Hu, Guowu Yu, Jian Li, Zhanbin Xu and Yubi Huang.Frontiers in plant science:2016,doi: 10.3389/fpls.2016.00667摘要In southwest China, some maize landraces have long been isolated geographically, and have phenotypes that differ from those of widely grown cultivars. These landraces may harbor rich genetic variation responsible for those phenotypes. Four-row Wax is one such landrace, with four rows of kernels on the cob. We resequenced the genome of Four-row Wax, obtaining 50.46 Gb sequence at 21.87× coverage, then identified and characterized 3,252,194 SNPs, 213,181 short InDels (1-5 bp) and 39,631 structural variations (greater than 5 bp). Of those, 312,511 (9.6% of) SNPs were novel compared to the most detailed haplotype map (HapMap) SNP database of maize. Characterization of variations in reported kernel row number (KRN) related genes and KRN QTL regions revealed potential causal mutations in fea2, td1, kn1 and te1. Genome-wide comparisons revealed abundant genetic variations in Four-row Wax, which may be associated with environmental adaptation. The sequence and SNP variations described here enrich genetic resources of maize, and provide guidance into study of seed numbers for crop yield improvement.
DRACULA2, a dynamic nucleoporin with a role in the regulation of the shade avoidance syndrome in ArabidopsisMarcal Gallemi, Anahit Galstyan, Sandi Paulisc, Christiane Then, Almudena Ferrandez-Ayela, Laura Lorenzo-Orts, Irma Roig-Villanova, Xuewen Wang, Jose Luis Micol, Maria Rosa Ponce,Paul Devlin, and Jaime Martinez-Garcia.Development:2016,143,1623-1631 doi: 10.1242/dev.130211摘要When plants grow in close proximity, basic resources such as light might become limiting. Under such conditions, plants respond to anticipate and/or adapt to the light shortage, a process known as the shade avoidance syndrome (SAS). After a genetic screening using a shade-responsive luciferase reporter line (PHYB:LUC), we identified DRACULA2 (DRA2) that encodes an Arabidopsis homolog to mammalian nucleoporin 98, a component of the nuclear pore complex (NPC). DRA2, together with other nucleoporines, positively participates in the control of the hypocotyl elongation response to plant proximity, a role that can be considered as dependent on the nucleocytoplasmic transport of macromolecules (i.e., transport-dependent). In addition, our results reveal a specific role for DRA2 in controlling shade-induced gene expression. We suggest that this novel regulatory role of DRA2 is transport-independent, and it might rely on its dynamic localization in and off the NPC. These results provide mechanistic insights on how SAS responses are rapidly established by light conditions. They also indicate that nucleoporins have an active role in plant signaling.
Current status and prospects for the study of Nicotiana genomics, genetics, and nicotine biosynthesis genesXuewen Wang, Jeffrey L. Bennetzen.Molecular Genetics and Genomics:2015,290 （1）,11-21摘要Nicotiana, a member of the Solanaceae family, is one of the most important research model plants, and of high agricultural and economic value worldwide. To better understand the substantial and rapid research progress with Nicotiana in recent years, its genomics, genetics, and nicotine gene studies are summarized, with useful web links. Several important genetic maps, including a high-density map of N. tabacum consisting of ~2,000 markers published in 2012, provide tools for genetics research. Four whole genome sequences are from allotetraploid species, including N. benthamiana in 2012, and three N. tabacum cultivars (TN90, K326, and BX) in 2014. Three whole genome sequences are from diploids, including progenitors N. sylvestris and N. tomentosiformis in 2013 and N. otophora in 2014. These and additional studies provide numerous insights into genome evolution after polyploidization, including changes in gene composition and transcriptome expression in N. tabacum. The major genes involved in the nicotine biosynthetic pathway have been identified and the genetic basis of the differences in nicotine levels among Nicotiana species has been revealed. In addition, other progress on chloroplast, mitochondrial, and NCBI-registered projects on Nicotiana are discussed. The challenges and prospects for genomic, genetic and application research are addressed. Hence, this review provides important resources and guidance for current and future research and application in Nicotiana.
A novel high throughput in vivo molecular screen for shade avoidance mutants identifies a novel phyA mutationWang, Xuewen ;Roig-Villanova, I. ; Khan, Safina ; Shanahan, Hugh ; Quail, P.H. ; Martinez-Garcia, Jaime ; Devlin, Paul.Journal of experimental botany:2011,62,2973-2987摘要4 citing articles by 2013 Dec in journals: Trends in plant science (IF 11) et al
The shade avoidance syndrome (SAS) allows plants to anticipate and avoid shading by neighbouring plants by initiating an elongation growth response. The phytochrome photoreceptors are able to detect a reduction in the red:far red ratio in incident light, the result of selective absorption of red and blue wavelengths by proximal vegetation. A shade-responsive luciferase reporter line (PHYB::LUC) was used to carry out a high-throughput screen to identify novel SAS mutants. The dracula 1 (dra1) mutant, that showed no avoidance of shade for the PHYB::LUC response, was the result of a mutation in the PHYA gene. Like previously characterized phyA mutants, dra1 showed a long hypocotyl in far red light and an enhanced hypocotyl elongation response to shade. However, dra1 additionally showed a long hypocotyl in red light. Since phyB levels are relatively unaffected in dra1, this gain-of-function red light phenotype strongly suggests a disruption of phyB signalling. The dra1 mutation, G773E within the phyA PAS2 domain, occurs at a residue absolutely conserved among phyA sequences. The equivalent residue in phyB is absolutely conserved as a threonine. PAS domains are structurally conserved domains involved in molecular interaction. Structural modelling of the dra1 mutation within the phyA PAS2 domain shows some similarity with the structure of the phyB PAS2 domain, suggesting that the interference with phyB signalling may be the result of non-functional mimicry. Hence, it was hypothesized that this PAS2 residue forms a key distinction between the phyA and phyB phytochrome species.
Reference genome sequence of the model plant SetariaJeffrey L. Bennetzen, Jeremy Schmutz, ... Xuewen Wang , ..., Katrien M Devos.Nature Biotechnology:2012,30,555-561摘要44 citing articles by 2013 Dec in journals:
Nature genetics (IF 35), Genome biology (IF 10.3), Current Opinion in Plant Biology (IF 9.2) et al
We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).
Genetic control and comparative genomic analysis of flowering time in Setaria (Poaceae)Margarita Mauro-Herrera, Xuewen Wang, Hugues Barbier,Thomas P. Brutnell, Katrien M. Devos, and Andrew N. Doust.G3:Genes|genomes|genetics:2013,3,283-295摘要2 citing articles by 2013 Dec in journals:
Nature reviews genetics, Volume: 14 Issue: 12 Pages: 840-852, Dec 2013, IF 41
We report the first study on the genetic control of flowering in Setaria, a panicoid grass closely related to switchgrass, and in the same subfamily as maize and sorghum. A recombinant inbred line mapping population derived from a cross between domesticated Setaria italica (foxtail millet) and its wild relative Setaria viridis (green millet), was grown in eight trials with varying environmental conditions to identify a small number of quantitative trait loci (QTL) that control differences in flowering time. Many of the QTL across trials colocalize, suggesting that the genetic control of flowering in Setaria is robust across a range of photoperiod and other environmental factors. A detailed comparison of QTL for flowering in Setaria, sorghum, and maize indicates that several of the major QTL regions identified in maize and sorghum are syntenic orthologs with Setaria QTL, although the maize large effect QTL on chromosome 10 is not. Several Setaria QTL intervals had multiple LOD peaks and were composed of multiple syntenic blocks, suggesting that observed QTL represent multiple tightly linked loci. Candidate genes from flowering time pathways identified in rice and Arabidopsis were identified in Setaria QTL intervals, including those involved in the CONSTANS photoperiod pathway. However, only three of the approximately seven genes cloned for flowering time in maize colocalized with Setaria QTL. This suggests that variation in flowering time in separate grass lineages is controlled by a combination of conserved and lineage specific genes.
Journal of Experimental Botany Volume: 64 Issue: 12 Pages: 3645-3655, SEP 2013, IF 5.2
Linkage maps of lowland and upland tetraploid ecotypesDesalegn Serba, Limin Wu, Guillaume Daverdin, Bochra A. Bahri, Xuewen Wang, Andrzej Kilian, Joseph H. Bouton, E. Charles Brummer, Malay C. Saha, Katrien M. Devos.Bioenergy research:2013,6,953-965摘要Switchgrass (Panicum virgatum L.) is a native perennial warm season (C4) grass that has been identified as a promising species for bioenergy research and production. Consequently, biomass yield and feedstock quality improvements are high priorities for switchgrass research. The objective of this study was to develop a switchgrass genetic linkage map using a full-sib pseudo-testcross mapping population derived from a cross between two heterozygous genotypes selected from the lowland cultivar ‘Alamo’ (AP13) and the upland cultivar ‘Summer’ (VS16). The female parent (AP13) map consists of 515 loci in 18 linkage groups (LGs) and spans 1,733 cM. The male parent (VS16) map arranges 363 loci in 17 LGs and spans 1,508 cM. No obvious cause for the lack of one LG in VS16 could be identified. Comparative analyses between the AP13 and VS16 maps showed that the two major ecotypic classes of switchgrass have highly colinear maps with similar recombination rates, suggesting that chromosomal exchange between the two ecotypes should be able to occur freely. The AP13 and VS16 maps are also highly similar with respect to marker orders and recombination levels to previously published switchgrass maps. The genetic maps will be used to identify quantitative trait loci associated with biomass and quality traits. The AP13 genotype was used for the whole genome-sequencing project and the map will thus also provide a tool for the anchoring of the switchgrass genome assembly.
马占相思的树龄和倍性对纤维性状的影响王学文,崔克明.林业科学:2000, 36(1)摘要Acacia mangium Willd. is an economic species for pulp and paper industry. The growth of the young tetraploid A.mangium trees was more superior than that of the diploid trees. The present study deals with the effects of age and multiploidy on fiber characteristics in tetraploid and diploid species. They were compared and analysed using Franklins method with hydrogen peroxide and glacial acetic acid treatment, the data were analysed from micromeasurements. With age increment, the fiber length in the diploid trees increased significantly(p
GMATo: A novel tool for the identification and analysis of microsatellites in large genomesXuewen Wang, Peng Lu, Zhaopeng Lu.bioinformation:2013,9(10),541-544摘要Simple Sequence Repeats (SSR), also called microsatellite, is very useful for genetic marker development and genome application. The increasing whole sequences of more and more large genomes provide sources for SSR mining in silico. However currently existing SSR mining tools can’t process large genomes efficiently and generate no or poor statistics. Genome-wide Microsatellite Analyzing Tool (GMATo) is a novel tool for SSR mining and statistics at genome aspects. It is faster and more accurate than existed tools SSR Locator and MISA. If a DNA sequence was too long, it was chunked to short segments at several Mb followed by motifs generation and searching using Perl powerful pattern match function. Matched loci data from each chunk were then merged to produce final SSR loci information. Only one input file is required which contains raw fasta DNA sequences and output files in tabular format list all SSR loci information and statistical distribution at four classifications. GMATo was programmed in Java and Perl with both graphic and command line interface, either executable alone in platform independent manner with full parameters control. Software GMATo is a powerful tool for complete SSR characterization in genomes at any size.
Mechanism of Dormancy in the Buds and Cambium of Eucommia ulmoidesKalima N'Koma MWANGE,Wang Xue-wen,Cui Ke-ming.Journal of Integrative Plant Biology:2003, 45(6),698-704摘要对杜仲(Eucommia ulmoides Oliv.)一年生枝条休眠中的芽和维管形成层的结构和蛋白质含量进行了研究,探讨了杜仲不同休眠期转化的生理生化机理.结果证实了杜仲树的休眠期包括2个被动休眠期和一个生理休眠期.在生理休眠期,无论用外源IAA处理,还是给予适当的温度和光照,形成层都不能恢复活动.而且,雌株进入各个休眠阶段的时间都比雄株早.树皮中的蛋白质含量在第一被动休眠期间(Q1)显著地逐步增高(PAbstract：This paper describes changes in the structure of buds and vascular cambium as well as in protein content of one-year-old dormant branches of Eucommia ulmoides Oliv. in water-culture conditions. Results confirm the existence of 2 quiescences (Q1, Q2) and 1 rest (R) phases in this tree during the dormancy period. In the R time, the E. ulmoides cambium was unable to reactivate even though the tree was subjected to exogenous IAA, suitable temperature or required luminosity. Furthermore, pistillate trees entered the dormant phase earlier than staminate ones. 全文下载http://www.jipb.net/pubsoft/content/2/2338/X020025%28PS2%29.pdf