Xingtan Zhang

ALLMAPS: robust scaffold ordering based on multiple maps

The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS.

Cloning and evolutionary analysis of tobacco MAPK gene family

The mitogen-activated protein (MAP) kinase cascade is an important signaling module which is involved in biotic and abiotic stress responses as well as plant growth and development. In this study, we identified 17 tobacco MAPKs including 11 novel tobacco MAPK genes that have not been identified before. Comparative analysis with MAPK gene families from other plants, such as Athaliana thaliana, rice and poplar, suggested that tobacco MAPKs (such as NtMPK1, NtMPK3 and NtMPK8) might play similar functions in response to abiotic and biotic stresses. QRT-PCR analysis revealed that a total of 14 NtMPKs were regulated by SA and/or MeJA, suggesting their potential roles involved in plant defense response. In addition, 6 NtMPKs were induced by drought treatment, implying their roles in response to drought stress. Our results indicated that most of tobacco MAPK might be involved in plant defense response, which provides the basis for further analysis on physiological functions of tobacco MAPKs.

Polyribosomal RNA-Seq reveals the decreased complexity and diversity of the Arabidopsis translatome.

Recent RNA-seq studies reveal that the transcriptomes in animals and plants are more complex than previously thought, leading to the inclusion of many more splice isoforms in annotated genomes. However, it is possible that a significant proportion of the transcripts are spurious isoforms that do not contribute to functional proteins. One of the current hypotheses is that commonly used mRNA extraction methods isolate both pre-mature (nuclear) mRNA and mature (cytoplasmic) mRNA, and these incompletely spliced pre-mature mRNAs may contribute to a large proportion of these spurious transcripts. To investigate this, we compared a traditional RNA-seq dataset (total RNA-seq) and a ribosome-bound RNA-seq dataset (polyribosomal RNA-seq) from Arabidopsis thaliana. An integrative framework that combined de novo assembly and genome-guided assembly was applied to reconstruct transcriptomes for the two datasets. Up to 44.8% of the de novo assembled transcripts in total RNA-seq sample were of low abundance, whereas only 0.09% in polyribosomal RNA-seq de novo assembly were of low abundance. The final round of assembly using PASA (Program to Assemble Spliced Alignments) resulted in more transcript assemblies in the total RNA-seq than those in polyribosomal sample. Comparison of alternative splicing (AS) patterns between total and polyribosomal RNA-seq showed a significant difference (G-test, p-value<0.01) in intron retention events: 46.4% of AS events in the total sample were intron retention, whereas only 23.5% showed evidence of intron retention in the polyribosomal sample. It is likely that a large proportion of retained introns in total RNA-seq result from incompletely spliced pre-mature mRNA. Overall, this study demonstrated that polyribosomal RNA-seq technology decreased the complexity and diversity of the coding transcriptome by eliminating pre-mature mRNAs, especially those of low abundance.

Evolution and expression of the fructokinase gene family in Saccharum

BackgroundSugarcane is an important sugar crop contributing up to about 80% of the world sugar production. Efforts to characterize the genes involved in sugar metabolism at the molecular level are growing since increasing sugar content is a major goal in the breeding of new sugarcane varieties. Fructokinases (FRK) are the main fructose phosphorylating enzymes with high substrate specificity and affinity.ResultsIn this study, by combining comparative genomics approaches with BAC resources, seven fructokinase genes were identified in S. spontaneum. Phylogenetic analysis based on representative monocotyledon and dicotyledon plant species suggested that the FRK gene family is ancient and its evolutionary history can be traced in duplicated descending order: SsFRK4, SsFRK6/SsFRK7,SsFRK5, SsFRK3 and SsFRK1/SsFRK2. Among the close orthologs, the number and position of exons in FRKs were conserved; in contrast, the size of introns varied among the paralogous FRKs in Saccharum. Genomic constraints were analyzed within the gene alleles and between S. spontaneum and Sorghum bicolor, and gene expression analysis was performed under drought stress and with exogenous applications of plant hormones. FRK1, which was under strong functional constraint selection, was conserved among the gene allelic haplotypes, and displayed dominant expression levels among the gene families in the control conditions, suggesting that FRK1 plays a major role in the phosphorylation of fructose. FRK3 and FRK5 were dramatically induced under drought stress, and FRK5 was also found to increase its expression levels in the mature stage of Saccharum. Similarly, FRK3 and FRK5 were induced in response to drought stress in Saccharum. FRK2 and FRK7 displayed lower expression levels than the other FRK family members; FRK2 was under strong genomic selection constraints whereas FRK7 was under neutral selection. FRK7 may have become functionally redundant in Saccharum through pseudogenization. FRK4 and FRK6 shared the most similar expression pattern: FRK4 was revealed to have higher expression levels in mature tissues than in premature tissues of Saccharum, and FRK6 presented a slight increase under drought stress.ConclusionsOur study presents a comprehensive genomic study of the entire FRK gene family in Saccharum, providing the foundations for approaches to characterize the molecular mechanism regulated by the SsFRK family in sugarcane.

Research on Surface Treatment of Magnesium Alloy and Its Wettability with Resin

After phosphatising disposal, the micro-morphology of the AZ31B sheet was observed. The contact angle of the sheet was measured. The surface energy of the sheet was calculated. The laminated sheet was prepared, with preliminary study of its performance. Results showed that the amount and grain size of phosphate were influenced by the phosphating process, as well as wettability of materials. After 30°C/5 min phosphating, a dense phosphating film consisting of zinc phosphate was obtained, and the advancing contact angle of magnesium alloy was 58.3°. Compared with 31.5 mN m−1 of the raw magnesium alloy sheet, the surface energy of the sheet after phosphating reached 90 mN m−1. The laminated sheet of fibre/resin–phosphated magnesium alloy–fibre/resin has good bonding interface, corrosion resistance and mechanical properties.

Recent polyploidization events in three Saccharum founding species

Summary The complexity of polyploid Saccharum genomes hindered progress of genome research and crop improvement in sugarcane. To understand their genome structure, transcriptomes of 59 F1 individuals derived from S. officinarum LA Purple and S. robustum Molokai 5829 (2n = 80, x = 10 for both) were sequenced, yielding 11 157 and 8998 SNPs and 83 and 105 linkage groups, respectively. Most markers in each linkage group aligned to single sorghum chromosome. However, 71 interchromosomal rearrangements were detected between sorghum and S. officinarum or S. robustum, and 24 (33.8%) of them were shared between S. officinarum and S. robustum, indicating their occurrence before the speciation event that separated these two species. More than 2000 gene pairs from S. spontaneum, S. officinarum and S. robustum were analysed to estimate their divergence time. Saccharum officinarum and S. robustum diverged about 385 thousand years ago, and the whole‐genome duplication events occurred after the speciation event because of shared interchromosomal rearrangements. The ancestor of these two species diverged from S. spontaneum about 769 thousand years ago, and the reduction in basic chromosome number from 10 to 8 in S. spontaneum occurred after the speciation event but before the two rounds of whole‐genome duplication. Our results proved that S. officinarum is a legitimate species in its own right and not a selection from S. robustum during the domestication process in the past 10 000 years. Our findings rejected a long‐standing hypothesis and clarified the timing of speciation and whole‐genome duplication events in Saccharum.

Functional analysis of NtMPK2 uncovers its positive role in response to Pseudomonas syringae pv. tomato DC3000 in tobacco

Mitogen-activated protein kinase cascades are highly conserved signaling modules downstream of receptors/sensors and play pivotal roles in signaling plant defense against pathogen attack. Extensive studies on Arabidopsis MPK4 have implicated that the MAP kinase is involved in multilayered plant defense pathways. In this study, we identified tobacco NtMPK2 as an ortholog of AtMPK4. Transgenic tobacco overexpressing NtMPK2 markedly enhances resistance to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) virulent and avirulent strains. Transcriptome analysis of NtMPK2-dependent genes shows that possibly the basal resistance system is activated by NtMPK2 overexpression. In addition to NtMPK2-mediated resistance, multiple pathways are involved in response to the avirulent bacteria based on analysis of Pst-responding genes, including SA and ET pathways. Notably, it is possible that biosynthesis of antibacterial compounds is responsible for inhibition of Pst DC3000 avirulent strain when programmed cell death processes in the host. Our results uncover that NtMPK2 positively regulate tobacco defense response to Pst DC3000 and improve our understanding of plant molecular defense mechanism.

Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations

F2 and recombinant inbred lines (RILs) populations are very commonly used in plant genetic mapping studies. Although genome-wide genetic markers like single nucleotide polymorphisms (SNPs) can be readily identified by a wide array of methods, accurate genotype calling remains challenging, especially for heterozygous loci and missing data due to low sequencing coverage per individual. Therefore, we developed Genotype-Corrector, a program that corrects genotype calls and imputes missing data to improve the accuracy of genetic mapping. Genotype-Corrector can be applied in a wide variety of genetic mapping studies that are based on low coverage whole genome sequencing (WGS) or Genotyping-by-Sequencing (GBS) related techniques. Our results show that Genotype-Corrector achieves high accuracy when applied to both synthetic and real genotype data. Compared with using raw or only imputed genotype calls, the linkage groups built by corrected genotype data show much less noise and significant distortions can be corrected. Additionally, Genotype-Corrector compares favorably to the popular imputation software LinkImpute and Beagle in both F2 and RIL populations. Genotype-Corrector is publicly available on GitHub at https://github.com/freemao/Genotype-Corrector.

From Alpha-Duplication to Triplication and Sextuplication

The Brassica napus is a truly great genome for the study of genome and gene family evolution, with a rich history of past whole-genome duplication (WGD) events. The genome has undergone a total of 5 rounds of duplications since the common ancestor with the basal angiosperm Amborella. This level of genetic redundancy is unparalleled by any other flowering plant genome that was sequenced prior to the release of the B. napus genome assembly. Three recent WGDs that occurred within the lineage of Brassicaceae are of significant value to polyploid research, namely the ‘alpha’ duplication event, the Brassica triplication and B. napus allotetraploidization. These events occurred at different evolutionary times and are representatives of paleo-polyploidy, meso-polyploidy, and neo-polyploidy, respectively. Studies of evolutionary changes and transcriptional regulation of duplicate genes derived from these WGD events have led to groundbreaking discoveries in the dynamics of polyploid genomes, including genome reorganization, gene fractionation (loss of duplicated genes), and genome dominance. These breakthroughs were largely facilitated by a number of innovations in computational methods, databases, and interconnected cyberinfrastructure that are devoted to plant comparative genomics research. With its genome now fully deciphered, B. napus continues to be one of the most important model organisms in post-polyploidy genome evolution research.

Identification and Characterization of microRNAs from Saccharum officinarum L by Deep Sequencing

In modern sugarcane cultivars, around 70–80% of the genetic information originates from Saccharum officinarum, which contributed important sugar content traits. Although several studies have identified microRNAs in Saccharum hybrids, they have not yet been studied in S. officinarum. In this study, by deep sequencing and in silico approaches, 268 miRNA candidates were predicted in S. officinarum, and 52 were found to likely be real miRNAs based on our analysis with stringent criteria. Among these 52 miRNAs, 43 miRNAs from 26 miRNA families were found to have homologous miRNAs in public miRBase Release 21, and 9 miRNAs were identified to be novel in S. officinarum. Out of the 52 miRNAs, 6 were randomly chosen and verified by stem-loop RT-PCR. The 52 miRNAs were predicted to have 237 and 76 targets in sugarcane and sorghum, respectively, including auxin response factor, MADS-box transcription factor, zinc finger-like protein. MicroRNAs were found to be involved in critical sugarcane pathways, such as sucrose metabolism and cellulose metabolism. In addition, the first miRNA (sof-novel1) derived from the Saccharum chloroplast genome was identified. These results provide the foundation for future studies to distinguish the miRNAs from S. spontaneum and S. officinarum in Saccharum hybrid, and valuable information to further study the miRNA functions in Saccharum species.