Multiple independent recombinations led to hermaphroditism in grapevine.

Hermaphroditic (perfect) flowers were a key trait in grapevine domestication, enabling a drastic increase in yields due to the efficiency of self-pollination in the domesticated grapevine (Vitis vinifera L. ssp. vinifera). In contrast, all extant wild Vitis species are dioecious, each plant having only male or female flowers. In this study, we identified the male (M) and female (f) haplotypes of the sex-determining region (SDR) in the wild grapevine species V. cinerea and confirmed the boundaries of the SDR. We also demonstrated that the SDR and its boundaries are precisely conserved across the Vitis genus using shotgun resequencing data of 556 wild and domesticated accessions from North America, East Asia, and Europe. A high linkage disequilibrium was found at the SDR in all wild grape species, while different recombination signatures were observed along the hermaphrodite (H) haplotype of 363 cultivated accessions, revealing two distinct H haplotypes, named H1 and H2. To further examine the H2 haplotype, we sequenced the genome of two grapevine cultivars, 'Riesling' and 'Chardonnay'. By reconstructing the first two H2 haplotypes, we estimated the divergence time between H1 and H2 haplotypes at ∼6 million years ago, which predates the domestication of grapevine (∼8,000 y ago). Our findings emphasize the important role of recombination suppression in maintaining dioecy in wild grape species and lend additional support to the hypothesis that at least two independent recombination events led to the reversion to hermaphroditism in grapevine.

Increases in vein length compensate for leaf area lost to lobing in grapevine.

PREMISE: Leaf lobing and leaf size vary considerably across and within species, including among grapevines (Vitis spp.), some of the best-studied leaves. We examined the relationship between leaf lobing and leaf area across grapevine populations that varied in extent of leaf lobing. METHODS: We used homologous landmarking techniques to measure 2632 leaves across 2 years in 476 unique, genetically distinct grapevines from five biparental crosses that vary primarily in the extent of lobing. We determined to what extent leaf area explained variation in lobing, vein length, and vein to blade ratio. RESULTS: Although lobing was the primary source of variation in shape across the leaves we measured, leaf area varied only slightly as a function of lobing. Rather, leaf area increases as a function of total major vein length, total branching vein length, and vein to blade ratio. These relationships are stronger for more highly lobed leaves, with the residuals for each model differing as a function of distal lobing. CONCLUSIONS: For leaves with different extents of lobing but the same area, the more highly lobed leaves have longer veins and higher vein to blade ratios, allowing them to maintain similar leaf areas despite increased lobing. These findings show how more highly lobed leaves may compensate for what would otherwise result in a reduced leaf area, allowing for increased photosynthetic capacity through similar leaf size.

It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data.

Biclustering is a powerful data mining technique that allows clustering of rows and columns, simultaneously, in a matrix-format data set. It was first applied to gene expression data in 2000, aiming to identify co-expressed genes under a subset of all the conditions/samples. During the past 17 years, tens of biclustering algorithms and tools have been developed to enhance the ability to make sense out of large data sets generated in the wake of high-throughput omics technologies. These algorithms and tools have been applied to a wide variety of data types, including but not limited to, genomes, transcriptomes, exomes, epigenomes, phenomes and pharmacogenomes. However, there is still a considerable gap between biclustering methodology development and comprehensive data interpretation, mainly because of the lack of knowledge for the selection of appropriate biclustering tools and further supporting computational techniques in specific studies. Here, we first deliver a brief introduction to the existing biclustering algorithms and tools in public domain, and then systematically summarize the basic applications of biclustering for biological data and more advanced applications of biclustering for biomedical data. This review will assist researchers to effectively analyze their big data and generate valuable biological knowledge and novel insights with higher efficiency.

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.

Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles that can be further analyzed using correlation analysis, co-expression analysis, clustering, differential gene expression (DGE), among many other studies. While these analyses can provide invaluable information related to gene expression, integration and interpretation of the results can prove challenging. Here we present a tool called IRIS-EDA, which is a Shiny web server for expression data analysis. It provides a straightforward and user-friendly platform for performing numerous computational analyses on user-provided RNA-Seq or Single-cell RNA-Seq (scRNA-Seq) data. Specifically, three commonly used R packages (edgeR, DESeq2, and limma) are implemented in the DGE analysis with seven unique experimental design functionalities, including a user-specified design matrix option. Seven discovery-driven methods and tools (correlation analysis, heatmap, clustering, biclustering, Principal Component Analysis (PCA), Multidimensional Scaling (MDS), and t-distributed Stochastic Neighbor Embedding (t-SNE)) are provided for gene expression exploration which is useful for designing experimental hypotheses and determining key factors for comprehensive DGE analysis. Furthermore, this platform integrates seven visualization tools in a highly interactive manner, for improved interpretation of the analyses. It is noteworthy that, for the first time, IRIS-EDA provides a framework to expedite submission of data and results to NCBI's Gene Expression Omnibus following the FAIR (Findable, Accessible, Interoperable and Reusable) Data Principles. IRIS-EDA is freely available at http://bmbl.sdstate.edu/IRIS/.

Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.).

BACKGROUND: Drought is an important constraint on grapevine sustainability. Vitis riparia, widely used in rootstock and scion breeding, has been studied in isolated leaf drying response studies; however, it is essential to identify key root and shoot water deficit signaling traits in intact plants. This information will aid improved scion and rootstock selection and management practices in grapevine. RNAseq data were generated from V. riparia roots and shoots under water deficit and well-watered conditions to determine root signaling and shoot responses to water deficit. RESULTS: Shoot elongation, photosynthetic rate, and stomatal conductance were significantly reduced in water deficit (WD) treated than in well-watered grapevines. RNAseq analysis indicated greater transcriptional differences in shoots than in roots under WD, with 6925 and 1395 genes differentially expressed, respectively (q-value < 0.05). There were 50 and 25 VitisNet pathways significantly enriched in WD relative to well-watered treatments in grapevine shoots and roots, respectively. The ABA biosynthesis genes beta-carotene hydroxylase, zeaxanthin epoxidase, and 9-cis-epoxycarotenoid dioxygenases were up-regulated in WD root and WD shoot. A positive enrichment of ABA biosynthesis genes and signaling pathways in WD grapevine roots indicated enhanced root signaling to the shoot. An increased frequency of differentially expressed reactive oxygen species scavenging (ROS) genes were found in the WD shoot. Analyses of hormone signaling genes indicated a strong ABA, auxin, and ethylene network and an ABA, cytokinin, and circadian rhythm network in both WD shoot and WD root. CONCLUSIONS: This work supports previous findings in detached leaf studies suggesting ABA-responsive binding factor 2 (ABF2) is a central regulator in ABA signaling in the WD shoot. Likewise, ABF2 may have a key role in V. riparia WD shoot and WD root. A role for ABF3 was indicated only in WD root. WD shoot and WD root hormone expression analysis identified strong ABA, auxin, ethylene, cytokinin, and circadian rhythm signaling networks. These results present the first ABA, cytokinin, and circadian rhythm signaling network in roots under water deficit. These networks point to organ specific regulators that should be explored to further define the communication network from soil to shoot.

Evaluation of Volatile Metabolites Emitted In-Vivo from Cold-Hardy Grapes during Ripening Using SPME and GC-MS: A Proof-of-Concept.

In this research, we propose a novel concept for a non-destructive evaluation of volatiles emitted from ripening grapes using solid-phase microextraction (SPME). This concept is novel to both the traditional vinifera grapes and the cold-hardy cultivars. Our sample models are cold-hardy varieties in the upper Midwest for which many of the basic multiyear grape flavor and wine style data is needed. Non-destructive sampling included a use of polyvinyl fluoride (PVF) chambers temporarily enclosing and concentrating volatiles emitted by a whole cluster of grapes on a vine and a modified 2 mL glass vial for a vacuum-assisted sampling of volatiles from a single grape berry. We used SPME for either sampling in the field or headspace of crushed grapes in the lab and followed with analyses on gas chromatography-mass spectrometry (GC-MS). We have shown that it is feasible to detect volatile organic compounds (VOCs) emitted in-vivo from single grape berries (39 compounds) and whole clusters (44 compounds). Over 110 VOCs were released to headspace from crushed berries. Spatial (vineyard location) and temporal variations in VOC profiles were observed for all four cultivars. However, these changes were not consistent by growing season, by location, within cultivars, or by ripening stage when analyzed by multivariate analyses such as principal component analysis (PCA) and hierarchical cluster analyses (HCA). Research into aroma compounds present in cold-hardy cultivars is essential to the continued growth of the wine industry in cold climates and diversification of agriculture in the upper Midwestern area of the U.S.

Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly.

BACKGROUND: De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC). RESULTS: The three new assemblies were greater in size than the AP assembly. PLAT*_GC had the greatest number of scaffolds aligning with a minimum of 95% identity and ≥1000 bp alignment length to V. vinifera (PN40024 12X.v2) reference genome. SNP analysis also identified additional high quality SNPs. A greater number of sequence reads mapped back with zero-mismatch to the PLAT_d, MERGE, and PLAT*_GC (>94%) than was found in the AP assembly (87%) indicating a greater fidelity to the original sequence data in the new assemblies than in AP assembly. A de novo gene prediction conducted using seedless RNA-seq data predicted > 30,000 coding sequences for the three new de novo assemblies, with the greatest number (30,544) in PLAT*_GC and only 26,515 for the AP assembly. Transcription factor analysis indicated good family coverage, but some genes found in the VCOST.v3 annotation were not identified in any of the de novo assemblies, particularly some from  the MYB and ERF families. CONCLUSIONS: The PLAT_d and PLAT*_GC had a greater number of synteny blocks with the V. vinifera (PN40024 12X.v2) reference genome than AP or MERGE. PLAT*_GC provided the most contiguous assembly with only 1.2% scaffold N, in contrast to AP (10.7% N), PLAT_d (6.6% N) and Merge (6.4% N). A PLAT*_GC pseudo-chromosome assembly with chromosome alignment to the reference genome V. vinifera, (PN40024 12X.v2) provides new information for use in seedless grape genetic mapping studies. An annotated de novo gene prediction for the PLAT*_GC assembly, aligned with VitisNet pathways provides new seedless grapevine specific transcriptomic resource that has excellent fidelity with the seedless short read sequence data.

QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data.

Motivation: Biclustering is widely used to identify co-expressed genes under subsets of all the conditions in a large-scale transcriptomic dataset. The program, QUBIC, is recognized as one of the most efficient and effective biclustering methods for biological data interpretation. However, its availability is limited to a C implementation and to a low-throughput web interface. Results: An R implementation of QUBIC is presented here with two unique features: (i) a 82% average improved efficiency by refactoring and optimizing the source C code of QUBIC; and (ii) a set of comprehensive functions to facilitate biclustering-based biological studies, including the qualitative representation (discretization) of expression data, query-based biclustering, bicluster expanding, biclusters comparison, heatmap visualization of any identified biclusters and co-expression networks elucidation. Availability and Implementation: The package is implemented in R (as of version 3.3) and is available from Bioconductor at the URL: http://bioconductor.org/packages/QUBIC, where installation and usage instructions can be found. Contact: qin.ma@sdstate.edu Supplimentary Information: Supplementary data are available at Bioinformatics online.

An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.

BACKGROUND: Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif prediction. RESULTS: Here we present an integrative phylogenetic footprinting framework for accurate motif predictions in prokaryotic genomes (MP(3)). The framework includes a new orthologous data preparation procedure, an additional promoter scoring and pruning method and an integration of six existing motif finding algorithms as basic motif search engines. Specifically, we collected orthologous genes from available prokaryotic genomes and built the orthologous regulatory regions based on sequence similarity of promoter regions. This procedure made full use of the large-scale genomic data and taxonomy information and filtered out the promoters with limited contribution to produce a high quality orthologous promoter set. The promoter scoring and pruning is implemented through motif voting by a set of complementary predicting tools that mine as many motif candidates as possible and simultaneously eliminate the effect of random noise. We have applied the framework to Escherichia coli k12 genome and evaluated the prediction performance through comparison with seven existing programs. This evaluation was systematically carried out at the nucleotide and binding site level, and the results showed that MP(3) consistently outperformed other popular motif finding tools. We have integrated MP(3) into our motif identification and analysis server DMINDA, allowing users to efficiently identify and analyze motifs in 2,072 completely sequenced prokaryotic genomes. CONCLUSION: The performance evaluation indicated that MP(3) is effective for predicting regulatory motifs in prokaryotic genomes. Its application may enhance progress in elucidating transcription regulation mechanism, thus provide benefit to the genomic research community and prokaryotic genome researchers in particular.

Protein identification and quantification from riverbank grape, Vitis riparia: Comparing SDS-PAGE and FASP-GPF techniques for shotgun proteomic analysis.

Protein sample preparation optimisation is critical for establishing reproducible high throughput proteomic analysis. In this study, two different fractionation sample preparation techniques (in-gel digestion and in-solution digestion) for shotgun proteomics were used to quantitatively compare proteins identified in Vitis riparia leaf samples. The total number of proteins and peptides identified were compared between filter aided sample preparation (FASP) coupled with gas phase fractionation (GPF) and SDS-PAGE methods. There was a 24% increase in the total number of reproducibly identified proteins when FASP-GPF was used. FASP-GPF is more reproducible, less expensive and a better method than SDS-PAGE for shotgun proteomics of grapevine samples as it significantly increases protein identification across biological replicates. Total peptide and protein information from the two fractionation techniques is available in PRIDE with the identifier PXD001399 (http://proteomecentral.proteomexchange.org/dataset/PXD001399).

Genome assembly of the hybrid grapevine Vitis 'Chambourcin'.

'Chambourcin' is a French-American interspecific hybrid grape grown in the eastern and midwestern United States and used for making wine. Few genomic resources are available for hybrid grapevines like 'Chambourcin'. Here, we assembled the genome of 'Chambourcin' using PacBio HiFi long-read, Bionano optical map, and Illumina short-read sequencing technologies. We generated an assembly for 'Chambourcin' with 26 scaffolds, with an N50 length of 23.3 Mb and an estimated BUSCO completeness of 97.9%. We predicted 33,791 gene models and identified 16,056 common orthologs between 'Chambourcin', V. vinifera 'PN40024' 12X.v2, VCOST.v3, Shine Muscat and V. riparia Gloire. We found 1,606 plant transcription factors from 58 gene families. Finally, we identified 304,571 simple sequence repeats (up to six base pairs long). Our work provides the genome assembly, annotation and the protein and coding sequences of 'Chambourcin'. Our genome assembly is a valuable resource for genome comparisons, functional genomic analyses and genome-assisted breeding research.

Genetic analysis of grapevine root system architecture and loci associated gene networks.

Own-rooted grapevines and grapevine rootstocks are vegetatively propagated from cuttings and have an adventitious root system. Unraveling the genetic underpinnings of the adventitious root system architecture (RSA) is important for improving own-rooted and grafted grapevine sustainability for a changing climate. Grapevine RSA genetic analysis was conducted in an Vitis sp. 'VRS-F2' population. Nine root morphology, three total root system morphology, and two biomass traits that contribute to root anchorage and water and nutrient uptake were phenotyped. Quantitative trait loci (QTL) analysis was performed using a high density integrated GBS and rhAmpSeq genetic map. Thirty-one QTL were detected for eleven of the RSA traits (surface area, root volume, total root length, fresh weight, number of tips, forks or links, longest root and average root diameter, link length, and link surface area) revealing many small effects. Several QTL were colocated on chromosomes 1, 9, 13, 18, and 19. QTL with identical peak positions on chromosomes 1 or 13 were enriched for AP2-EREBP, AS2, C2C2-CO, HMG, and MYB transcription factors, and QTL on chromosomes 9 or 13 were enriched for the ALFIN-LIKE transcription factor and regulation of autophagy pathways. QTL modeling for individual root traits identified eight models explaining 13.2 to 31.8% of the phenotypic variation. 'Seyval blanc' was the grandparent contributing to the allele models that included a greater surface area, total root length, and branching (number of forks and links) traits promoting a greater root density. In contrast, V. riparia 'Manitoba 37' contributed the allele for greater average branch length (link length) and diameter, promoting a less dense elongated root system with thicker roots. LATERAL ORGAN BOUNDARY DOMAIN (LBD or AS2/LOB) and the PROTODERMAL FACTOR (PFD2 and ANL2) were identified as important candidate genes in the enriched pathways underlying the hotspots for grapevine adventitious RSA. The combined QTL hotspot and trait modeling identified transcription factors, cell cycle and circadian rhythm genes with a known role in root cell and epidermal layer differentiation, lateral root development and cortex thickness. These genes are candidates for tailoring grapevine root system texture, density and length in breeding programs.

Berry Anthocyanin, Acid, and Volatile Trait Analyses in a Grapevine-Interspecific F2 Population Using an Integrated GBS and rhAmpSeq Genetic Map.

Increased map density and transferability of markers are essential for the genetic analysis of fruit quality and stress tolerance in interspecific grapevine populations. We used 1449 GBS and 2000 rhAmpSeq markers to develop a dense map for an interspecific F2 population (VRS-F2) that was derived by selfing a single F1 from a Vitis riparia x 'Seyval blanc' cross. The resultant map contained 2519 markers spanning 1131.3 cM and was highly collinear with the Vitis vinifera 'PN40024' genome. Quantitative trait loci (QTL) for berry skin color and flower type were used to validate the map. Four rhAmpSeq transferable markers were identified that can be used in pairs (one pistillate and one hermaphroditic) to predict pistillate and hermaphrodite flower type with ≥99.7% accuracy. Total and individual anthocyanin diglucoside QTL mapped to chromosome 9 near a 5-O-GLUCOSYLTRANSFERASE candidate gene. Malic acid QTL were observed on chromosome 1 and 6 with two MALATE DEHYRDROGENASE CYTOPLASMIC 1 and ALUMINUM-ACTIVATED MALATE TRANSPORTER 2-LIKE (ALMT) candidate genes, respectively. Modeling malic acid identified a potential QTL on chromosome 8 with peak position in proximity of another ALMT. A first-ever reported QTL for the grassy smelling volatile (E)-2-hexenal was found on chromosome 2 with a PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE candidate gene near peak markers.

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine.

Transition of grapevine buds from paradormancy to endodormancy is coordinated by changes in gene expression, phytohormones, transcription factors, and other molecular regulators, but the mechanisms involved in transcriptional and post-transcriptional regulation of dormancy stages are not well delineated. To identify potential regulatory targets, an integrative analysis of differential gene expression profiles and their inverse relationships with miRNA abundance was performed in paradormant (long day (LD) 15 h) or endodormant (short day (SD), 13 h) Vitis riparia buds. There were 400 up- and 936 downregulated differentially expressed genes in SD relative to LD budsGene set and gene ontology enrichment analysis indicated that hormone signaling and cell cycling genes were downregulated in SD relative to LD buds. miRNA abundance and inverse expression analyses of miRNA target genes indicated increased abundance of miRNAs that negatively regulate genes involved with cell cycle and meristem development in endodormant buds and miRNAs targeting starch metabolism related genes in paradormant buds. Analysis of interactions between abundant miRNAs and transcription factors identified a network with coinciding regulation of cell cycle and epigenetic regulation related genes in SD buds. This network provides evidence for cross regulation occurring between miRNA and transcription factors both upstream and downstream of MYB3R1.

Multi-dimensional leaf phenotypes reflect root system genotype in grafted grapevine over the growing season.

BACKGROUND: Modern biological approaches generate volumes of multi-dimensional data, offering unprecedented opportunities to address biological questions previously beyond reach owing to small or subtle effects. A fundamental question in plant biology is the extent to which below-ground activity in the root system influences above-ground phenotypes expressed in the shoot system. Grafting, an ancient horticultural practice that fuses the root system of one individual (the rootstock) with the shoot system of a second, genetically distinct individual (the scion), is a powerful experimental system to understand below-ground effects on above-ground phenotypes. Previous studies on grafted grapevines have detected rootstock influence on scion phenotypes including physiology and berry chemistry. However, the extent of the rootstock's influence on leaves, the photosynthetic engines of the vine, and how those effects change over the course of a growing season, are still largely unknown. RESULTS: Here, we investigate associations between rootstock genotype and shoot system phenotypes using 5 multi-dimensional leaf phenotyping modalities measured in a common grafted scion: ionomics, metabolomics, transcriptomics, morphometrics, and physiology. Rootstock influence is ubiquitous but subtle across modalities, with the strongest signature of rootstock observed in the leaf ionome. Moreover, we find that the extent of rootstock influence on scion phenotypes and patterns of phenomic covariation are highly dynamic across the season. CONCLUSIONS: These findings substantially expand previously identified patterns to demonstrate that rootstock influence on scion phenotypes is complex and dynamic and underscore that broad understanding necessitates volumes of multi-dimensional data previously unmet.

Differential floral development and gene expression in grapevines during long and short photoperiods suggests a role for floral genes in dormancy transitioning.

Daylength is an important environmental cue for synchronizing growth, flowering, and dormancy with seasonality. As many floral development genes are photoperiod regulated, it has been suggested that they could have a regulatory role in bud endodormancy. Therefore, the influence of photoperiod was studied on inflorescence primordia differentiation and floral pathway related gene expression during the development of overwintering buds in Vitis riparia and V. spp. 'Seyval'. Photoperiod treatments were imposed 35 days after budbreak, and histological and transcriptomic analyses were conducted during the subsequent 42 days of bud development. Long day (LD, 15 h) and short day (SD, 13 h) buds were floral competent by 21 days of photoperiod treatment (56 days after budbreak); however, the floral meristem developed faster in LD than in SD buds. Analysis of 132 floral pathway related genes represented on the Affymetrix Grape Genome array indicated 60 were significantly differentially expressed between photoperiod treatments. Genes predominantly related to floral transition or floral meristem development were identified by their association with distinct grape floral meristem development and an expression pattern in LD consistent with their previously identified roles in flowering literature. Genes with a potential dual role in floral development and dormancy transitioning were identified using photoperiod induced differences in floral development between LD and SD buds and uncharacteristic gene expression trends in relation to floral development. Candidate genes with the potential to play a dual role in SD dormancy induction include circadian rhythm or flowering transition related genes: AP2, BT1, COL-13, EIN3, ELF4, DDTR, GAI and HY5.

Proteomic analysis of shoot tissue during photoperiod induced growth cessation in V. riparia Michx. grapevines.

BACKGROUND: Growth cessation, cold acclimation and dormancy induction in grapevines and other woody perennial plants native to temperate continental climates is frequently triggered by short photoperiods. The early induction of these processes by photoperiod promotes winter survival of grapevines in cold temperate zones. Examining the molecular processes, in particular the proteomic changes in the shoot, will provide greater insight into the signaling cascade that initiates growth cessation and dormancy induction. To begin understanding transduction of the photoperiod signal, Vitis riparia Michx. grapevines that had grown for 35 days in long photoperiod (long day, LD, 15 h) were subjected to either a continued LD or a short photoperiod (short day, SD, 13 h) treatment. Shoot tips (4-node shoot terminals) were collected from each treatment at 7 and 28 days of LD and SD for proteomic analysis via two-dimensional (2D) gel electrophoresis. RESULTS: Protein profiles were characterized in V. riparia shoot tips during active growth or SD induced growth cessation to examine physiological alterations in response to differential photoperiod treatments. A total of 1054 protein spots were present on the 2D gels. Among the 1054 proteins, 216 showed differential abundance between LD and SD (>/= two-fold ratio, p-value

Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. 'Manitoba 37'.

Vitis riparia, a critically important Native American grapevine species, is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic. This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species. Here we report an Illumina short-read 369X coverage, draft de novo heterozygous genome sequence of V. riparia Michx. 'Manitoba 37' with the size of ~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp. Using RNAseq data, 40,019 coding sequences were predicted and annotated. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models found 96% of the complete BUSCOs in this assembly. The assembly continuity and completeness were further validated using V. riparia ESTs, BACs, and three de novo transcriptome assemblies of three different V. riparia genotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of the V. riparia assembly and predicted CDS with the latest V. vinifera 'PN40024' CDS and genome assembly showed 99% CDS alignment and a high degree of synteny. An analysis of plant transcription factors indicates a high degree of homology with the V. vinifera transcription factors. QTL mapping to V. riparia 'Manitoba 37' and V. vinifera PN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understanding V. riparia's genetic contributions in grape breeding and research.

Water Deficit Transcriptomic Responses Differ in the Invasive Tamarix chinensis and T. ramosissima Established in the Southern and Northern United States.

Tamarix spp. (saltcedar) were introduced from Asia to the southern United States as windbreak and ornamental plants and have spread into natural areas. This study determined differential gene expression responses to water deficit (WD) in seedlings of T. chinensis and T. ramosissima from established invasive stands in New Mexico and Montana, respectively. A reference de novo transcriptome was developed using RNA sequences from WD and well-watered samples. Blast2GO analysis of the resulting 271,872 transcripts yielded 89,389 homologs. The reference Tamarix (Tamaricaceae, Carophyllales order) transcriptome showed homology with 14,247 predicted genes of the Beta vulgaris subsp. vulgaris (Amaranthaceae, Carophyllales order) genome assembly. T. ramosissima took longer to show water stress symptoms than T. chinensis. There were 2068 and 669 differentially expressed genes (DEG) in T. chinensis and T. ramosissima, respectively; 332 were DEG in common between the two species. Network analysis showed large biological process networks of similar gene content for each of the species under water deficit. Two distinct molecular function gene ontology networks (binding and transcription factor-related) encompassing multiple up-regulated transcription factors (MYB, NAC, and WRKY) and a cellular components network containing many down-regulated photosynthesis-related genes were identified in T. chinensis, in contrast to one small molecular function network in T. ramosissima.

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.

Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.