Mining and Survey of Simple Sequence Repeats in Expressed Sequence Tags of Tomato Species

Expressed Sequence Tags (ESTs) of three tomato species were computationally mined for simple sequence repeats (SSRs). A total of 4,490, 291 and 1,270 simple sequence repeats identified in analyzed non-redundant ESTs of Solanum lycoperisicum, Solanum pennellii and Solanum habrochaites, respectively. In S. lycopersucum, 416 sequences contained more than one SSR and 264 motifs were present in compound formation. 24 and 137 EST sequences contained more than one SSR, and 16 and 93 motifs were found in compound formation in S. pennellii and S. habrochaites, respectively. The frequency of repeats within all retrieved S. lycopersicum EST sequences were 7.6%, whereas this number was corresponded to 6.5% in S. pennellii and 9% in S. habrochaites. An average density was one SSR per 9 kb in S. lycopersicum, per 7.9 kb in S. pennellii and per 9.4 kb in S. habrochaites. AT/AT, AG/CT and AAG/CTT motifs, considering sequence complementary, detected more frequently among all types of identified repeats

Predicting promoters in phage genomes using machine learning models

The renewed interest in phages as antibacterial agents has led to the exponentially growing number of sequenced phage genomes. Therefore, the development of novel bioinformatics methods to automate and facilitate phage genome annotation is of utmost importance. The most difficult step of phage genome annotation is the identification of promoters. As the existing methods for predicting promoters are not well suited for phages, we used machine learning models for locating promoters in phage genomes. Several models were created, using different algorithms and datasets, which consisted of known phage promoter and non-promoter sequences. All models showed good performance, but the ANN model provided better results for the smaller dataset (92% of accuracy, 89% of precision and 87% of recall) and the SVM model returned better results for the larger dataset (93% of accuracy, 91% of precision and 80% of recall). Both models were applied to the genome of Pseudomonas phage phiPsa17 and were able to identify both types of promoters, host and phage, found in phage genomes.This study was supported by the Portuguese Foundation for Science andTechnology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 unit and theProject POCI-01-0145-FEDER-029628. This work was also supported by BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fundunder the scope of Norte2020 - Programa Operacional Regional do Norte.info:eu-repo/semantics/publishedVersio

PlantProm: a database of plant promoter sequences

PlantProm DB, a plant promoter database, is an annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species. The first release (2002.01) of PlantProm DBcontains 305 entries including 71, 220 and 14 promoters from monocot, dicot and other plants, respectively. It provides DNA sequence of the promoter regions ( 200: þ51) with TSS on the fixed position þ201, taxonomic/promoter type classification of promoters and Nucleotide Frequency Matrices (NFM) for promoter elements: TATA-box, CCAAT-box and TSS-motif (Inr). Analysis of TSS-motifs revealed that their composition is different in dicots and monocots, as well as for TATA and TATA-less promoters. The database serves as learning set in developing plant promoter prediction programs. One such program (TSSP) based on discriminant analysis has been created by Softberry Inc. and the application of a support vector machine approach for promoter identification is under development

Robust analysis of 5′-transcript ends (5′-RATE): a novel technique for transcriptome analysis and genome annotation

Complicated cloning procedures and the high cost of sequencing have inhibited the wide application of serial analysis of gene expression and massively parallel signature sequencing for genome-wide transcriptome profiling of complex genomes. Here we describe a new method called robust analysis of 5′-transcript ends (5′-RATE) for rapid and cost-effective isolation of long 5′ transcript ends (∼80 bp). It consists of three major steps including 5′-oligocapping of mRNA, NlaIII tag and ditag generation, and pyrosequencing of NlaIII tags. Complicated steps, such as purification and cloning of concatemers, colony picking and plasmid DNA purification, are eliminated and the conventional Sanger sequencing method is replaced with the newly developed pyrosequencing method. Sequence analysis of a maize 5′-RATE library revealed complex alternative transcription start sites and a 5′ poly(A) tail in maize transcripts. Our results demonstrate that 5′-RATE is a simple, fast and cost-effective method for transcriptome analysis and genome annotation of complex genomes

Low temperature and light regulate delta 12 fatty acid desaturases (FAD2) at a transcriptional level in cotton (Gossypium hirsutum)

Lipid modifying enzymes play a key role in the development of cold stress tolerance in cold-resistant plants such as cereals. However, little is known about the role of the endogenous enzymes in cold-sensitive species such as cotton. Delta 12 fatty acid desaturases (FAD2), known to participate in adaptation to low temperatures through acyl chain modifications were used in gene expression studies in order to identify parameters of plant response to low temperatures. The induction of microsomal delta 12 fatty acid desaturases at an mRNA level under cold stress in plants is shown here for first time. Quantitative PCR showed that though both delta 12 omega 6 fatty acid desaturase genes FAD2-3 and FAD2-4 identified in cotton are induced under cold stress, FAD2-4 induction is significantly higher than FAD2-3. The induction of both isoforms was light regulated, in contrast a third isoform FAD2-2 was not affected by cold or light. Stress tolerance and light regulatory elements were identified in the predicted promoters of both FAD2-3 and FAD2-4 genes. Di-unsaturated fatty acid species rapidly increased in the microsomal fraction isolated from cotton leaves, following cold stress. Expression analysis patterns were correlated with the observed increase in both total and microsomal fatty acid unsaturation levels suggesting the direct role of the FAD2 genes in membrane adaptation to cold stress

The gene encoding Arabidopsis acyl-CoA-binding protein 3 is pathogen inducible and subject to circadian regulation

In Arabidopsis thaliana, acyl-CoA-binding protein 3 ( ACBP3), one of six ACBPs, is unique in terms of the C-terminal location of its acyl-CoA-binding domain. It promotes autophagy-mediated leaf senescence and confers resistance to Pseudomonas syringae pv. tomato DC3000. To understand the regulation of ACBP3, a 1.7 kb 5'-flanking region of ACBP3 and its deletion derivatives were characterized using β-glucuronidase (GUS) fusions. A 374 bp minimal fragment (–151/+223) could drive GUS expression while a 1698 bp fragment (–1475/+223) conferred maximal activity. Further, histochemical analysis on transgenic Arabidopsis harbouring the largest (1698 bp) ACBP3pro::GUS fusion displayed ubiquitous expression in floral organs and vegetative tissues (vascular bundles of leaves and stems), consistent with previous results showing that extracellularly localized ACBP3 functions in plant defence. A 160 bp region (–434/–274) induced expression in extended darkness and caused down-regulation in extended light. Electrophoretic mobility shift assay (EMSA) and DNase I footprinting assay showed that the DNA-binding with one finger box (Dof-box, –341/–338) interacted specifically with leaf nuclear proteins from dark-treated Arabidopsis, while GT-1 (–406/–401) binds both dark- and light-treated Arabidopsis, suggesting that Dof and GT-1 motifs are required to mediate circadian regulation of ACBP3. Moreover, GUS staining and fluorometric measurements revealed that a 109 bp region (–543/–434) was responsive to phytohormones and pathogens. An S-box of AT-rich sequence (–516/–512) was identified to bind nuclear proteins from pathogen-infected Arabidopsis leaves, providing the basis for pathogen-inducible regulation of ACBP3 expression. Thus, three cis-responsive elements (Dof, GT-1, and the S-box) in the 5'-flanking region of ACBP3 are proven functional in the regulation of ACBP3

Root Suberin Forms an Extracellular Barrier That Affects Water Relations and Mineral Nutrition in Arabidopsis

Though central to our understanding of how roots perform their vital function of scavenging water and solutes from the soil, no direct genetic evidence currently exists to support the foundational model that suberin acts to form a chemical barrier limiting the extracellular, or apoplastic, transport of water and solutes in plant roots. Using the newly characterized enhanced suberin1 (esb1) mutant, we established a connection in Arabidopsis thaliana between suberin in the root and both water movement through the plant and solute accumulation in the shoot. Esb1 mutants, characterized by increased root suberin, were found to have reduced day time transpiration rates and increased water-use efficiency during their vegetative growth period. Furthermore, these changes in suberin and water transport were associated with decreases in the accumulation of Ca, Mn, and Zn and increases in the accumulation of Na, S, K, As, Se, and Mo in the shoot. Here, we present direct genetic evidence establishing that suberin in the roots plays a critical role in controlling both water and mineral ion uptake and transport to the leaves. The changes observed in the elemental accumulation in leaves are also interpreted as evidence that a significant component of the radial root transport of Ca, Mn, and Zn occurs in the apoplast

Barley grain (1,3;1,4)-β-glucan content:effects of transcript and sequence variation in genes encoding the corresponding synthase and endohydrolase enzymes

The composition of plant cell walls is important in determining cereal end uses. Unlike other widely consumed cereal grains barley is comparatively rich in (1,3;1,4)-β-glucan, a source of dietary fibre. Previous work showed Cellulose synthase-like genes synthesise (1,3;1,4)-β-glucan in several tissues. HvCslF6 encodes a grain (1,3;1,4)-β-glucan synthase, whereas the function of HvCslF9 is unknown. Here, the relationship between mRNA levels of HvCslF6, HvCslF9, HvGlbI (1,3;1,4)-β-glucan endohydrolase, and (1,3;1,4)-β-glucan content was studied in developing grains of four barley cultivars. HvCslF6 was differentially expressed during mid (8-15 DPA) and late (38 DPA) grain development stages while HvCslF9 transcript was only clearly detected at 8-10 DPA. A peak of HvGlbI expression was detected at 15 DPA. Differences in transcript abundance across the three genes could partially explain variation in grain (1,3;1,4)-β-glucan content in these genotypes. Remarkably narrow sequence variation was found within the HvCslF6 promoter and coding sequence and does not explain variation in (1,3;1,4)-β-glucan content. Our data emphasise the genotype-dependent accumulation of (1,3;1,4)-β-glucan during barley grain development and a role for the balance between hydrolysis and synthesis in determining (1,3;1,4)-β-glucan content, and suggests that other regulatory sequences or proteins are likely to be involved in this trait in developing grain.Guillermo Garcia-Gimenez, Joanne Russell, Matthew K. Aubert, Geoffrey B. Fincher, Rachel A. Burton, Robbie Waugh, Matthew R. Tucker, Kelly Housto

Transcription of nuclear organellar DNA in a model plant system

Endosymbiotic gene transfer from cytoplasmic organelles (chloroplasts and mitochondria) to the nucleus is an ongoing process in land plants. Although the frequency of organelle DNA migration is high, functional gene transfer is rare because a nuclear promoter is thought necessary for activity in the nucleus. Here we show that a chloroplast promoter, 16S rrn, drives nuclear transcription, suggesting that a transferred organellar gene may become active without obtaining a nuclear promoter. Examining the chromatin status of a known de novo chloroplast integrant indicates that plastid DNA inserts into open chromatin and that this relaxed condition is maintained after integration. Transcription of nuclear organelle DNA integrants was explored at the whole genome level by analyzing RNA-seq data of Oryza sativa subsp. japonica, and utilizing sequence polymorphisms to unequivocally discriminate nuclear organelle DNA transcripts from those of bona fide cytoplasmic organelle DNA. Nuclear copies of organelle DNA that are transcribed show a spectrum of transcriptional activity but at comparatively low levels compared with the majority of other nuclear genes.Dong Wang, Zhipeng Qu, David L. Adelson, Jian-Kang Zhu, and Jeremy N. Timmi