Genome-Wide Identification and Tissue-Specific Expression Analysis of UDP-Glycosyltransferases Genes Confirm Their Abundance in <i>Cicer arietinum</i> (Chickpea) Genome

<div><p>UDP-glycosyltransferases (EC 2.4.1.x; UGTs) are enzymes coded by an important gene family of higher plants. They are involved in the modification of secondary metabolites, phytohormones, and xenobiotics by transfer of sugar moieties from an activated nucleotide molecule to a wide range of acceptors. This modification regulates various functions like detoxification of xenobiotics, hormone homeostasis, and biosynthesis of secondary metabolites. Here, we describe the identification of 96 <i>UGT</i> genes in <i>Cicer arietinum</i> (<i>CaUGT</i>) and report their tissue-specific differential expression based on publically available RNA-seq and expressed sequence tag data. This analysis has established medium to high expression of 84 <i>CaUGTs</i> and low expression of 12 <i>CaUGTs</i>. We identified several closely related orthologs of <i>Ca</i>UGTs in other genomes and compared their exon-intron arrangement. An attempt was made to assign functional specificity to chickpea UGTs by comparing substrate binding sites with experimentally determined specificity. These findings will assist in precise selection of candidate genes for various applications and understanding functional genomics of chickpea.</p></div

Phylogenetic analysis of <i>Ca</i>UGTs.

<p>Dendrogram showing clustering of 96 <i>Ca</i>UGTs along with two recent gene duplication events marked by arrows.</p

Docked complexes of <i>Ca</i>UGTs with their respective acceptor and sugar donor.

<p><b>A.</b> The docked complex of <i>Ca</i>UGT of group A1 with cyanidin (shown in stick form) interacting with H26 and H155. <b>B.</b> The docked complex of <i>Ca</i>UGT of group B with cytokinin (shown in stick form) interacting with H21 and H404. <b>C.</b> The docked complex of <i>Ca</i>UGT of group A2 in which 3-OH group of quercetin (shown in stick form) interacting with H22. <b>D.</b> The docked complex of <i>Ca</i>UGT of group A2 in which 7-OH group of quercetin (shown in stick form) is pointing towards H22. <b>E.</b> The docked complex of <i>Ca</i>UGT of group E with hydroquinone (shown in stick form) interacting with H19 and E83 shown in stick form. <b>F.</b> The docked complex of <i>Ca</i>UGT of group G with hydroquinone (shown in stick form) interacting with H19.</p

Expression level for chickpea <i>UGT</i> genes in various tissues by RNA-seq data analysis.

<p>Heatmap showing relative gene expression in various tissue samples. The color scale (−1 to 1) represents Z-score, calculated by comparing Fragments Per Kilobase of transcript per Million (FPKM) value for UGT genes in different tissues. The <i>UGT</i> genes with FPKM>0 are included in the analysis. Dendrogram on the top and side of the heatmap shows hierarchical clustering of tissues and genes using complete linkage approach.</p

Functional annotation of <i>Ca</i>UGTs.

<p>Dendrogram showing clustering of 96 <i>Ca</i>UGTs with 38 well characterized UGT proteins from other plant species. The image shows distinct clustering of <i>Ca</i>UGTs with the functionally related UGTs.</p

Genomic distribution of <i>CaUGTs</i>.

<p>Chromosomal distribution of <i>CaUGTs</i> in chickpea genome.</p

Improving the Annotation of <i>Arabidopsis lyrata</i> Using RNA-Seq Data

<div><p>Gene model annotations are important community resources that ensure comparability and reproducibility of analyses and are typically the first step for functional annotation of genomic regions. Without up-to-date genome annotations, genome sequences cannot be used to maximum advantage. It is therefore essential to regularly update gene annotations by integrating the latest information to guarantee that reference annotations can remain a common basis for various types of analyses. Here, we report an improvement of the <i>Arabidopsis lyrata</i> gene annotation using extensive RNA-seq data. This new annotation consists of 31,132 protein coding gene models in addition to 2,089 genes with high similarity to transposable elements. Overall, ~87% of the gene models are corroborated by evidence of expression and 2,235 of these models feature multiple transcripts. Our updated gene annotation corrects hundreds of incorrectly split or merged gene models in the original annotation, and as a result the identification of alternative splicing events and differential isoform usage are vastly improved.</p></div

Heat stress induces alternative splicing events.

<p><b>(A)</b> Examples of differentially expressed isoforms in response to heat stress in <i>A</i>. <i>lyrata</i>. AL3G42820 expresses a second isoform that lacks the middle exon in heat-treated samples (HS). Transcripts from wild-type (WT) and recovery (REC) samples contain all three exons. AL2G15640 retains an intron in response to heat stress (HS) while wild-type (WT) and recovery (REC) samples show partial intron splicing. <b>(B)</b> Number of differential splicing events, including alternative 5’ and 3’ splice sites, mutually exclusive exons, intron retention, and exon skipping events identified with MATs based on version-1 and version-2 annotations.</p

Examples of version-1 gene models split and merged in <i>A</i>. <i>lyrata</i> gene annotation version-2.

<p><b>(A)</b> Example of a gene model that was split into two gene models in version-2. Reverse transcription-PCR could not confirm the connection of both. <b>(B)</b> Example of version-1 gene models that were merged during the annotation update. Reverse transcription-PCR confirmed presence of a transcript bridging the two version-1 genes.</p

Updating the gene model annotation of <i>A</i>. <i>lyrata</i>.

<p><b>(A)</b> Left, version-2 gene models predicted by Augustus [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137391#pone.0137391.ref028" target="_blank">28</a>]. Number of gene models overlapping with version-1 (yellow), genes predicted with Cufflinks (red), and genes with expression evidence (blue). Right, gene models of the version-1 annotation. Number of models without overlap to version-2 models (yellow), without orthologs in five other Brassicaceae (red), and without significant expression evidence (blue). <b>(B)</b> Correlation of the lengths of <i>A</i>. <i>lyrata</i> gene models with the length of their orthologous gene models in <i>A</i>. <i>thaliana</i>. Left, <i>A</i>. <i>lyrata</i> version-1 gene models. Correlations using version-1 gene models (left), version-2 gene models before (middle) and after (right) the homology-based correction of gene models. <b>(C)</b> Length distribution of gene models including genes that were removed or newly added in the version-2.</p