Genome-wide identification of rubber tree (Hevea brasiliensis Muell. Arg.) aquaporin genes and their response to ethephon stimulation in the laticifer, a rubber-producing tissue

Expression profiles of the 51 HbAQP genes in the laticifer of rubber tree clone RRIM928. (PDF 36 kb

Gene Structures, Evolution and Transcriptional Profiling of the WRKY Gene Family in Castor Bean (Ricinus communis L.).

WRKY proteins comprise one of the largest transcription factor families in plants and form key regulators of many plant processes. This study presents the characterization of 58 WRKY genes from the castor bean (Ricinus communis L., Euphorbiaceae) genome. Compared with the automatic genome annotation, one more WRKY-encoding locus was identified and 20 out of the 57 predicted gene models were manually corrected. All RcWRKY genes were shown to contain at least one intron in their coding sequences. According to the structural features of the present WRKY domains, the identified RcWRKY genes were assigned to three previously defined groups (I-III). Although castor bean underwent no recent whole-genome duplication event like physic nut (Jatropha curcas L., Euphorbiaceae), comparative genomics analysis indicated that one gene loss, one intron loss and one recent proximal duplication occurred in the RcWRKY gene family. The expression of all 58 RcWRKY genes was supported by ESTs and/or RNA sequencing reads derived from roots, leaves, flowers, seeds and endosperms. Further global expression profiles with RNA sequencing data revealed diverse expression patterns among various tissues. Results obtained from this study not only provide valuable information for future functional analysis and utilization of the castor bean WRKY genes, but also provide a useful reference to investigate the gene family expansion and evolution in Euphorbiaceus plants

Exon-intron structures of the 58 identified <i>RcWRKY</i> genes.

<p>The graphic representation of the optimized gene models is displayed using GSDS.</p

Motif sequences of 58 <i>RcWRKY</i> proteins identified by the MEME tools.

<p>Motif sequences of 58 <i>RcWRKY</i> proteins identified by the MEME tools.</p

Distribution of the 58 <i>RcWRKY</i> genes and their <i>Arabidopsis</i> and physic nut homologs in subgroups.

<p>Distribution of the 58 <i>RcWRKY</i> genes and their <i>Arabidopsis</i> and physic nut homologs in subgroups.</p

Gene Structures, Evolution, Classification and Expression Profiles of the Aquaporin Gene Family in Castor Bean (<i>Ricinus communis</i> L.)

<div><p>Aquaporins (AQPs) are a class of integral membrane proteins that facilitate the passive transport of water and other small solutes across biological membranes. Castor bean (<i>Ricinus communis</i> L., Euphobiaceae), an important non-edible oilseed crop, is widely cultivated for industrial, medicinal and cosmetic purposes. Its recently available genome provides an opportunity to analyze specific gene families. In this study, a total of 37 full-length AQP genes were identified from the castor bean genome, which were assigned to five subfamilies, including 10 plasma membrane intrinsic proteins (PIPs), 9 tonoplast intrinsic proteins (TIPs), 8 NOD26-like intrinsic proteins (NIPs), 6 X intrinsic proteins (XIPs) and 4 small basic intrinsic proteins (SIPs) on the basis of sequence similarities. Functional prediction based on the analysis of the aromatic/arginine (ar/R) selectivity filter, Froger’s positions and specificity-determining positions (SDPs) showed a remarkable difference in substrate specificity among subfamilies. Homology analysis supported the expression of all 37 RcAQP genes in at least one of examined tissues, e.g., root, leaf, flower, seed and endosperm. Furthermore, global expression profiles with deep transcriptome sequencing data revealed diverse expression patterns among various tissues. The current study presents the first genome-wide analysis of the AQP gene family in castor bean. Results obtained from this study provide valuable information for future functional analysis and utilization.</p></div

Phylogenetic analysis of deduced amino acid sequences of the 37 RcAQPs with Arabidopsis and poplar homologs.

<p>Deduced amino acid sequences were aligned using ClustalX and the phylogenetic tree was constructed using bootstrap maximum likelihood tree (1000 replicates) method and MEGA6 software. The distance scale denotes the number of amino acid substitutions per site. The name of each subfamily and subgroup is indicated next to the corresponding group. Species and accession numbers are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141022#pone.0141022.t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141022#pone.0141022.s007" target="_blank">S1 Table</a>.</p

Expression profiles of the 37 RcAQP genes in leaf, flower, endosperm II/III, endosperm V/VI and seed.

<p>Color scale represents RPKM normalized log₁₀ transformed counts where green indicates low expression and red indicates high expression.</p

Structural and phylogenetic analysis of <i>RcWRKY</i> proteins.

<p>The unrooted phylogenetic tree resulting from the full-length amino acid alignment of all the RcWRKY proteins is shown on the left side of the figure. The different colored balls at the bottom of the figure indicate different groups. The distribution of conserved motifs among the <i>RcWRKY</i> proteins is shown on the right side of the figure. Different motif types are represented by different color blocks as indicated at the bottom of the figure. The same color in different proteins indicates the same group or motif.</p