Genome-wide investigation of WRKY gene family in pineapple: evolution and expression profiles during development and stress

Abstract

BackgroundWRKY proteins comprise a large family of transcription factors that play important roles in many aspects of physiological processes and adaption to environment. However, little information was available about the WRKY genes in pineapple (Ananas comosus), an important tropical fruits. The recent release of the whole-genome sequence of pineapple allowed us to perform a genome-wide investigation into the organization and expression profiling of pineapple WRKY genes.ResultsIn the present study, 54 pineapple WRKY (AcWRKY) genes were identified and renamed on the basis of their respective chromosome distribution. According to their structural and phylogenetic features, the 54 AcWRKYs were further classified into three main groups with several subgroups. The segmental duplication events played a major role in the expansion of pineapple WRKY gene family. Synteny analysis and phylogenetic comparison of group III WRKY genes provided deep insight into the evolutionary characteristics of pineapple WRKY genes. Expression profiles derived from transcriptome data and real-time quantitative PCR analysis exhibited distinct expression patterns of AcWRKY genes in various tissues and in response to different abiotic stress and hormonal treatments.ConclusionsFifty four WRKY genes were identified in pineapple and the structure of their encoded proteins, their evolutionary characteristics and expression patterns were examined in this study. This systematic analysis provided a foundation for further functional characterization of WRKY genes with an aim of pineapple crop improvement.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4880-x) contains supplementary material, which is available to authorized users.

Genome-Wide Identification and Characterization of the NAC Transcription Factor Family in Musa Acuminata and Expression Analysis during Fruit Ripening

“…As presented in Table S4, the Ka/Ks of all MaNAC gene pairs were less than one, indicating that the MaNAC gene family might have been subject to purifying selection and functional constraints during its evolution, which is consistent with the NAC genes reported in Populus trichocarpa [47]. [45], and the results were visualized by Circos and are illustrated in Figure 2. According to the analysis, four genes were clustered into two tandem duplication events (MaNAC001/002 and MaNAC014/015) ( Figure 1).…”

“…In addition to WGD, tandem duplication and segmental duplication also play a vital role in the expansion of the large gene families in plants [44]. Therefore, BLASTP and Multiple Collinearity Scan Toolkit (MCScanX) were employed to analyze the duplication events for each MaNAC gene with default parameters [45], and the results were visualized by Circos and are illustrated in Figure 2. According to the analysis, four genes were clustered into two tandem duplication events (MaNAC001/002 and MaNAC014/015) ( Figure 1).…”

“…All the MaNACs genes were mapped to the banana chromosomes with MapChart software, according to their positions in the database. The Multiple Collinearity Scan Toolkit (MCScanX, Athens, Greece) was employed to analyze the duplication events for each MaNAC gene using the default parameters [45].…”

Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses

“…Morus005757 shows significant up-regulation in response to dehydration stress, salinity stress, and SA and ABA (Abscisic acid) treatments [27]. Similar results were also found in wheat, common bean [28], grape [29], pineapple [30], soybean [31], moso bamboo [32], Caragana intermedia [33], peanut [34], and broomcorn millet [35]. These observations suggest that studying the WRKY gene families may provide valuable insights into the mechanism underlying abiotic stress tolerance in plants.…”

Identification and Validation a Major QTL from “Sea Rice 86” Seedlings Conferred Salt Tolerance

“…Coincidentally, SKC1 was also located in qST1.1, and SR86 had the same amino acid sequence as Nona Bokra ( Figure S4). The balance of cations, such as Na + , K + , and Ca 2+ , and their transport ability played key roles in the salt tolerance response of rice [31,34,35]. Whether the ions transport affects salt tolerance in SR86 remains to be further explored.…”