mRNA-seq Analysis of the Gossypium arboreum transcriptome Reveals Tissue Selective Signaling in Response to Water Stress during Seedling Stage

Abstract

The cotton diploid species, Gossypium arboreum, shows important properties of stress tolerance and good genetic stability. In this study, through mRNA-seq, we de novo assembled the unigenes of multiple samples with 3h H2O, NaCl, or PEG treatments in leaf, stem and root tissues and successfully obtained 123,579 transcripts of G. arboreum, 89,128 of which were with hits through BLAST against known cotton ESTs and draft genome of G. raimondii. About 36,961 transcripts (including 1,958 possible transcription factor members) were identified with differential expression under water stresses. Principal component analysis of differential expression levels in multiple samples suggested tissue selective signalling responding to water stresses. Venn diagram analysis showed the specificity and intersection of transcripts’ response to NaCl and PEG treatments in different tissues. Self-organized mapping and hierarchical cluster analysis of the data also revealed strong tissue selectivity of transcripts under salt and osmotic stresses. In addition, the enriched gene ontology (GO) terms for the selected tissue groups were differed, including some unique enriched GO terms such as photosynthesis and tetrapyrrole binding only in leaf tissues, while the stem-specific genes showed unique GO terms related to plant-type cell wall biogenesis, and root-specific genes showed unique GO terms such as monooxygenase activity. Furthermore, there were multiple hormone cross-talks in response to osmotic and salt stress. In summary, our multidimensional mRNA sequencing revealed tissue selective signalling and hormone crosstalk in response to salt and osmotic stresses in G. arboreum. To our knowledge, this is the first such report of spatial resolution of transcriptome analysis in G. arboreum. Our study will potentially advance understanding of possible transcriptional networks associated with water stress in cotton and other crop species.

Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes

“…Two or more genotypes with contrasting salt tolerance have only been used in a few reported investigations [46, 55–57]. To identify genes responsible for salt tolerance, analysis of genotypes with similar genetic backgrounds and contrasting salt tolerances is preferable.…”

“…In those studies, it was consequently difficult to accurately distinguish true salt tolerance-related genes from salt-responsive ones. Furthermore, most research for salt stress focused on root [31, 46]. However, the previous results show that when subjected to salt stress in upland cotton, mostly absorbed Na + accumulated in the shoot through the roots, and the root of K + transport to the leaves to maintain high K + / Na + in the leaves [9].…”

Phytochrome Interacting Factors (PIFs) in Solanum lycopersicum: Diversity, Evolutionary History and Expression Profiling during Different Developmental Processes

“…thaliana transcription factors involved in light signaling, such as PIFs and HY5, were found in both sequences. SlPIF1a promoter showed PIF and HY5 binding-motifs, PBE-box and CA-hybrid, respectively [41,42]. Additionally, CArG motifs, which are recognized by the ripening inducer transcription factor RIN [43], were also found in SlPIF1a promoter region.…”

“…Motif positions are indicated by triangles. CArG [42], PBE-box [40], CA-hybrid, CG-hybrid and ACE-motif [41]. …”

RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants

“…To identify differentially expressed genes under drought stress in cotton, RNAseq experiments have been performed in the tetraploid Gossypium hirsutum cotton (Bowman et al 2013 ) and the diploid Gossypium arboretum cotton (Zhang et al 2013c ). RNA-seq experiments have also provided insight into transcriptional drought responsive in trees such as poplars (Cossu et al 2013 ;Tang et al 2013 ) and eucalyptus (Villar et al 2011 ).…”