Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses

Abstract

BackgroundWUSCHEL-related homeobox (WOX) family members play significant roles in plant growth and development, such as in embryo patterning, stem-cell maintenance, and lateral organ formation. The recently published cotton genome sequences allow us to perform comprehensive genome-wide analysis and characterization of WOX genes in cotton.ResultsIn this study, we identified 21, 20, and 38 WOX genes in Gossypium arboreum (2n = 26, A2), G. raimondii (2n = 26, D5), and G. hirsutum (2n = 4x = 52, (AD)t), respectively. Sequence logos showed that homeobox domains were significantly conserved among the WOX genes in cotton, Arabidopsis, and rice. A total of 168 genes from three typical monocots and six dicots were naturally divided into three clades, which were further classified into nine sub-clades. A good collinearity was observed in the synteny analysis of the orthologs from At and Dt (t represents tetraploid) sub-genomes. Whole genome duplication (WGD) and segmental duplication within At and Dt sub-genomes played significant roles in the expansion of WOX genes, and segmental duplication mainly generated the WUS clade. Copia and Gypsy were the two major types of transposable elements distributed upstream or downstream of WOX genes. Furthermore, through comparison, we found that the exon/intron pattern was highly conserved between Arabidopsis and cotton, and the homeobox domain loci were also conserved between them. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of WOX genes under different stress treatments showed that the different genes were induced by different stresses.ConclusionIn present work, WOX genes, classified into three clades, were identified in the upland cotton genome. Whole genome and segmental duplication were determined to be the two major impetuses for the expansion of gene numbers during the evolution. Moreover, the expression patterns suggested that the duplicated genes might have experienced a functional divergence. Together, these results shed light on the evolution of the WOX gene family, and would be helpful in future research.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-1065-8) contains supplementary material, which is available to authorized users.

Genome-Wide Characterization and Analysis of CIPK Gene Family in Two Cultivated Allopolyploid Cotton Species: Sequence Variation, Association with Seed Oil Content, and the Role of GhCIPK6

“…After gene duplication, the new gene could be considered a redundant gene compared with the existing gene, and it can be considered a driving force for evolutionary innovation [61]. Inserting or deleting tissue-specific enhancers or repressors in the coding regions of duplicated genes could obtain a new regulatory context, which might be the cause of functional divergence [62]. Overexpression of GhCIPK6 in cotton could reduce oil content, and increased C18:1 and C18:1+C18:1d6 in transgenic cotton lines, as compared to wild-type plants (Figure 7), indicated that GhCIPK6 plays a negative role in oil synthesis.…”

A genome-wide analysis of SWEET gene family in cotton and their expressions under different stresses

“…Each AtSWEET gene corresponded to approximately one to ten cotton SWEET genes, respectively. The naming rules were performed based on a published paper (Yang et al 2017). Ga, Gr, Gh, Gb, and At were used as prefixes before the names of SWEET genes from G. arboreum, G. raimondii, G. hirsutum, G. barbadense, and Arabidopsis, respectively.…”

“…A line between two genes indicates a paralog genes during growth and development of G. hirsutum plant. The transcription levels in various tissues or organs of RNA-seq data from NCBI and COTTONFGD (http:// www.cottonfgd.org/) were downloaded and analyzed (Yuan et al 2015;Yang et al 2017), including the vegetative (root, stem, and leaf) and reproductive (torus, petal, stamen, pistil, calycle, − 3 and − 1 days post anthesis (DPA) ovule, 0, 1, 3, 5, 10, 20, 25, and 35 days post anthesis (DPA) seed) tissues as well as in the fiber (5, 10, 20, and 25 DPA), and germinating seeds at 0 h, 5 h,10 h and from roots and cotyledons at 24 h, 48 h, 72 h, 96 h, and 120 h after imbibition. Their expression levels were varied (Figs.…”

Genetic and evolution analysis of extrafloral nectary in cotton

“…Each sample was sequenced at~309 coverage of the assembled genome with 150-bp paired-end reads for each sample from the Illumina HiSeq X-ten platform. For mRNA-seq, total RNA was extracted with a previously reported workflow (Qin et al, 2018;Yang et al, 2017;Yang et al, 2018;Zhang et al, 2019). The mRNA was used to synthesis cDNA for building paired-end sequencing libraries.…”

“…The petal, flowering bud, stamen, fibre (10 DPA), root, stem cotyledon, hypocotyl, leaf and foliar nectary were harvested for qPCR analysis. The total RNA was extracted using a previous workflow (Qin et al, 2018;Yang et al, 2017;Yang et al, 2018;Zhang et al, 2019). The cDNA was synthesized using PrimeScript RT reagent Kit with gDNA Eraser (Takara, China).…”