Identification and Expression Profiling of Protein Phosphatases (PP2C) Gene Family in Gossypium hirsutum L.

Abstract

The protein phosphatase (PP2C) gene family, known to participate in cellular processes, is one of the momentous and conserved plant-specific gene families that regulate signal transduction in eukaryotic organisms. Recently, PP2Cs were identified in Arabidopsis and various other crop species, but analysis of PP2C in cotton is yet to be reported. In the current research, we found 87 (Gossypium arboreum), 147 (Gossypium barbadense), 181 (Gossypium hirsutum), and 99 (Gossypium raimondii) PP2C-encoding genes in total from the cotton genome. Herein, we provide a comprehensive analysis of the PP2C gene family in cotton, such as gene structure organization, gene duplications, expression profiling, chromosomal mapping, protein motif organization, and phylogenetic relationships of each species. Phylogenetic analysis further categorized PP2C genes into 12 subgroups based on conserved domain composition analysis. Moreover, we observed a strong signature of purifying selection among duplicated pairs (i.e., segmental and dispersed) of Gossypium hirsutum. We also observed the tissue-specific response of GhPP2C genes in organ and fiber development by comparing the RNA-sequence (RNA-seq) data reported on different organs. The qRT-PCR validation of 30 GhPP2C genes suggested their critical role in cotton by exposure to heat, cold, drought, and salt stress treatments. Hence, our findings provide an overview of the PP2C gene family in cotton based on various bioinformatic tools that demonstrated their critical role in organ and fiber development, and abiotic stress tolerance, thereby contributing to the genetic improvement of cotton for the resistant cultivar.

Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.)

“…In flax, four types of gene duplications were observed in the 210 ABC transporter and HMA genes. Segmental (WGD) duplications (77.14%) contributed by far the most to the expansion of the two gene families in flax, a common mode of expansion of gene families across various plant species [58][59][60]. The selection pressure analysis of duplicated gene pairs based on three categories (i.e., purifying, positive, and neutral selection) tends to provide valuable evolutionary information [61].…”

Genome-wide Identification of ATP Binding Cassette (ABC) Transporter and Heavy Metal Associated (HMA) Gene Families in Flax (Linum usitatissimum L.)

“…In ax, four types of gene duplications were observed in 210 ABC transporter and HMA genes. Segmental (WGD) duplications (77.14%) contributed by far the most to the expansion of the two gene families in ax, a common mode of expansion of gene families across various plant species [62][63][64]. The selection pressure analysis of duplicated gene pairs based on three categories (i.e., purifying, positive, and neutral selection) tends to provide valuable evolutionary information [65].…”

Identification, Evolution, and Expression Profiling of Histone Lysine Methylation Moderators in Brassica rapa

“…The divergence time for both SET and JmjC for paralogous gene pairs indicates that their divergence occurred during the divergence of B. rapa from A. thaliana (9.6-16.1 MYA) [45]. Generally, if the value of Ka/Ks is < 1, indicates gene pairs may have evolved from purifying selection (also called negative selection); Ka/Ks = 1 suggests neutral selection, while Ka/Ks > 1 means positive selection [56][57][58]. Three pairs of SET had a Ka/Ks > 1, specifying positive selection, the remaining SET showed values less than 1.00.…”