Molecular Characterization of the Acyl-CoA-Binding Protein Genes Reveals Their Significant Roles in Oil Accumulation and Abiotic Stress Response in Cotton.

Members of the acyl-CoA-binding protein (ACBP) gene family play vital roles in diverse processes related to lipid metabolism, growth and development, and environmental response. Plant ACBP genes have been well-studied in a variety of species including Arabidopsis, soybean, rice and maize. However, the identification and functions of ACBP genes in cotton remain to be elucidated. In this study, a total of 11 GaACBP, 12 GrACBP, 20 GbACBP, and 19 GhACBP genes were identified in the genomes of Gossypium arboreum, Gossypium raimondii, Gossypium babardense, and Gossypium hirsutum, respectively, and grouped into four clades. Forty-nine duplicated gene pairs were identified in Gossypium ACBP genes, and almost all of which have undergone purifying selection during the long evolutionary process. In addition, expression analyses showed that most of the GhACBP genes were highly expressed in the developing embryos. Furthermore, GhACBP1 and GhACBP2 were induced by salt and drought stress based on a real-time quantitative PCR (RT-qPCR) assay, indicating that these genes may play an important role in salt- and drought-stress tolerance. This study will provide a basic resource for further functional analysis of the ACBP gene family in cotton.

Genome-wide characterization of the UDP-glycosyltransferase gene family reveals their potential roles in leaf senescence in cotton.

Uridine diphosphate (UDP) glycosyltransferases (UGTs) involved in many metabolic processes and are essential for plant growth and development. Although UGTs proteins have been studied in many plants, the biological functions of UGT genes in cotton leaf senescence are still unknown. In the present study, we performed a genome-wide survey and identified 157 GrUGT, 152 GaUGT and 261 GHUGT genes in Gossypium raimondii, G. arboreum, and G. hirsutum, respectively, that were classified into 15 groups. Analysis of protein motif and gene structure demonstrated that structural and functional conservation occurred within same groups but diverged among the different groups. Gene duplication analysis indicated the different duplication ways happened between tetraploid G. hirsutum and the two diploid species. Whole genome or segmental duplications played a main role in the expansion of the GHUGT family in cotton, and experienced purifying selection during the long evolutionary process in cotton. Cis-acting regulatory elements analysis indicated that they were associated with complex hormone regulatory networks and the stress response. Additionally, to identify GHUGT candidate genes responsive to leaf senescence, we analyzed the expression patterns of GHUGT genes using our transcriptome data from two cultivars of upland cotton with contrasting tolerance to leaf senescence. Subsequently, gene expression profiling based on real-time quantitative PCR showed that selected GHUGT candidate genes might be involved in ABA and JA regulation. Through further functional verification, silencing GHUGT116 gene via VIGS (Virus-induced gene silencing) delayed dark-induced leaf senescence. Overall, the results provide useful and valuable information for understanding the evolution of cotton UGTs genes and the function in leaf senescence.

Genome-Wide Identification and Expression Analyses of the Cotton AGO Genes and Their Potential Roles in Fiber Development and Stress Response.

Argonaute proteins (AGOs) are indispensable components of RNA silencing. However, systematic characterization of the AGO genes have not been completed in cotton until now. In this study, cotton AGO genes were identified and analyzed with respect to their evolution and expression profile during biotic and abiotic stresses. We identified 14 GaAGO, 14 GrAGO, and 28 GhAGO genes in the genomes of Gossypium arboreum, Gossypium raimondii, and Gossypium hirsutum. Cotton AGO proteins were classified into four subgroups. Structural and functional conservation were observed in the same subgroups based on the analysis of the gene structure and conserved domains. Twenty-four duplicated gene pairs were identified in GhAGO genes, and all of them exhibited strong purifying selection during evolution. Moreover, RNA-seq analysis showed that most of the GhAGO genes exhibit high expression levels in the fiber initiation and elongation processes. Furthermore, the expression profiles of GhAGO genes tested by quantitative real-time polymerase chain reaction (qPCR) demonstrated that they were sensitive to Verticillium wilt infection and salt and drought stresses. Overall, our results will pave the way for further functional investigation of the cotton AGO gene family, which may be involved in fiber development and stress response.

Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt.

As one of the largest plant-specific gene families, the NAC transcription factor gene family plays important roles in various plant physiological processes that are related to plant development, hormone signaling, and biotic and abiotic stresses. However, systematic investigation of the NAC gene family in sea-island cotton (Gossypium babardense L.) has not been reported, to date. The recent release of the complete genome sequence of sea-island cotton allowed us to perform systematic analyses of G. babardense NAC GbNAC) genes. In this study, we performed a genome-wide survey and identified 270 GbNAC genes in the sea-island cotton genome. Genome mapping analysis showed that GbNAC genes were unevenly distributed on 26 chromosomes. Through phylogenetic analyses of GbNACs along with their Arabidopsis counterparts, these proteins were divided into 10 groups (I-X), and each contained a different number of GbNACs with a similar gene structure and conserved motifs. One hundred and fifty-four duplicated gene pairs were identified, and almost all of them exhibited strong purifying selection during evolution. In addition, various cis-acting regulatory elements in GbNAC genes were found to be related to major hormones, defense and stress responses. Notably, transcriptome data analyses unveiled the expression profiles of 62 GbNAC genes under Verticillium wilt (VW) stress. Furthermore, the expression profiles of 15 GbNAC genes tested by quantitative real-time PCR (qPCR) demonstrated that they were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatments and that they could be involved in pathogen-related hormone regulation. Taken together, the genome-wide identification and expression profiling pave new avenues for systematic functional analysis of GbNAC candidates, which may be useful for improving cotton defense against VW.

Molecular characterization of a stress-induced NAC gene, GhSNAC3, from Gossypium hirsutum.

NAC genes, specific to plants, play important roles in plant development as well as in response to biotic and abiotic stresses. Here, a novel gene encoding a NAC domain, named as GhSNAC3, was isolated from upland cotton (Gossypium hirsutum L.). Sequence analyses showed that GhSNAC3 encodes a protein of 346 amino acids with an estimated molecular mass of 38.4 kDa and pI of 8.87. Transient localization assays in onion epidermal cells confirmed GhSNAC3 is a nuclear protein. Transactivation studies using a yeast system revealed that GhSNAC3 functions as a transcription activator. Quantitative real-time polymerase chain reaction analysis indicated that GhSNAC3 was induced by high salinity, drought and abscisic acid treatments. We overexpressed GhSNAC3 in tobacco by using Agrobacterium-mediated transformation. Transgenic lines produced longer primary roots and more fresh weight under salt and drought stresses as compared to wild-type plants. Collectively, our results indicated that overexpression of GhSNAC3 in tobacco can enhance drought and salt tolerances.

Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog.

Amino acids show apparent propensities toward their neighbors. In addition to preferences of amino acids for their neighborhood context, amino acid substitutions are also considered to be context-dependent. However, context-dependence patterns of amino acid substitutions still remain poorly understood. Using relative entropy, we investigated the neighbor preferences of 20 amino acids and the context-dependent effects of amino acid substitutions with protein sequences in human, mouse, and dog. For 20 amino acids, the highest relative entropy was mostly observed at the nearest adjacent site of either N- or C-terminus except C and G. C showed the highest relative entropy at the third flanking site and periodic pattern was detected at G flanking sites. Furthermore, neighbor preference patterns of amino acids varied greatly in different secondary structures. We then comprehensively investigated the context-dependent effects of amino acid substitutions. Our results showed that nearly half of 380 substitution types were evidently context dependent, and the context-dependent patterns relied on protein secondary structures. Among 20 amino acids, P elicited the greatest effect on amino acid substitutions. The underlying mechanisms of context-dependent effects of amino acid substitutions were possibly mutation bias at a DNA level and natural selection. Our findings may improve secondary structure prediction algorithms and protein design; moreover, this study provided useful information to develop empirical models of protein evolution that consider dependence between residues.

Evolution of the F-box gene family in Euarchontoglires: gene number variation and selection patterns.

F-box proteins are substrate adaptors used by the SKP1-CUL1-F-box protein (SCF) complex, a type of E3 ubiquitin ligase complex in the ubiquitin proteasome system (UPS). SCF-mediated ubiquitylation regulates proteolysis of hundreds of cellular proteins involved in key signaling and disease systems. However, our knowledge of the evolution of the F-box gene family in Euarchontoglires is limited. In the present study, 559 F-box genes and nine related pseudogenes were identified in eight genomes. Lineage-specific gene gain and loss events occurred during the evolution of Euarchontoglires, resulting in varying F-box gene numbers ranging from 66 to 81 among the eight species. Both tandem duplication and retrotransposition were found to have contributed to the increase of F-box gene number, whereas mutation in the F-box domain was the main mechanism responsible for reduction in the number of F-box genes, resulting in a balance of expansion and contraction in the F-box gene family. Thus, the Euarchontoglire F-box gene family evolved under a birth-and-death model. Signatures of positive selection were detected in substrate-recognizing domains of multiple F-box proteins, and adaptive changes played a role in evolution of the Euarchontoglire F-box gene family. In addition, single nucleotide polymorphism (SNP) distributions were found to be highly non-random among different regions of F-box genes in 1092 human individuals, with domain regions having a significantly lower number of non-synonymous SNPs.