Genome-wide identification and expression analysis of the SAUR gene family in foxtail millet (Setaria italica L.)

Abstract Background Auxin performs important functions in plant growth and development processes, as well as abiotic stress. Small auxin-up RNA (SAUR) is the largest gene family of auxin-responsive factors. However, the knowledge of the SAUR gene family in foxtail millet is largely obscure. Results In the current study, 72 SiSAUR genes were identified and renamed according to their chromosomal distribution in the foxtail millet genome. These SiSAUR genes were unevenly distributed on nine chromosomes and were classified into three groups through phylogenetic tree analysis. Most of the SiSAUR members from the same group showed similar gene structure and motif composition characteristics. Analysis of cis-acting elements showed that many hormone and stress response elements were identified in the promoter region of SiSAURs. Gene replication analysis revealed that many SiSAUR genes were derived from gene duplication events. We also found that the expression of 10 SiSAURs was induced by abiotic stress and exogenous hormones, which indicated that SiSAUR genes may participated in complex physiological processes. Conclusions Overall, these results will be valuable for further studies on the biological role of SAUR genes in foxtail development and response to stress conditions and may shed light on the improvement of the genetic breeding of foxtail millet

Interspecific Gene Flow and Selective Sweeps in Picea wilsonii, P. neoveitchii and P. likiangensis

Genome-wide single nucleotide polymorphism (SNP) markers were obtained by genotyping-by-sequencing (GBS) technology to study the genetic relationships, population structure, gene flow and selective sweeps during species differentiation of Picea wilsonii, P. neoveitchii and P. likiangensis from a genome-wide perspective. We used P. jezoensis and P. pungens as outgroups, and three evolutionary branches were obtained: P. likiangensis was located on one branch, two P. wilsonii populations were grouped onto a second branch, and two P. neoveitchii populations were grouped onto a third branch. The relationship of P. wilsonii with P. likiangensis was closer than that with P. neoveitchii. ABBA-BABA analysis revealed that the gene flow between P. neoveitchii and P. wilsonii was greater than that between P. neoveitchii and P. likiangensis. Compared with the background population of P. neoveitchii, the genes that were selected in the P. wilsonii population were mainly related to plant stress resistance, stomatal regulation, plant morphology and flowering. The genes selected in the P. likiangensis population were mainly related to plant stress resistance, leaf morphology and flowering. Selective sweeps were beneficial for improving the adaptability of spruce species to different habitats as well as to accelerate species differentiation. The frequent gene flow between spruce species makes their evolutionary relationships complicated. Insight into gene flow and selection pressure in spruce species will help us further understand their phylogenetic relationships and provide a scientific basis for their introduction, domestication and genetic improvement

Statistics of splicing results of transcriptome sequencing data.

<p>Statistics of splicing results of transcriptome sequencing data.</p

Top 20 genes enriched in cyan module.

<p>Top 20 genes enriched in cyan module.</p

Phylogenetic analysis of ABI-like and Ca²⁺ ATPase genes.

<p>(A) Evolutionary analysis of ABI-like genes in K14, KT1, and Tri with their homologs from different plant species and with ABI proteins from Arabidopsis. (B) Evolutionary analysis of Ca²⁺-ATPase genes in K14, KT1, and Tri with Arabidopsis homologs. Length of branch lines indicates the extent of divergence.</p

WGCNA module building, Hubgenes cluster analysis, and EigenGene expression statistics.

<p>(A, B) Hierarchical clustering of co-expression data. (C) Heatmap cluster of Hubgenes from cyan module. (D) Heatmap cluster of Hubgenes from light yellow module. (E) Eigengenes expression pattern in cyan module. (F) Eigengenes expression pattern in light yellow module.</p

Top 20 genes enriched in light yellow module.

<p>Top 20 genes enriched in light yellow module.</p

Number of genes enriched in each module.

<p>Number of genes enriched in each module.</p