The complete chloroplast genome sequence and phylogenetic analysis of Chuanminshen (Chuanminshenviolaceum Sheh et Shan).

Chloroplast genome sequences are very useful for species identification and phylogenetics. Chuanminshen (Chuanminshen violaceum Sheh et Shan) is an important traditional Chinese medicinal plant, for which the phylogenetic position is still controversial. In this study, the complete chloroplast genome of Chuanminshen violaceum Sheh et Shan was determined. The total size of Chuanminshen chloroplast genome was 154,529 bp with 37.8% GC content. It has the typical quadripartite structure, a large single copy (17,800 bp) and a small single copy (84,171 bp) and a pair of inverted repeats (26,279 bp). The whole genome harbors 132 genes, which includes 85 protein coding genes, 37 tRNA genes, eight rRNA genes, and two pseudogenes. Thirty-nine SSR loci, 32 tandem repeats and 49 dispersed repeats were found. Phylogenetic analyses results with the help of MEGA showed a new insight for the Chuanminshen phylogenetic relationship with the reported chloroplast genomes in Apiales plants.

Integrative analysis of metabolome and transcriptome reveals the improvements of seed quality in vegetable soybean (Glycine max (L.) Merr.).

Vegetable soybean is derived from grain soybean. Seeds of vegetable soybean are bigger, sweeter, and have smoother texture and better flavor than those of grain soybean. To better understand the improvements of seed quality in vegetable soybean, comparative metabolome and transcriptome analyses were performed in the developing seeds between grain (Williams 82) and vegetable (Jiaoda 133) soybeans. A total of 299 differential metabolites were identified between two genotypes, with an increase in free amino acids, carbohydrates, sterols, and flavonoids and a decrease in fatty acid in vegetable soybean. Thousands of differentially expressed genes (DEGs) were identified by transcriptome analysis. DEGs were used for weighted gene co-expression network analysis (WGCNA), yielding 16 co-expression modules. The expression patterns of DEGs within these modules were distinct between two genotypes. Functional enrichment analysis revealed that metabolic pathways, including alanine, aspartate and glutamate metabolism, fatty acid degradation, starch and sucrose metabolism, sucrose transport, and flavonoid biosynthesis, were up-regulated, whereas photosynthesis, arginine biosynthesis, arginine and proline metabolism, glycolysis/gluconeogenesis, and fatty acid biosynthesis were down-regulated in vegetable soybean. Reasonably, the alterations of metabolic pathways corresponding to DEGs partly explained the formation of differential metabolites. These findings provide a better understanding of seed development and breeding improvements of vegetable soybean.

TMT-based quantitative proteomics analyses of sterile/fertile anthers from a genic male-sterile line and its maintainer in cotton (Gossypium hirsutum L.).

Genetic male sterility (GMS) in cotton is important for utilization of heterosis. However, the molecular mechanism of GMS is poorly known. In this study, cytological and proteomics analyses of anthers were conducted in three stages (stage 3 to 5) between GMS line (GA18) and its maintainer (GA18M). The cross-section observation revealed that the tapetal layer in stage 3 was thinner in GA18 compared to GA18M, and the tapetum cells did not degrade in stage 4 in GA18, thus providing no material for microspore development. A total of 1952 differentially expressed proteins (DEPs) were identified between GA18 and GA18M anthers. They were annotated to 52 gene ontology (GO) terms and enriched in 115 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which formed several complex regulator networks, and dozens of important nodes were identified. Moreover, DEPs were also identified between two consecutive stages of GA18 and GA18M, with functional analyses indicating that numerous developmental differences existed between fertile and sterile anthers. The metabolic pathways were significantly altered, including decreased carbohydrate metabolism, ribosome defects, disturbed protein synthesis, disrupted flavonoids synthesis, etc., that may be involved in male sterility. Overall, these results provide genetic resources that help decipher the molecular mechanisms behind GMS. SIGNIFICANCE: Male sterility is a common phenomenon in flowering plant species, and plays a role in the application of heterosis. However, the molecular mechanism of it remains to be elucidated. Using cytological and proteomics approaches, we found that the tapetal layer development retardation may be the reason of male sterility, which was different from the delayed degradation described in previous studies. More than one thousand differentially expressed proteins were identified between male sterile line and its maintainer, forming a complex regulatory network, and the key nodes were remarked that could be used as candidate proteins related to male sterility in future study. Dozens of metabolic pathways were significantly altered, among them, ribosome defects was a novel pathway that may be involved in male sterility. These results enhance our understanding of the molecular mechanism governing male sterility and lay a foundation for clone of genes association with male sterility.