ALBERT

Description: Background Suaeda glauca (S. glauca) is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also admired as a landscape plant with high development prospects and scientific research value. The S. glauca chloroplast (cp) genome has recently been reported; however, the mitochondria (mt) genome is still unexplored. Results The mt genome of S. glauca were assembled based on the reads from Pacbio and Illumina sequencing platforms. The circular mt genome of S. glauca has a length of 474,330 bp. The base composition of the S. glauca mt genome showed A (28.00%), T (27.93%), C (21.62%), and G (22.45%). S. glauca mt genome contains 61 genes, including 27 protein-coding genes, 29 tRNA genes, and 5 rRNA genes. The sequence repeats, RNA editing, and gene migration from cp to mt were observed in S. glauca mt genome. Phylogenetic analysis based on the mt genomes of S. glauca and other 28 taxa reflects an exact evolutionary and taxonomic status of S. glauca. Furthermore, the investigation on mt genome characteristics, including genome size, GC contents, genome organization, and gene repeats of S. gulaca genome, was investigated compared to other land plants, indicating the variation of the mt genome in plants. However, the subsequently Ka/Ks analysis revealed that most of the protein-coding genes in mt genome had undergone negative selections, reflecting the importance of those genes in the mt genomes. Conclusions In this study, we reported the mt genome assembly and annotation of a halophytic model plant S. glauca. The subsequent analysis provided us a comprehensive understanding of the S. glauca mt genome, which might facilitate the research on the salt-tolerant plant species.

Description: Background SQUAMOSA promoter binding proteins (SBPs) genes encode a family of plant-specific transcription factors involved in various growth and development processes, including flower and fruit development, leaf initiation, phase transition, and embryonic development. The SBP gene family has been identified and characterized in many species, but no systematic analysis of the SBP gene family has been carried out in sugarcane. Results In the present study, a total of 50 sequences for 30 SBP genes were identified by the genome-wide analysis and designated SsSBP1 to SsSBP30 based on their chromosomal distribution. According to the phylogenetic tree, gene structure and motif features, the SsSBP genes were classified into eight groups (I to VIII). By synteny analysis, 27 homologous gene pairs existed in SsSBP genes, and 37 orthologous gene pairs between sugarcane and sorghum were found. Expression analysis in different tissues, including vegetative and reproductive organs, showed differential expression patterns of SsSBP genes, indicating their functional diversity in the various developmental processes. Additionally, 22 SsSBP genes were predicted as the potential targets of miR156. The differential expression pattern of miR156 exhibited a negative correlation of transcription levels between miR156 and the SsSBP gene in different tissues. Conclusions The sugarcane genome possesses 30 SsSBP genes, and they shared similar gene structures and motif features in their subfamily. Based on the transcriptional and qRT-PCR analysis, most SsSBP genes were found to regulate the leaf initial and female reproductive development. The present study comprehensively and systematically analyzed SBP genes in sugarcane and provided a foundation for further studies on the functional characteristics of SsSBP genes during different development processes.