Temporal small RNA transcriptome profiling unraveled partitioned miRNA expression in developing maize endosperms between reciprocal crosses

In angiosperms, the endosperm nurtures embryo and provides nutrients for seed germination. We have performed high-throughput small RNA transcriptome sequencing of kernels at 0, 3, and 5 days after pollination (DAP) and endosperms at 7, 10, and 15 DAP by using B73 and Mo17 reciprocal crosses in previous study. Here, we further explored these small RNA-seq data to investigate the potential roles of miRNAs in regulating gene expression process. In total, 57 conserved miRNAs and 18 novel miRNAs were observed highly expressed in maize endosperm. Temporal expression profiling indicates these miRNAs exhibited dynamic and partitioned expression patterns at different developmental stages between maize reciprocal crosses, and qRT-PCR results further confirmed our observation. In addition, we found a subset of distinct tandem miRNAs are generated from a single stem-loop structure in maize which might be conserved in monocots. Furthermore, a SNP variation of Zma-miR408-5p at 11th base position was characterized between B73 and Mo17 which leads to completely different functions in repressing targets. More interestingly, Zma-miR408-5p exhibited B73-biased expression pattern in the B73 and Mo17 reciprocal hybrid endosperms at 7, 10 and 15 DAP according to the reads abundance with SNPs and CAPS experiment

The reference genome of the halophytic plant Eutrema salsugineum

A halophyte refers to a plant that can naturally tolerate high concentrations of salt in the soil, and its tolerance to salt stress may occur through various evolutionary and molecular mechanisms. Eutrema salsugineum is one of the halophytic species in the Brassicaceae family that can naturally tolerate multiple types of abiotic stresses that typically limit crop productivity, such as extreme salinity and cold. It has been widely used as a laboratorial model for stress biology research in plants. Here, we present the reference genome sequence (241 Mb) of E. salsugineum at 8x coverage sequenced by traditional Sanger sequencing-based approach with comparison to its close relative Arabidopsis thaliana. The E. salsugineum genome contains 26,531 protein-coding genes and 51.4% of its genome is composed of repetitive sequences that mostly reside in pericentromeric regions. Comparative analyses of the genome structures, protein-coding genes, microRNAs, stress-related pathways and estimated translation efficiency of proteins between E. salsugineum and A. thaliana suggest adaptation of halophyte to environmental stresses may occur via a global network adjustment of multiple regulatory mechanisms. The E. salsugineum genome provides a resource to identify naturally occurring genetic alterations contributing to the adaptation of the halophyte plants to salinity might be bioengineered in related crop species