Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.)

BACKGROUND

Long noncoding RNAs (lncRNAs) have several known functions involving various biological regulatory processes in plant. However, the possible roles of lncRNAs during peanut seed development have not been fully explored.

RESULTS

In this study, two peanut recombinant inbred lines (RIL₈) that differ in seed size were used to investigate comprehensive lncRNA profiles derived from the seed development at 15 and 35 days after flowering (DAF). We identified a total of 9388 known and 4037 novel lncRNAs, from which 1437 were differentially expressed lncRNAs. Interestingly, the expression patterns of a number of lncRNAs can be very different between two closely related inbred lines and these lncRNAs were expressed predominantly in only one RIL at 35 DAF. Some differentially expressed lncRNAs were found related to putative cis-acting target genes and predicted to be involved in transcription, transport, cell division, and plant hormone biosynthesis. The expression patterns of several representative lncRNAs and 12 protein-coding genes were validated by qPCR. Same expression pattern was observed between most lncRNAs and their target genes. 11 lncRNAs, XR_001593099.1, MSTRG.18462.1, MSTRG.34915.1, MSTRG.41848.1, MSTRG.22884.1, MSTRG.12404.1, MSTRG.26719.1, MSTRG.35761.1, MSTRG.20033.1, MSTRG.13500.1, and MSTRG.9304.1 and their cis-acting target genes may play key roles in peanut seed development.

CONCLUSIONS

These results provided new information on lncRNA-mediated regulatory roles in peanut seed development, contributing to the comprehensive understanding of the molecular mechanisms involved in peanut seed development.

A novel Gateway®-compatible binary vector allows direct selection of recombinant clones in Agrobacterium tumefaciens

BACKGROUND

Cloning genes into plasmid vectors is one of the key steps for studying gene function. Recently, Invitrogen™ developed a convenient Gateway® cloning system based on the site-specific DNA recombination properties of bacteriophage lambda and the cytotoxic protein ccdB, which is lethal to most E. coli strains. The ccdB protein, however, is not toxic to Agrobacterium tumefaciens, an important player often used for studying gene function in planta. This limits the direct application of the Gateway® cloning system in plant transformation-mediated research.

RESULTS

In this study, we constructed a novel Gateway®-compatible destination vector, pEG101-SacB/R, by replacing the ccdB gene with a SacB-SacR gene cassette as the negative selectable marker.

CONCLUSION

Our results demonstrate that the new pEG101-SacB/R destination vector can be used for Gateway® cloning in Agrobacterium tumefaciens. pEG101-SacB/R will be a valuable tool for high-throughput functional analysis of genes in planta.