Yuanda Lv

Proteome-wide lysine acetylation identification in developing rice (Oryza sativa) seeds and protein co-modification by acetylation, succinylation, ubiquitination, and phosphorylation

Protein lysine acetylation is a highly conserved post-translational modification with various biological functions. However, only a limited number of acetylation sites have been reported in plants, especially in cereals, and the function of non-histone protein acetylation is still largely unknown. In this report, we identified 1003 lysine acetylation sites in 692 proteins of developing rice seeds, which greatly extended the number of known acetylated sites in plants. Seven distinguished motifs were detected flanking acetylated lysines. Functional annotation analyses indicated diverse biological processes and pathways engaged in lysine acetylation. Remarkably, we found that several key enzymes in storage starch synthesis pathway and the main storage proteins were heavily acetylated. A comprehensive comparison of the rice acetylome, succinylome, ubiquitome and phosphorylome with available published data was conducted. A large number of proteins carrying multiple kinds of modifications were identified and many of these proteins are known to be key enzymes of vital metabolic pathways. Our study provides extending knowledge of protein acetylation. It will have critical reference value for understanding the mechanisms underlying PTM mediated multiple signal integration in the regulation of metabolism and development in plants.

mInDel: an efficient pipeline for high-throughput InDel marker discovery

Background Next-Generation Sequencing (NGS) technologies have emerged as a powerful tool to reveal nucleotide polymorphisms in a high-throughput and cost-effective manner. However, it remains a daunting task to proficiently analyze the enormous volume of data generated from NGS and to identify length polymorphisms for molecular marker discovery. The development of insertion-deletion polymorphism (InDel) markers is in particular computationally intensive, calling for integrated high performance methods to identify InDels with high sensitivity and specificity, which would directly benefit areas from genomic studies to molecular breeding. Results We present here a NGS-based tool for InDel marker discovery (mInDel), a high-performance computing pipeline for the development of InDel markers between any two genotypes. The mInDel pipeline proficiently develops InDel markers by comparing shared region size using sliding alignments between assembled contigs or reference genomes. mInDel has successfully designed thousands of InDel markers from maize NGS data locally and genome-wide. The program needs less than 2 hours to run when using 20 threads on a high-performance computing server to implement 40G data. Conclusions mInDel is an efficient, integrated pipeline for a high-throughput design of InDel markers between genotypes. It will be particularly applicable to the crop species which require a sufficient amount of DNA markers for molecular breeding selection. mInDel is freely available for downloading at www.github.com/lyd0527/mInDel website.