Genome-wide evolutionary analysis of two gene families related to plant disease resistance

Abstract

Plants have evolved elaborate defense systems against pathogens. There are various gene families playing roles for defense response. To date, genome data of plants from green algae to angiosperms are available and they allow us to identify and compare certain gene families that we are interested in. Here, I performed genome-wide identification and evolutionary analyses of two gene families related to plant disease resistance

nucleotide-binding and leucine rich repeat (NLR) and Autophagy (ATG). NLRs are known to recognize effectors from pathogens and induce downstream signaling for defense responses. ATGs play roles in degradation and recycling of intracellular materials and are related to programmed cell death (PCD). Among ATG gene family, ATG4 cleaves ATG8 for genesis of autophagosome and subsequent process. The numbers of NLRs were diverse even among related species, pepper, tomato and potato. Phylogenetic and clustering analysis classified them into 14 subgroups. Among them, certain subgroups of NLRs in pepper were dramatically expanded and subgroup- or species-specific duplication after speciation might result in divergent evolution of NLRs in Solanaceae. In addition, computational prediction and degradome analysis revealed that some of NLRs were regulated by microRNAs (miRNAs). Interestingly, a novel miRNA targets many NLRs which belong to the expanded subgroup (CNL-G1) in pepper. This indicates that miRNAs are one of the most important regulators of NLRs and have evolved to regulate diverse NLRs. In addition, conserved or novel miRNAs might regulate NLRs by producing secondary small RNAs, such as phased siRNAs (phasiRNAs). In contrast, ATG4 and ATG8 for genesis of autophagosome showed mostly conserved sequences and the numbers of exons among 18 plants, although the number of genes was different. ATG8s were divided into 3 subgroups and most of them appear to be duplicated by whole genome duplication or dispersed duplication. Cross-kingdom processing activity of ATG8s by ATG4s revealed that yeast and plant ATG4s can cleave ATG8s from both yeast and plants, while human ATG4 can cleave ATG8s from human, yeast, and plants. Identification, classification and evolutionary analyses of these gene families might provide important information for functional study of the genes.