Identification Of Genes And Biosynthesis Gene Clusters For Allelopathy Between Rice And Barnyardgrass

As one of the most agronomically critical weeds,the hexaploidy species barnyardgrass(Echinochloa crus-galli)causes tremendous losses of global crop yields.Research showed that the reduction of ~ 35% of rice yield is caused by barnyardgrass over the world.Allelopathy is a central process in crop–weed interactions and is mediated by the release of allelochemicals that result in adverse growth effects on one or another plant in the interaction.Recently,many studies have used crop allelopathy as the method for weeds controlling.However,the knowledge for the molecular mechanisms of the interaction of rice and barnyardgrass are quite limited.Particularly,the genomic mechanism for the biosynthesis of many critical allelochemicals remains largely unknown.In this study,we have investigated the allelopathic interactions between rice and barnyardgrass using the transcriptomics data for their mono-culture and co-culture for different time points.Also,we used a unified analysis to identify the vital biosynthesis gene clusters and hub gene modules controlling and involving allelopathic mechanisms in rice and barnyardgrass interaction.The major findings are as follows:(1)Transcriptomic profiling reveals rice allelochemical genes involving in the ricebarnyardgrass interactionIn this study,transcriptomes from rice(mono-and co-cultured with barnyardgrass)were generated to identify the genes and their functional relationship controlling ricebarnyardgrass interactions at 3 hours(3h)and 3 days(3d)time points.Using a pairwise comparison approach,3,453 up-regulated and 2,231 down-regulated differentially expressed genes(DEGs)were identified in this study.Among them,393 common genes have identified in all-time points,and these genes were involved in different allelochemical pathways.Gene ontology(GO)results showed that a total of 35 and 64 GO terms were enriched at 3h and 3d time points,respectively,and more up-regulated genes involved in diverse biological and cellular processes as well as various responses to environmental stimuli.KEGG pathway analysis results indicated that various allelopathic biosynthesis pathways including “phenylpropanoid biosynthesis” and “glutathione metabolism” pathways might be play important role for controlling rice and barnyardgrass interaction in this study.Four highly significant(p-value < 0.05)major temporal RNA expression profiles showed physiologically consistent patterns of change in their protein abundance over the time course in rice and barnyardgrass interaction.In addition,we have identified 90 and 68 new phenolic acid and momilactone associated biosynthesis pathways genes,respectively,at both 3h and 3d time points.Also,various secondary metabolic pathways,including terpenoids,phenylpropanoids,simple phenols,lignin and lignans,and different flavonoids pathways,were noticeably up-regulated in this study.We supposed that the momilactone pathway might be more sensitive against barnyardgrass than other phenolic acid pathways involved in phenylpropanoid biosynthesis.These results offer an essential basis for the identification of candidate genes responsible for rice and barnyardgrass interaction,as well as contribute valuable resources for genomics and molecular mechanisms controlling rice allelopathy with barnyardgrass.(2)Identification of new biosynthetic gene clusters(BGCs)for allelopathy in rice and barnyardgrass genomesBased on the allelopathic transcriptomes and genomes of rice and barnyardgrass with known metabolic databases such as Plant Metabolic Network,we investigate the candidate gene clusters and their regulatory gene modules involved in the allelopathic interactions of these two plants.In addition to the already known biosynthetic gene clusters in barnyardgrass,we identified three potential new clusters including one for quercetin biosynthesis and potentially involved in allelopathic interaction with rice.Based on the construction of gene networks,we identified one gene regulatory module containing hub transcription factors,significantly positively co-regulated with both the momilactone A and phytocassane clusters in rice.In barnyardgrass,gene modules and hub genes co-expressed with the gene clusters responsible for 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one(DIMBOA)biosynthesis were also identified.In addition,we found three genes in barnyardgrass encoding indole-3-glycerolphosphate synthase that regulate the expression of the DIMBOA cluster.Our findings offer new insights into the regulatory mechanisms of biosynthetic gene clusters involved in allelopathic interactions between rice and barnyardgrass,and have potential implications in controlling weeds for crop protection.