Identification and Functional Analysis of LncRNAs in Response to Seed Aging in Metasequoia glyptostroboides by Third Generation Sequencing Technology

Abstract

The seeds of Metasequia glyptostroboides Hu et Cheng, an endangered species, are susceptible to aging, making natural population renewal difficult and increasing the risk of extinction. LncRNAs play important roles in plant growth and development and biotic and abiotic stress responses, but the functions of lncRNAs in the aging process of M. glyptostroboides seeds are still unclear. In this study, we used single molecule real-time (SMRT) sequencing technology in combination with Illumina RNA-seq to analyze lncRNA changes during M. glyptostroboides seed aging. We identified 403 intergenic lncRNAs (lincRNAs), 29 intronic lncRNAs, and 25 antisense lncRNAs; screened 9000 differentially expressed mRNAs (DEGs) and 128 differentially expressed lncRNAs (DELs); and predicted 844 cis-target genes and 8098 trans-target genes. GO and KEGG functional annotation of target genes revealed that the regulation of the reactive oxygen species metabolic process, protein processing in the endoplasmic reticulum, and the MAPK signaling pathway and other pathways were significantly enriched, showing a high correlation with the mRNA enrichment results. In addition, we constructed a ceRNA network consisting of 18 lncRNAs, 38 miRNAs, and 69 mRNAs, in which some miRNAs and mRNAs related to seed aging were found. Among them, miR167(a,b,c,d) may compete with lncRNA_00185, which is related to plant aging, to regulate the expression of the RCD1(Radical-induced Cell Death1) gene, thus promoting the balance of seed reactive oxygen species and enhancing seed-aging resistance. These results will have significant reference value in elucidating the molecular mechanism of the seed aging of M. glyptostroboides sequoia, improving the storage capacity for crop seeds, and protecting rare germplasm resources.