Whole-transcriptome sequencing reveals the regulatory roles of non-coding RNAs during xylem development in Ginkgo biloba L.

Wood formation in Ginkgo biloba is a seasonal process that is regulated by complex molecular networks. However, studies of the molecular mechanisms of xylem development in ginkgo are limited; in particular, the roles the roles of non-coding RNAs (ncRNAs) in the development of secondary cell wall (SCW) in ginkgo xylem have not been investigated. In this study, we performed whole-transcriptome sequencing of ginkgo xylem tissues collected in April, June, August, and October and identified numerous differentially expressed mRNAs and ncRNAs. Weighted gene co-expression network analysis (WGCNA) highlighted key module 21 positively correlated with lignin, cellulose, and hemicellulose, and we noted that the hub gene evm_TU_chr10_1387 in module 21 was involved in nucleotide sugar transport for mannan/glucomannan synthesis and co-expressed with multiple lncRNAs/circRNAs. Cis-regulatory analysis revealed that lncRNAs regulate several lignin/hemicellulose biosynthesis genes (e.g., PAL , CAD , LAC , GMPP , XXT , and GATL1 ) and WRKY19 , a negative regulator of SCW formation, via cis-action. Notably, the lncRNA –miR319–PLT2 and miR160–ARF16 modules collectively promoted cambium–to–xylem differentiation and SCW biosynthesis during the vigorous growth period of ginkgo, whereas the miR171–SCL6 and lncRNA –miR159–MYB33 modules coordinated GA synthesis and ABA signaling to prioritize seasonal resources for SCW development. Additionally, we identified multiple miRNAs ( miR396 , miR319 , miR159 , miR164 , miR166 , and miR11534 ) that directly target enzyme-encoding genes ( UXS1 , XGOAT , EG ) and TF-encoding genes ( WRKY19 , HB15 , SPL2 ) associated with SCW formation. These regulatory modules collectively promote SCW biosynthesis and development during the vigorous growth period in ginkgo, revealing a multilayered ncRNA network regulating seasonal wood formation. • 28,692 mRNAs, 4253 lncRNAs, 1899 circRNAs, and 331 miRNAs were identified in ginkgo xylem. • 344 pairs of significantly correlated lncRNA mRNA cis-regulatory relationships were constructed. • A ceRNA regulatory network consisting of 76 lncRNAs, 3 circRNAs, 32 miRNAs and 100 mRNAs were constructed. • Multiple regulatory modules regulating ginkgo xylem SCW development were identified.