Identification And Analysis Of LncRNA During Early Shoot Development In Moso Bamboo

Moso bamboo(Phyllostachys edulis)is a large woody grass-like plant with fast growth rate and strong carbon sequestration capacity,which has important ecological,humanistic and economic values.It has been shown that the growth stages of bamboo shoots are closely related to metabolic process,resistance response,mutual regulation of phytohormones and abiotic stress,which is an important grip to reveal the secret of rapid growth of bamboo.In this study,we used early bamboo shoots as experimental material to explore the lncRNA regulatory pathways of shoot development through transcriptome data analysis.Samples of stem-apex meristem(sm)and base tissue(bt)were collected from bamboo shoots at different heights of 20 cm,30 cm and 50 cm,each with three sets of replicates,and strand-specific sequencing was performed to identify and analyze the bamboo shoot lncRNAs.The results of the study showed that:(1)The Q20 and Q30 of transcriptome sequencing data were above 90%,indicating high reliability of the sequencing results;based on the reference genome of moso bamboo,the accuracy of the sequencing data is above 86%.A series of screening criteria were set to identify 1 091 lncRNAs,and the families predicted that these lncRNAs were concentrated in 53 families,indicating that lncRNA families were diversity.(2)Differential expression lncRNA analysis was performed according to the expression levels,and nine groups of differentially expressed lncRNAs were obtained;1 013 differential lncRNAs were obtained by venn analysis of the nine groups of differentially expressed lncRNAs.(3)Through cis-acting and trans-acting analysis of differential target genes,KEGG enrichment results showed that trans-acting target genes were significantly enriched in the phytohormone metabolic pathway,suggesting that lncRNAs regulate shoot growth by regulating target genes in response to phytohormones.In addition,834 target genes belonging to 34 transcription factor families were identified among the differential genes,suggesting that transcription factor family proteins play an important role in the regulation of shoot development.Expression analysis of 28 pairs of lncRNAs and their target genes were performed for the gluconeogenesis pathway and amino acid metabolism pathway in the cis-acting pathway,respectively.The results revealed diverse expression trends of lncRNAs and target genes in the metabolism pathways,suggesting that they may have complex regulatory mechanisms in the metabolic pathways.(4)Analysis of lncRNA interaction network revealed that there were 1 297 sets of lncRNA-mi RNA-m RNA relationships,and 18 mi R156-targeted SPL genes were identified.Analysis of lncRNA-m RNAs in the ce RNA interaction network revealed 16 m RNAs that function in the plant hormone metabolic pathway,and two lncRNAs were co-expressed with m RNAs that respond to auxin.This result suggests that these two lncRNAs may be involved in the metabolic pathway of auxin and thus play an important role in the development of bamboo shoots.(5)Based on WGCNA analysis,a significant module(r value of 0.9)associated with the slub phenotype of moso bamboo shoots was explored,and analysis revealed that the module contained 163 lncRNAs and 2 630 m RNAs;and one m RNA gene(LRR gene PH02Gene06623.t1)was a regulatory target gene of mi R156.It is hypothesized that lncRNAs could play an important role as ce RNAs in the metabolic network of shoot slub phenotype regulated by mi R156.Transcription factor analysis of the hub genes of this module revealed three genes belonging to the MYB family.The characteristics of the transcription factor binding site of MYB(PH02Gene31429.t1)gene were further analyzed,and 10 target genes involved in the phenylpropanoid synthesis pathway were identified.This phenylpropanoid pathway was significantly related to lignin and stress resistance during shoot growth.In this study,we used transcriptome data to identify lncRNAs involved in sm and bt development of moso bamboo shoots initially.And through the enrichment analysis of target genes,we learned the metabolic pathways involved in related lncRNAs and the preliminary mechanism of lncRNAs as ce RNA regulation.Further,the hub genes and related functions associated with the phenotype of bamboo shoots were analyzed by WGCNA.The analysis have laid an important foundation for the regulatory mechanism of lncRNA during the development of bamboo shoots in the future.