Honeysuckle Genome Assembly And Evolution And Expression Analysis Of NLR Gene Family

Lonicera japonica is an important medicinal plant,which is widely used in traditional Chinese medicine.However,pests and disease seriously affect the quality and yield of honeysuckle,which restricts the development of its industry.The acquisition of high-quality reference genome is helpful to study molecular evolution,excavate important agronomic traits genes and analyze their genetic mechanism at genome-wide level,which is of great importance for promoting the resistant varieties breeding of honeysuckle.The R gene(Resistance gene)plays an important role in the process of plants resisting the invasion of external pathogens.Among all known types of R gene,the nucleotide-binding site-leucine-rich repeat(NBS-LRR or NLR)gene family the largest disease-resistance gene family in plants.Accurate and comprehensive identification of R genes can accelerate the process of unearthing disease-resistance genes.In this study,the chromosome-level genome of honeysuckle was assembled using PacBio sequencing,Illumina sequencing and Hi-C technology,which was then annotated.Based on the assembled and annotated honeysuckle genome,we identified the members of NLR gene family in the honeysuckle genome by homology search,and performed subfamilies division,chromosomal distribution,gene structure visualization,conserved motifs identification,cis-regulatory elements prediction,phylogenetic analysis and duplication types identification of candidate NLR genes.Finally,we analyzed the expression abundance of NLR genes in different flower development stages of honeysuckle,and found a group of NLR genes that may play an important role in flower development.Here are the main results of this study:1.The honeysuckle chromosome-level genome was successfully assembled by using PacBio sequencing,Illumina sequencing and Hi-C technology,and a total of 9 chromosomes were assembled with a length of 886 Mb,of which the scaffold N50 was 79.57 Mb.In addition,39,320protein-coding genes annotation as well as repeat annotation,non-coding RNA annotation,pseudogenes annotation and functional annotation were accomplished.2.561 candidate NLR genes were identified in the honeysuckle genome and subdivide into 3 subfamilies,namely TNL(156),CNL(397)and RNL(8).We accomplished the gene structure and conserved motifs analysis of NLR genes,and reconstructed the phylogenetic relationship and predicted the cis-regulatory elements of them.3.Transcriptomics were used to analyze the expression of NLR genes in different flower development stages of honeysuckle,We found that the expression of NLR genes may be related to flower development,and identified 68 differentially expressed NLR genes during flower development.In conclusion,the assembly of the chromosome-level genome of honeysuckle not only contributes to the study of its molecular evolution and important agronomic traits genes,but also provides theoretical resources for the study of honeysuckle genomics and comparative genomics.In addition,the identification,evolution and transcriptomic analysis of the NLR gene in honeysuckle revealed the evolution and expression of NLR genes in honeysuckle genome,providing theoretical basis and technical support for disease resistance breeding of honeysuckle.