Chromosome-scale genome assembly provides insights into the molecular mechanisms of tissue development of Populus wilsonii

Abstract

Populus wilsonii is an important species of section Leucoides, and the natural populations mainly grow in southwest China. In this study, a single genotype of wild P. wilsonii was sequenced and assembled at genome size of 477.35 Mb in 19 chromosomes with contig N50 of 16.3 Mb. A total of 38,054 genes were annotated, and 49.95% of the genome was annotated as repetitive elements. Phylogenetic analysis identified that the divergence between P. wilsonii and the ancestor of P. deltoides and P. trichocarpa was 12 (3–23) Mya. 4DTv and Ks distributions supported the occurrence of the salicoid WGD event (~65 Mya). The highly conserved collinearity supports the close evolutionary relationship among these species. Some key enzyme-encoding gene families related to the biosynthesis of lignin and flavonoids were expanded and highly expressed in the stems or leaves, which probably resist the damage of the natural environment. In addition, some key gene families related to cellulose biosynthesis were highly expressed in stems, accounting for the high cellulose content of P. wilsonii variety. Our findings provided deep insights into the genetic evolution of P. wilsonii and will contribute to further biological research and breeding as well as for other poplars in Salicaceae.

Genome ofPhyllanthus emblica: the medicinal plant Amla with super antioxidant properties

“…The lignin biosynthesis genes were observed to be highly expanded and among the MSA genes in P. emblica genome, which hints towards the evolutionary significance of lignified endocarp in this stone fruit. The lignin biosynthesis gene families were also reported to be expanded in the other stone fruit genomes such as pear and Populus, which are economically important due to their fruit and wood, respectively, where lignin is the main content of pear's stone cells and poplar's wood (Wu, Wang et al 2013;Li, Xing et al 2022).…”

Genome of Phyllanthus emblica: the medicinal plant Amla with super antioxidant properties

“…The lignin biosynthesis genes were observed to be highly expanded and among the MSA genes in P. emblica genome, which hints towards the evolutionary significance of lignified endocarp in this stone fruit. The lignin biosynthesis gene families were also reported to be expanded in the other stone fruit genomes such as pear and Populus , which are economically important due to their fruit and wood, respectively, where lignin is the main content of pear’s stone cells and poplar’s wood ( Wu et al., 2013 ; Li et al., 2022 ).…”

Genome Assembly of Docynia delavayi Provides New Insights into α-Farnesene Biosynthesis

“…Five representative species in Rosaceae family ( M. domestica, P. communis, Prunus persica, Rosa rugosa and F. vesca ), three representative fruit species ( Solanum lycopersicum, Vitis vinifera and Ziziphus jujuba ), two model plants ( Populus trichocarpa and Arabidopsis thaliana ) and a monocotyledon plant ( Oryza sativa ) were selected for comparative genomic analysis (Table S1). The ortholog clusters of protein-coding genes in D. delavayi and 11 other species were identified referred to previous study (Liu et al, 2023). Referring to the method of pervious study (Liu et al, 2023), we selected the single-copy genes of D. delavayi and the nine species mentioned above to construct the phylogenetic tree, identify the expansion and contraction gene families, and predict the divergence time.…”

“…The ortholog clusters of protein-coding genes in D. delavayi and 11 other species were identified referred to previous study (Liu et al, 2023). Referring to the method of pervious study (Liu et al, 2023), we selected the single-copy genes of D. delavayi and the nine species mentioned above to construct the phylogenetic tree, identify the expansion and contraction gene families, and predict the divergence time. Last, the GO and KEGG databases was used to perform the functional annotation of the expansion gene families.…”

“…The TR elements were searched using the TRF software (Benson, 1999). The TEs were annotated using homologous prediction and de novo prediction, and the method was consistent with the description of Liu et al (2023). The structural annotation of D. delavayi were carried out through de novo, homologous and transcript-based prediction (Shen et al, 2023).…”