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Accession PRJCA021875
Title A high-quality haplotype-resolved genome of Japanese knotweed (Reynoutria japonica) provides insights into polyploid origin, adaptive evolution and fast growth
Relevance Evolution
Data types Whole genome sequencing
genome
Organisms Reynoutria japonica
Description Reynoutria japonica Houtt., a traditional Chinese herb in Polygonaceae, is one of the top 100 most destructive invasive species worldwide due to its aggressive growth and strong adaptability. Here, we report a 8.04 Gb chromosome-scale assembly of R. japonica with 88 chromosomes across eight homolgous sets. Combing with phylogenetic and genomic analysis, we demonstrate F. japonica is a mixed auto/allo-octaploid genome (AAAABBBB) with SubA showing closer relationship with its related species F. multiflora, and unveil its origin and evolutionary scenario based on 90 resequencing data with different ploidy in Reynoutria. Comparative genomic analysis reveals the genetic basis underlying the strong environmental adaptation of R. japonica and the significantly expanded ARF gene family through tandem repeats and their higher expression in rhizome in R. japonica. We also investigate the collaboration and differentiation of the duplicated genes from auto- and allo-polyploid events at the level of genomic variations, gene families evolution and gene expression in R. japonica. Transcriptome analysis of stem- internodes and tips with different developmental stages reveals that the octuplation and significant expansion of SAUR19 and SAUR63 subfamily with higher expression in stem potentially contribute to the rapid growth of R. japonica. Our study provides important understandings of adaptive evolution and polyploid dominant traits in invasive plants, and will also provide important guidance for the breeding of polyploid crops.
Sample scope Monoisolate
Release date 2023-12-19
Grants
Agency program Grant ID Grant title
National Natural Science Foundation of China 32100500
National Natural Science Foundation of China 32160438
Natural Science Foundation of Hebei Province C2021201048
Young Elite Scientists Sponsorship Program by CAST YESS20210080
Submitter Minghao    Li  (1830762433@qq.com)
Organization Hebei University
Submission date 2023-12-08

Project Data

Resource name Description
BioSample (43)  show -
GSA (3) -
CRA013835 HiC
CRA013826 illumina
CRA013823 RNA-Seq of R. japonica