Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research

doi:10.1093/gigascience/giz136

KIB OpenIR

	Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research
	Strijk,Joeri S.; Hinsinger,Damien D.; Zhang,Fengping; Cao,Kunfang
	2019
发表期刊	GIGASCIENCE
ISSN	2047-217X
卷号	8 期号:11 页码:giz136
摘要	Background: The wheel tree (Trochodendron aralioides) is one of only 2 species in the basal eudicot order Trochodendrales. Together with Tetracentron sinense, the family is unique in having secondary xylem without vessel elements, long considered to be a primitive character also found in Amborella and Winteraceae. Recent studies however have shown that Trochodendraceae belong to basal eudicots and demonstrate that this represents an evolutionary reversal for the group. Trochodendron aralioides is widespread in cultivation and popular for use in gardens and parks. Findings: We assembled the T. aralioides genome using a total of 679.56 Gb of clean reads that were generated using both Pacific Biosciences and Illumina short-reads in combination with 10XGenomics and Hi-C data. Nineteen scaffolds corresponding to 19 chromosomes were assembled to a final size of 1.614 Gb with a scaffold N50 of 73.37 Mb in addition to 1,534 contigs. Repeat sequences accounted for 64.226% of the genome, and 35,328 protein-coding genes with an average of 5.09 exons per gene were annotated using de novo, RNA-sequencing, and homology-based approaches. According to a phylogenetic analysis of protein-coding genes, T. aralioides diverged in a basal position relative to core eudicots, similar to 121.8-125.8 million years ago. Conclusions: Trochodendron aralioides is the first chromosome-scale genome assembled in the order Trochodendrales. It represents the largest genome assembled to date in the basal eudicot grade, as well as the closest order relative to the core-eudicots, as the position of Buxales remains unresolved. This genome will support further studies of wood morphology and floral evolution, and will be an essential resource for understanding rapid changes that took place at the base of the Eudicot tree. Finally, it can further genome-assisted improvement for cultivation and conservation efforts of the wheel tree.
DOI	10.1093/gigascience/giz136
收录类别	SCI
WOS记录号	WOS:000500759800009
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/71093
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Strijk,Joeri S.,Hinsinger,Damien D.,Zhang,Fengping,et al. Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research[J]. GIGASCIENCE,2019,8(11):giz136.
APA	Strijk,Joeri S.,Hinsinger,Damien D.,Zhang,Fengping,&Cao,Kunfang.(2019).Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research.GIGASCIENCE,8(11),giz136.
MLA	Strijk,Joeri S.,et al."Trochodendron aralioides, the first chromosome-level draft genome in Trochodendrales and a valuable resource for basal eudicot research".GIGASCIENCE 8.11(2019):giz136.

条目包含的文件		下载所有文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
Strijk-2019-Trochode（2088KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	浏览下载