Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii

A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequenc...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jielong Zhou, Peifu Wu, Zhongping Xiong, Naiyong Liu, Ning Zhao, Mei Ji, Yu Qiu, Bin Yang
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	lepidoptera Dendrolimus kikuchii nanopore Hi-C chromosome-level genome gene expansion Genetics QH426-470
Acceso en línea:	https://doaj.org/article/9d75ccd72e0f413e84bbc49a6f0186fa
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:9d75ccd72e0f413e84bbc49a6f0186fa
record_format	dspace
spelling	oai:doaj.org-article:9d75ccd72e0f413e84bbc49a6f0186fa2021-11-30T14:30:24ZChromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii1664-802110.3389/fgene.2021.728418https://doaj.org/article/9d75ccd72e0f413e84bbc49a6f0186fa2021-10-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.728418/fullhttps://doaj.org/toc/1664-8021A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.Jielong ZhouPeifu WuZhongping XiongNaiyong LiuNing ZhaoMei JiYu QiuBin YangFrontiers Media S.A.articlelepidopteraDendrolimus kikuchiinanoporeHi-Cchromosome-level genomegene expansionGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	lepidoptera Dendrolimus kikuchii nanopore Hi-C chromosome-level genome gene expansion Genetics QH426-470
spellingShingle	lepidoptera Dendrolimus kikuchii nanopore Hi-C chromosome-level genome gene expansion Genetics QH426-470 Jielong Zhou Peifu Wu Zhongping Xiong Naiyong Liu Ning Zhao Mei Ji Yu Qiu Bin Yang Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii
description	A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.
format	article
author	Jielong Zhou Peifu Wu Zhongping Xiong Naiyong Liu Ning Zhao Mei Ji Yu Qiu Bin Yang
author_facet	Jielong Zhou Peifu Wu Zhongping Xiong Naiyong Liu Ning Zhao Mei Ji Yu Qiu Bin Yang
author_sort	Jielong Zhou
title	Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii
title_short	Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii
title_full	Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii
title_fullStr	Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii
title_full_unstemmed	Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii
title_sort	chromosome-level genome assembly reveals significant gene expansion in the toll and imd signaling pathways of dendrolimus kikuchii
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/9d75ccd72e0f413e84bbc49a6f0186fa
work_keys_str_mv	AT jielongzhou chromosomelevelgenomeassemblyrevealssignificantgeneexpansioninthetollandimdsignalingpathwaysofdendrolimuskikuchii AT peifuwu chromosomelevelgenomeassemblyrevealssignificantgeneexpansioninthetollandimdsignalingpathwaysofdendrolimuskikuchii AT zhongpingxiong chromosomelevelgenomeassemblyrevealssignificantgeneexpansioninthetollandimdsignalingpathwaysofdendrolimuskikuchii AT naiyongliu chromosomelevelgenomeassemblyrevealssignificantgeneexpansioninthetollandimdsignalingpathwaysofdendrolimuskikuchii AT ningzhao chromosomelevelgenomeassemblyrevealssignificantgeneexpansioninthetollandimdsignalingpathwaysofdendrolimuskikuchii AT meiji chromosomelevelgenomeassemblyrevealssignificantgeneexpansioninthetollandimdsignalingpathwaysofdendrolimuskikuchii AT yuqiu chromosomelevelgenomeassemblyrevealssignificantgeneexpansioninthetollandimdsignalingpathwaysofdendrolimuskikuchii AT binyang chromosomelevelgenomeassemblyrevealssignificantgeneexpansioninthetollandimdsignalingpathwaysofdendrolimuskikuchii
_version_	1718406520612323328

Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii

Ejemplares similares