Supporting data for "Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano and Hi-C analysis"

Dataset type: Genomic
Data released on January 10, 2020

Ning D; Wu T; Xiao L; Ma T; Fang W; Dong R; Cao F (2020): Supporting data for "Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano and Hi-C analysis" GigaScience Database. http://dx.doi.org/10.5524/100693

DOI10.5524/100693

Juglans sigillata (NCBI: txid224355), belonging to Juglandales order, is an economically important tree species in Asia, especially in Yunnan province of China. However, little research has been conducted on J. sigillata at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to the plateau environment. To address these issues, a high-quality reference genome of J. sigillata would be a very useful resource.
To construct a high-quality reference genome for J. sigillata, we first generated 38.0 Gb short reads and 66.31 Gb long reads using Illumina and Nanopore sequencing platforms, respectively. The sequencing data were assembled into a 536.50 Mb genome assembly with a contig N50 length of 4.31 Mb. Additionally, we applied BioNano technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with scaffold N50 length of 16.43 Mb and contig N50 length of 4.34 Mb. To obtain a chromosome-level genome assembly, we constructed one Hi-C library and sequenced 79.97 Gb raw reads using the Illumina HiSeq platform. We anchored approximately 93% of the scaffold sequences into 16 chromosomes and evaluated the quality of our assembly using the high contact frequency heatmap. Repetitive elements account for 50.06% of the genome, and 30,387 protein-coding genes were predicted from the genome, of which 99.8% have been functionally annotated. The genome-wide phylogenetic tree indicated the divergence time between J. sigillata and J.regia was estimated to be 49 million years ago (Mya) based on single-copy orthologous genes.
We provide the first chromosome-level genome for J. sigillata. The genome will lay a valuable foundation for future research on genetic improvement of J. sigillata.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 32101299)

Accessions (data generated as part of this study):

BioProject: PRJNA509030





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Yangpao walnut224355  Juglans sigillata Description:DNA extracted from the leaves of a 116...
Alternative accession-BioProject:PRJNA509030
Alternative accession-BioSample:SAMN10535804
...
+
Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
OtherFASTA0.8 KB2019-12-21
Coding sequenceFASTA37.75 MB2019-12-21
AnnotationFASTA7.76 MB2019-12-21
AnnotationGFF27.69 MB2019-12-21
Sequence assemblyFASTA548.02 MB2019-12-21
Phylogenetic treeFASTA4.06 KB2019-12-21
AnnotationGFF428.23 KB2019-12-21
Protein sequenceFASTA13.76 MB2019-12-21
OtherTSV89.71 KB2019-12-21
AnnotationGFF164.62 MB2019-12-21
Displaying 1-10 of 15 File(s).
Funding body Awardee Award ID Comments
Yunnan Provincial Science and Technology Major Project D-L Ning 2018ZG001
Yunnan Provincial Science and Technology Major Project D-L Ning 2018ZG002
Science and Technology Innovation Program of Forestry Department of Yunnan Province T Wu ([2016]cx03)
Science and Technology Innovation Program of Forestry Department of Yunnan Province D-L Ning ([2014]cx01)
Date Action
January 10, 2020 Dataset publish
January 29, 2020 Manuscript Link added : 10.1093/gigascience/giaa006
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
September 24, 2021 Sample Attribute added : of Sample Yangpao walnut
October 7, 2022 Manuscript Link updated : 10.1093/gigascience/giaa006