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Juglans sigillata

ABSTRACT: Raw sequence reads ofJuglans sigllata underwent different soil pH stresss

PROVIDER: PRJNA464180 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR7311300.fastq.gz	Fastqsanger.gz
	SRR7311301.fastq.gz	Fastqsanger.gz
	SRR7311302.fastq.gz	Fastqsanger.gz
	SRR7311303.fastq.gz	Fastqsanger.gz
	SRR7311304.fastq.gz	Fastqsanger.gz

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Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano, and Hi-C analysis.

Project description:Juglans sigillata, or iron walnut, belonging to the order Juglandales, is an economically important tree species in Asia, especially in the 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 its plateau environment. To address these issues, a high-quality reference genome of J. sigillata would be useful. 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 1 Hi-C library and sequenced 79.97 Gb raw reads using the Illumina HiSeq platform. We anchored ∼93% of the scaffold sequences into 16 chromosomes and evaluated the quality of our assembly using the high contact frequency heat map. 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 an estimated divergence time between J. sigillata and Juglans regia of 49 million years ago on the basis of single-copy orthologous genes. We provide the first chromosome-level genome for J. sigillata. It will lay a valuable foundation for future research on the genetic improvement of J. sigillata.

| S-EPMC7043058 | biostudies-literature

Development of 32 novel microsatellite loci in <i>Juglans sigillata</i> using genomic data.

Project description:PremiseA novel set of microsatellite markers was developed for Juglans sigillata (Juglandaceae), an endemic walnut species in southwestern China, to facilitate cultivar identification and future investigations into the genetic structure and domestication history of this species and its close relatives.Methods and resultsWe developed 32 microsatellite loci for J. sigillata using genomic data and used them to examine 60 individuals from three natural populations. A high level of polymorphism was detected by these primers, with up to eight alleles observed per locus, and an average of four alleles across populations. The levels of observed and expected heterozygosity ranged from 0.000-1.000 and 0.000-0.785, respectively. All but two of the loci were also successfully amplified in three closely related Eurasian Juglans species (J. regia, J. cathayensis, and J. mandshurica).ConclusionsThe microsatellite loci identified here provide a powerful resource for examining the genetic structure and domestication history of Juglans, as well as identification of its cultivars.

| S-EPMC7073327 | biostudies-literature

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