Chromosome-level genome assembly and annotation of the loquat (Eriobotrya japonica) genome.

GigaScience
Shuang JiangXueying Zhang

Abstract

The loquat (Eriobotrya japonica) is a species of flowering plant in the family Rosaceae that is widely cultivated in Asian, European, and African countries. It blossoms in the winter and ripens in the early summer. The genome of loquat has to date not been published, which limits the study of molecular biology in this cultivated species. Here, we used the third-generation sequencing technology of Nanopore and Hi-C technology to sequence the genome of Eriobotrya. We generated 100.10 Gb of long reads using Oxford Nanopore sequencing technologies. Three types of Illumina high-throughput sequencing data, including genome short reads (47.42 Gb), transcriptome short reads (11.06 Gb), and Hi-C short reads (67.25 Gb), were also generated to help construct the loquat genome. All data were assembled into a 760.1-Mb genome assembly. The contigs were mapped to chromosomes by using Hi-C technology based on the contacts between contigs, and then a genome was assembled exhibiting 17 chromosomes and a scaffold N50 length of 39.7 Mb. A total of 45,743 protein-coding genes were annotated in the Eriobotrya genome, and we investigated the phylogenetic relationships between the Eriobotrya and 6 other Rosaceae species. Eriobotrya shows a close relat...Continue Reading

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Citations

May 28, 2020·Journal of Experimental Botany·Kathryn DumschottBjörn Usadel
Dec 11, 2020·GigaScience·Chaoyang LiuYehua He
Nov 19, 2020·Plants·Félix MoránAna Belén Ruiz-García
Jan 19, 2021·Mitochondrial DNA. Part B, Resources·Jongsun ParkKyeong-In Heo
Jul 25, 2021·International Journal of Molecular Sciences·Pengfei ZhangZexiao Yang

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Methods Mentioned

BETA
PCR
Hi-C
gypsy
RNA-seq
Hi-C.

Key Resources (RRID) Mentioned

SCR_016386
SCR_017987
SCR_015880
SCR_017622
SCR_017642
SCR_014731
SCR_010910
SCR_017643
SCR_017644
SCR_015055

Software Mentioned

Genscan
BLAST
tRNAscan
LACHESIS
TIMETREE
Basic Local Alignment Search Tool Aligner
BWA
MCScan
SE
Pro

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