火炬松疱锈病菌的基因组草图组装

Draft genome assembly of Passalora sequoiae a needle blight pathogen on Leyland cypress.

机构信息

USDA ARS Thad Cochran Southern Horticultural Laboratory, Poplarville, MS, 39470, USA.

Dept. of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.

出版信息

BMC Res Notes. 2020 Nov 4;13(1):505. doi: 10.1186/s13104-020-05328-3.

DOI:10.1186/s13104-020-05328-3

PMID:33148306

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7640444/

Abstract

OBJECTIVE

Passalora sequoiae (family Mycosphaerellaceae) causes a twig blight on Leyland cypress that requires numerous fungicide applications annually to minimize economic losses for ornamental plant nursery and Christmas tree producers. The objective was to generate a high-quality draft assembly of the genome of P. sequoiae as a resource for primer development to investigate genotype diversity.

DATA DESCRIPTION

We report here the genome sequence of P. sequoiae 9LC2 that was isolated from Leyland cypress 'Leighton Green' in 2017 in southern Mississippi, USA. The draft genome was obtained using Pacific Biosciences (PacBio) SMRT and Illumina HiSeq 2500 sequencing. Illumina reads were mapped to PacBio assembled contigs to determine base call consistency. Based on a total of 44 contigs with 722 kilobase (kb) average length (range 9.4 kb to 3.4 Mb), the whole genome size was estimated at 31,768,716 bp. Mapping of Illumina reads to PacBio contigs resulted in a 1000 × coverage and were used to confirm accuracy of the consensus sequences.

摘要

目的

Passalora sequoiae（属 Mycosphaerellaceae）引起的湿地柏嫩枝枯萎病，需要每年多次使用杀菌剂处理，以最大限度地减少观赏植物苗圃和圣诞树生产者的经济损失。本研究的目的是生成 Passalora sequoiae 的高质量基因组草图，作为开发引物以调查基因型多样性的资源。

数据描述

我们在此报告了 2017 年在美国密西西比州南部从莱兰柏 'Leighton Green' 中分离出的 P. sequoiae 9LC2 的基因组序列。该草图基因组是使用 Pacific Biosciences（PacBio）SMRT 和 Illumina HiSeq 2500 测序技术获得的。将 Illumina reads 映射到 PacBio 组装的 contigs 上，以确定碱基调用的一致性。基于总共 44 个长度为 722kb（范围为 9.4kb 至 3.4Mb）的 contigs，全基因组大小估计为 31,768,716bp。Illumina reads 映射到 PacBio contigs 的覆盖率达到 1000×，用于确认共识序列的准确性。