Diaphorina citri genome assembly Diaci 1.1

The International Psyllid Genome Consortium has generated a genome assembly Diaci 1.1 of the Asian citrus psyllid (Diaphorina citri). This assembly is also available and accessioned at the National Center for Biotechnology Information:
https://www.ncbi.nlm.nih.gov/assembly/GCF_000475195.1/.
DNA extraction and library preparation
High-molecular weight DNA was extracted using the BioRad AquaPure Genomic DNA isolation kit from fresh intact D. citri collected from a citrus grove in Ft. Pierce, FL and reared at the USDA, ARS, U.S. Horticultural Research Laboratory, Ft. Pierce, FL. To generate PacBio libraries, DNA was sheared using a Covaris g-Tube and SMRT-bell library was prepared using the 10Kb protocol (PacBio DNA template prep kit 2.0; 3-10Kb), cat #001-540-835.
Genome sequencing and assembly
Samples were prepared for sequencing using the TruSeq DNA library preparation kits for paired-end as well as long-insert mate-pair libraries. All were sequenced on the Illumina HiSeq2000 using 100bp or longer reads. Seven libraries were sequenced, with inserts ranging from "short" (ca. 275bp) to 10Kb. These are available in NCBI SRA and included 99.7 million paired-end reads (NCBI SRA:SRX057205), 35.1 million 2kb mate-pair reads (NCBI SRA: SRX057204), 30 million 5kb mate-pair reads (NCBI SRA: SRX058250) and 30 million 10kb mate-pair reads (NCBI SRA: SRX216330). A second round of DNA sequencing was done with PacBio at 12X coverage (NCBI SRA: SRX218985) for scaffolding the Diaci1.0 Illumina assembly to create the Diaci1.1 version of the D. citri genome. Thirty-nine SMRTcells of the library were sequenced, all with 2×45 minute movies. A total of 2,750,690 post-filter reads were generated, with an average of 70,530 reads per SMRTcell. The post-filter mean read length was 2,504 bp with an error rate of 15%.
Velvet was used with kmer 59 for generating the original assembly. PacBio long reads were mapped to the draft assembly using blasr with the folowing parameters: -minMatch 8 -minPctIdentity 70 -bestn 5 -nCandidates 30 -maxScore -500 -nproc 8 -noSplitSubreads. These alignments were parsed using PBJelly with default parameters.
Resources in this dataset:Resource Title: Diaphorina citri genome assembly Diaci 1.1. File Name: 121845_ref_Diaci_psyllid_genome_assembly_version_1.1_chrUn.mfa_.gzResource Description: This resource contains a fasta file of the Diaphorina citri genome assembly Diaci 1.1.

国际柑橘木虱基因组联盟已构建了亚洲柑橘木虱（Diaphorina citri）的基因组装配版本 Diaci 1.1。该装配版本亦可在国家生物技术信息中心检索，访问号：https://www.ncbi.nlm.nih.gov/assembly/GCF_000475195.1/。

DNA 提取与文库制备：采用 BioRad AquaPure 基因组 DNA 纯化试剂盒，从佛罗里达州皮茨堡市一柑橘园采集的完整新鲜 D. citri 样本中提取高分子量 DNA，并在美国农业部农业研究服务局、美国园艺研究实验室（佛罗里达州皮茨堡市）进行饲养。为构建 PacBio 文库，使用 Covaris g-Tube 进行 DNA 梯度切割，并采用 10Kb 协议（PacBio DNA 模板制备试剂盒 2.0；3-10Kb，货号 001-540-835）制备 SMRT-bell 文库。

基因组测序与装配：使用 TruSeq DNA 文库制备试剂盒对成对末端以及长插入体配对文库进行样本制备。所有样本均使用 Illumina HiSeq2000 进行测序，测序长度为 100bp 或更长。共测序七个文库，插入片段长度从“短”（约 275bp）到 10Kb 不等。这些数据可在 NCBI SRA 中找到，包括 9970 万个成对末端读段（NCBI SRA：SRX057205），3510 万个 2kb 配对末端读段（NCBI SRA：SRX057204），3000 万个 5kb 配对末端读段（NCBI SRA：SRX058250）和 3000 万个 10kb 配对末端读段（NCBI SRA：SRX216330）。对 Diaci1.0 Illumina 装配进行了第二轮 DNA 测序，以 PacBio 测序技术进行 12X 覆盖度测序（NCBI SRA：SRX218985），以构建 Diaci1.1 版本的 D. citri 基因组。对 39 个 SMRTcell 文库进行了测序，每个 SMRTcell 均进行了 2×45 分钟的拍摄。共生成了 2750690 个经过过滤的读段，平均每个 SMRTcell 产生 70530 个读段。经过过滤的平均读段长度为 2504 bp，错误率为 15%。

使用 Velvet 工具和 kmer 59 参数生成原始装配。使用 blasr 将 PacBio 长读段映射到草图装配上，参数如下：-minMatch 8 -minPctIdentity 70 -bestn 5 -nCandidates 30 -maxScore -500 -nproc 8 -noSplitSubreads。这些对齐结果使用 PBJelly 工具进行解析。

本数据集包含的资源：
资源标题：Diaphorina citri 基因组装配 Diaci 1.1
文件名：121845_ref_Diaci_psyllid_genome_assembly_version_1.1_chrUn.mfa_.gz
资源描述：此资源包含 Diaphorina citri 基因组装配 Diaci 1.1 的 fasta 文件。