Cosmopolites sordidus genome assemblies

PacBio HiFi sequencing was employed in combination with metagenomic binning to produce a high-quality reference genome of Cosmopolites sordidus. We compared k-mer and alignment reference-based pre-binning and post-binning approaches to remove contamination. We were also interested to know if the post-binning approach had interspersed Bacterial contamination within intragenic regions of Arthropoda-binned contigs. Our analyses identified 3,433 genes that were composed with reads identified as of putative bacterial origins. The pre-binning approach yielded a C. sordidus genome of 1.07Gb genome composed of 3,089 contigs with 98.6% and 97.1% complete and single copy genome and protein BUSCO scores respectively. In this paper, we demonstrate that in this case, the pre-binning approach does not sacrifice assembly quality for more stringent metagenomic filtering. We also determine post-binning allows for increased intragenic contamination increased with increasing coverage, but the frequency of..., PacBio HiFi Sequencing of high molecular weight DNA from Cosmopolites sordidus pupa. Briefly, assembly via hifiasm, repeat masking via RepeatModeler and RepeatMasker, gene prediction via Braker2 followed by functional annotation via blastx to swissprot, DIAMOND to eggNog, and OrthoFinder., , ############################################################################################################

Data from: Metagenomic binning of PacBio HiFi data prior to assembly reveals a complete

genome of Cosmopolites sordidus (Germar) (Coleopterea: Curculionidae, Dryophthorinae) the

most damaging arthropod pest of bananas and plantains

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DESCRIPTION: Genome assemblies and associated gene prediction and annotation via

pre-binning out contamination before genome assembly or post-binning of contamination

after genome assembly.

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DIRECTORY: /Users/alexvandam/Cosmo/prefilt

\|\-\-\- \.DS\_Store \#should have been hidden but these files are used by the Mac OS to store custom attributes of a folder\, such as the position of icons\, the choice of a background image\, or ot...

PacBio HiFi测序结合宏基因组分箱（metagenomic binning）技术，获得了香蕉象甲（Cosmopolites sordidus）的高质量参考基因组（reference genome）。我们比较了基于k-mer和参考序列比对（alignment reference-based）的预分箱（pre-binning）与后分箱（post-binning）方法以去除污染（contamination）。我们还关注后分箱方法是否会在节肢动物分箱的contig（contig）基因内区（intragenic regions）中存在散在的细菌污染。我们的分析鉴定出3433个基因，其序列包含疑似细菌来源的reads（reads）。预分箱方法得到的香蕉象甲基因组大小为1.07Gb，由3089个contig组成，其基因组和蛋白质的BUSCO完整单拷贝评分（BUSCO scores）分别为98.6%和97.1%。本文中，我们证明在此案例中，预分箱方法在更严格的宏基因组过滤（metagenomic filtering）下并未牺牲组装质量（assembly quality）。我们还发现后分箱方法中基因内污染随覆盖度（coverage）增加而增多，但频率为...，对香蕉象甲蛹的高分子量DNA（high molecular weight DNA）进行PacBio HiFi测序。简要流程如下：通过hifiasm组装（assembly），使用RepeatModeler和RepeatMasker进行重复序列屏蔽（repeat masking），通过Braker2进行基因预测（gene prediction），随后通过blastx比对swissprot、DIAMOND比对eggNog以及OrthoFinder进行功能注释（functional annotation）。,,,,############################################################################################################

Data from: 组装前对PacBio HiFi数据进行宏基因组分箱（metagenomic binning），揭示了香蕉象甲（Cosmopolites sordidus, Germar）（鞘翅目：象甲科，隐喙象亚科）的完整基因组（reference genome），该虫是香蕉和大蕉最具破坏性的节肢动物害虫（arthropod pest）。############################################################################################################

DESCRIPTION: 基因组组装（genome assembly）及相关基因预测（gene prediction）与注释（annotation），通过组装前预分箱（pre-binning）去除污染（contamination）或组装后后分箱（post-binning）去除污染。############################################################################################################

DIRECTORY: /Users/alexvandam/Cosmo/prefilt |--- .DS\_Store #本应隐藏，但这些文件被Mac OS用于存储文件夹的自定义属性，例如图标位置、背景图片选择或其他...