Annotated genome assemblies for Geoscapheus dilatatus, Panesthia cribrata and Neogeoscapheus hanni

Genetic changes that enabled the evolution of eusociality have long captivated biologists. More recently, attention has focussed on the consequences of eusociality on genome evolution. Studies have reported higher molecular evolutionary rates in eusocial hymenopteran insects compared with their solitary relatives. To investigate the genomic consequences of eusociality in termites, we analysed nine genomes, including newly sequenced genomes from three non-eusocial cockroaches. Using a phylogenomic approach, we found that termite genomes have experienced lower rates of synonymous substitutions than those of cockroaches, possibly as a result of longer generation times. We identified higher rates of non-synonymous substitutions in termite genomes than in cockroach genomes, and identified pervasive relaxed selection in the former (24–31% of the genes analysed) compared with the latter (2–4%). We infer that this is due to reductions in effective population size, rather than gene-specific effe..., Three Blaberidae genomes (Geoscapheus dilatatus, Panesthia cribrata and Neogeoscapheus hanni) were sequenced and assembled to investigate the evolution of this group, and to provide genomic resources for studies on Blattodea. These genomes were assembled using a combination of linked-read, long-read and Hi-C data (the raw seqeunce data are avalable on the SRA database under BioSample accessions SAMN39450771, SAMN39450772 and SAMN39450773 for Geoscapheus dilatatus, Neogeoscapheus hanni and Panesthia cribrata respectively). Assembly methods are outlined in the associated manuscript. Briefly, an initial de novo Geoscapheus dilatatus genome assembly was generated using the program Supernova with linked-read stLFR data. Gaps were filled using the program TGS-GapCloser with low-coverage long-read PacBio HiFi data, and the assembly was subsequently scaffolded using the SALSA2 with Hi-C reads. An initial Panesthia cribrata genome assembly was generated using the program Supernova with linked-re..., , # De novo assemblies of Blaberidae genomes This repository contains genome assemblies and associated annotations for three Blaberidae species: *Geoscapheus dilatatus*, *Neogeoscapheus hanni* and *Panesthia cribrata*. The genome were assembled using a combination of linked-read, long-read and Hi-C data. An initial *Geoscapheus dilatatus* genome assembly was generated using linked-read data, then gaps were filled using low-coverage long-read data, and the assembly was subsequently scaffolded using Hi-C reads. ## Description of the data and file structure Five files are available for each of the three species: * Full genome assembly (fasta file) * *Geoscapheus dilatatus* genome assembly: 'Geoscapheus-dilatatus_genome-assembly.fa' * *Neogeoscapheus hanni* genome assembly: 'Neogeoscapheus-hanni_genome-assembly.fa' * *Panesthia cribrata* genome assembly: 'Panesthia-cribrata_genome-assembly.fa' * Genome annotation (gff3) * *Geoscapheus dilatatus* genome anno...长期以来，驱动真社会性（eusociality）演化的遗传改变一直令生物学家着迷。近年来，研究焦点转向了真社会性对基因组演化的影响。已有研究报道，与独居近亲相比，真社会性膜翅目昆虫的分子演化速率更高。为探究真社会性在白蚁中的基因组层面影响，我们分析了9个基因组，其中包含3个非真社会性蜚蠊（蟑螂）的新测序基因组。通过系统基因组学（phylogenomic）分析方法，我们发现白蚁基因组的同义替换（synonymous substitution）速率低于蜚蠊基因组，这可能源于更长的世代时间。我们还发现，白蚁基因组的非同义替换（non-synonymous substitution）速率高于蜚蠊基因组，且前者普遍存在更为广泛的放松选择（relaxed selection）现象——在所分析的基因中占比24%~31%，而后者仅为2%~4%。我们推测，这一现象源于有效种群大小（effective population size）的缩减，而非基因特异性的效应…… 为探究折翅蠊科（Blaberidae）类群的演化并为蜚蠊目（Blattodea）研究提供基因组资源，我们对3个折翅蠊科基因组（*Geoscapheus dilatatus*、*Panesthia cribrata*及*Neogeoscapheus hanni*）进行了测序与组装。这些基因组采用链接读长（linked-read）、长读长（long-read）与Hi-C技术相结合的策略进行组装（原始测序数据可于SRA数据库获取，对应生物样本（BioSample）编号分别为：*Geoscapheus dilatatus*：SAMN39450771、*Neogeoscapheus hanni*：SAMN39450772、*Panesthia cribrata*：SAMN39450773）。组装方法详见相关手稿。简言之，我们首先利用Supernova软件结合stLFR链接读长数据，生成了*Geoscapheus dilatatus*的初始从头（de novo）基因组组装结果；随后使用TGS-GapCloser软件结合低覆盖度长读长PacBio HiFi数据填补组装间隙；最后利用SALSA2软件结合Hi-C reads完成支架挂载。*Panesthia cribrata*的初始基因组组装则采用Supernova软件结合链接读长数据完成…… # 折翅蠊科基因组从头组装 本仓库包含3种折翅蠊科物种的基因组组装结果及相关注释：*Geoscapheus dilatatus*、*Neogeoscapheus hanni*及*Panesthia cribrata*。 我们采用链接读长、长读长与Hi-C技术相结合的策略完成基因组组装。首先基于链接读长数据生成*Geoscapheus dilatatus*的初始基因组组装结果，随后利用低覆盖度长读长数据填补组装间隙，最终通过Hi-C reads完成支架挂载。 ## 数据与文件结构说明 3个物种各对应5个可用文件： * 全基因组组装文件（FASTA格式） * *Geoscapheus dilatatus*基因组组装文件：'Geoscapheus-dilatatus_genome-assembly.fa' * *Neogeoscapheus hanni*基因组组装文件：'Neogeoscapheus-hanni_genome-assembly.fa' * *Panesthia cribrata*基因组组装文件：'Panesthia-cribrata_genome-assembly.fa' * 基因组注释文件（GFF3格式） * *Geoscapheus dilatatus*基因组注释……