Table_1_Benchmark study for evaluating the quality of reference genomes and gene annotations in 114 species.XLSX

IntroductionFor reference genomes and gene annotations are key materials that can determine the limits of the molecular biology research of a species; however, systematic research on their quality assessment remains insufficient.MethodsWe collected reference assemblies, gene annotations, and 3,420 RNA-sequencing (RNA-seq) data from 114 species and selected effective indicators to simultaneously evaluate the reference genome quality of various species, including statistics that can be obtained empirically during the mapping process of short reads. Furthermore, we newly presented and applied transcript diversity and quantification success rates that can relatively evaluate the quality of gene annotations of various species. Finally, we proposed a next-generation sequencing (NGS) applicability index by integrating a total of 10 effective indicators that can evaluate the genome and gene annotation of a specific species.Results and discussionBased on these effective evaluation indicators, we successfully evaluated and demonstrated the relative accessibility of NGS applications in all species, which will directly contribute to determining the technological boundaries in each species. Simultaneously, we expect that it will be a key indicator to examine the direction of future development through relative quality evaluation of genomes and gene annotations in each species, including countless organisms whose genomes and gene annotations will be constructed in the future.

引言：就参考基因组与基因注释而言，它们是决定物种分子生物学研究界限的关键材料；然而，对它们质量评估的系统研究尚显不足。方法：我们从114种物种中收集了参考组装、基因注释以及3,420个RNA测序（RNA-seq）数据，并选取了有效的指标，以同时评估多种物种的参考基因组质量，包括在短读序列映射过程中可以经验性地获得的统计数据。此外，我们提出并应用了转录多样性与量化成功率，这些指标可以相对评估各种物种基因注释的质量。最终，我们通过整合总计10个有效指标，提出了一种下一代测序（NGS）适用性指数，用以评估特定物种的基因组与基因注释。结果与讨论：基于这些有效的评估指标，我们成功评估并证明了所有物种中NGS应用的相对可及性，这将直接有助于确定每种物种的技术边界。同时，我们期望这将成为一个关键指标，通过评估每种物种基因组与基因注释的相对质量，来检验未来发展的方向，包括未来将构建其基因组与基因注释的无尽生物体。