USDA-ARS, Southeastern Fruit & Tree Nut Research Laboratory, 21 Dunbar Rd. Byron, GA 31008, USA.
G3 (Bethesda). 2023 Jun 1;13(6). doi: 10.1093/g3journal/jkad086.
De novo transcriptome assembly of next-generation sequencing information has become a powerful tool for the study of non-model species. Transcriptomes generated by this method can have high variability due to endless combinations of user-defined variables and programs available for assembly. Many methods have been developed for evaluating the quality of these assemblies. Here, raw sequencing information for Green ash (Fraxinus pennsylvanica Marshall) that was previously published has been re-evaluated. An updated assembly has been developed by including additional sequencing information not used for the currently accepted transcriptome in combination with more stringent trimming parameters. Input reads were assembled with Trinity and Abyss assembly programs. The resulting Trinity assembly has a 7.3-fold increase in genomic breadth of coverage, a 2.4-fold increase in predicted complete open reading frames, an increased L50 value, and increased Benchmarking Universal Single-Copy Ortholog completeness compared to the earlier published transcriptome. This updated transcriptome can be leveraged to help fight the rapid decline of green ash due to pathogens.
从头转录组组装技术利用新一代测序信息，已经成为研究非模式物种的有力工具。由于用户定义的变量和可用的组装程序组合无穷无尽，因此通过这种方法生成的转录组可能具有高度的可变性。已经开发出许多方法来评估这些组装的质量。在这里，重新评估了先前发表的绿灰（Fraxinus pennsylvanica Marshall）的原始测序信息。通过结合更严格的修剪参数，包含先前未用于当前接受的转录组的其他测序信息，开发了一个更新的组装。使用 Trinity 和 Abyss 组装程序对输入读取进行组装。与早期发表的转录组相比，该 Trinity 组装的基因组覆盖广度增加了 7.3 倍，预测的完整开放阅读框增加了 2.4 倍，L50 值增加，并且 Benchmarking Universal Single-Copy Ortholog 的完整性也增加。与早期发表的转录组相比，该 Trinity 组装的基因组覆盖广度增加了 7.3 倍，预测的完整开放阅读框增加了 2.4 倍，L50 值增加，并且 Benchmarking Universal Single-Copy Ortholog 的完整性也增加。这个更新的转录组可以用来帮助对抗由于病原体导致的绿灰的快速减少。
