AIT Austrian Institute of Technology, Center for Health and Bioresources, Tulln, Austria.
Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, Austria.
BMC Bioinformatics. 2021 Mar 22;22(1):146. doi: 10.1186/s12859-021-04078-8.
Polyploidy is very common in plants and can be seen as one of the key drivers in the domestication of crops and the establishment of important agronomic traits. It can be the main source of genomic repatterning and introduces gene duplications, affecting gene expression and alternative splicing. Since fully sequenced genomes are not yet available for many plant species including crops, de novo transcriptome assembly is the basis to understand molecular and functional mechanisms. However, in complex polyploid plants, de novo transcriptome assembly is challenging, leading to increased rates of fused or redundant transcripts. Since assemblers were developed mainly for diploid organisms, they may not well suited for polyploids. Also, comparative evaluations of these tools on higher polyploid plants are extremely rare. Thus, our aim was to fill this gap and to provide a basic guideline for choosing the optimal de novo assembly strategy focusing on autotetraploids, as the scientific interest in this type of polyploidy is steadily increasing.
We present a comparison of two common (SOAPdenovo-Trans, Trinity) and one recently published transcriptome assembler (TransLiG) on diploid and autotetraploid species of the genera Acer and Vaccinium using Arabidopsis thaliana as a reference. The number of assembled transcripts was up to 11 and 14 times higher with an increased number of short transcripts for Acer and Vaccinium, respectively, compared to A. thaliana. In diploid samples, Trinity and TransLiG performed similarly good while in autotetraploids, TransLiG assembled most complete transcriptomes with an average of 1916 assembled BUSCOs vs. 1705 BUSCOs for Trinity. Of all three assemblers, SOAPdenovo-Trans performed worst (1133 complete BUSCOs).
All three assembly tools produced complete assemblies when dealing with the model organism A. thaliana, independently of its ploidy level, but their performances differed extremely when it comes to non-model autotetraploids, where specifically TransLiG and Trinity produced a high number of redundant transcripts. The recently published assembler TransLiG has not been tested yet on any plant organism but showed highest completeness and full-length transcriptomes, especially in autotetraploids. Including such species during the development and testing of new assembly tools is highly appreciated and recommended as many important crops are polyploid.
多倍体在植物中非常普遍，可以看作是作物驯化和重要农艺性状形成的关键驱动力之一。它可以作为基因组重新排列的主要来源，并引入基因复制，影响基因表达和选择性剪接。由于包括作物在内的许多植物物种尚未有完整测序的基因组，从头转录组组装是理解分子和功能机制的基础。然而，在复杂的多倍体植物中，从头转录组组装具有挑战性，导致融合或冗余转录本的比例增加。由于组装器主要是为二倍体生物开发的，它们可能不适合多倍体。此外，对这些工具在更高倍性植物上的比较评估极为罕见。因此，我们的目标是填补这一空白，并提供一个基本的指导方针，以选择最佳的从头组装策略，重点是自交四倍体，因为自交四倍体的科学兴趣正在稳步增加。
我们使用拟南芥作为参考，比较了两种常见的（SOAPdenovo-Trans、Trinity）和一种最近发表的转录组组装器（TransLiG）在 Acer 和 Vaccinium 属的二倍体和自交四倍体物种上的表现。与拟南芥相比，Acer 和 Vaccinium 的组装转录本数量分别高达 11 倍和 14 倍，且短转录本数量增加。在二倍体样本中，Trinity 和 TransLiG 的表现相似，而在自交四倍体中，TransLiG 组装了最多完整的转录组，平均有 1916 个组装的 BUSCOs，而 Trinity 为 1705 个 BUSCOs。在所有三种组装器中，SOAPdenovo-Trans 的表现最差（1133 个完整 BUSCOs）。
当处理模式生物拟南芥时，所有三种组装工具都能产生完整的组装，而与多倍体水平无关，但当涉及到非模式自交四倍体时，它们的表现却截然不同，其中 TransLiG 和 Trinity 产生了大量的冗余转录本。最近发表的组装器 TransLiG 尚未在任何植物物种上进行测试，但在自交四倍体中表现出最高的完整性和全长转录组。在新组装工具的开发和测试中包含此类物种是非常值得赞赏和推荐的，因为许多重要的作物都是多倍体。
