CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy.
PLoS One. 2020 Jun 19;15(6):e0234782. doi: 10.1371/journal.pone.0234782. eCollection 2020.
A functional Non-Tandem Duplicated Cluster (FNTDC) is a group of non-tandem-duplicated genes that are located closer than expected by mere chance and have a role in the same biological function. The identification of secondary-compounds-related FNTDC has gained increased interest in recent years, but little ab-initio attempts aiming to the identification of FNTDCs covering all biological functions, including primary metabolism compounds, have been carried out. We report an extensive FNTDC dataset accompanied by a detailed assessment on parameters used for genome scanning and their impact on FNTDC detection. We propose 70% identity and 70% alignment coverage as intermediate settings to exclude tandem duplicated genes and a dynamic scanning window of 24 genes. These settings were applied to rice, arabidopsis and grapevine genomes to call for FNTDCs. Besides the best-known secondary metabolism clusters, we identified many FNTDCs associated to primary metabolism ranging from macromolecules synthesis/editing, TOR signalling, ubiquitination, proton and electron transfer complexes. Using the intermediate FNTDC setting parameters (at P-value 1e-6), 130, 70 and 140 candidate FNTDCs were called in rice, arabidopsis and grapevine, respectively, and 20 to 30% of GO tags associated to called FNTDC were common among the 3 genomes. The datasets developed along with this work provide a rich framework for pinpointing candidate FNTDCs reflecting all GO-BP tags covering both primary and secondary metabolism with large macromolecular complexes/metabolons as the most represented FNTDCs. Noteworthy, several FNTDCs are tagged with GOs referring to organelle-targeted multi-enzyme complex, a finding that suggest the migration of endosymbiont gene chunks towards nuclei could be at the basis of these class of candidate FNTDCs. Most FNTDC appear to have evolved prior of genome duplication events. More than one-third of genes interspersed/adjacent to called FNTDCs lacked any functional annotation; however, their co-localization may provide hints towards a candidate biological role.
一个功能上非串联重复簇（FNTDC）是一组位于比仅仅通过偶然位置更接近的非串联重复基因，它们具有相同的生物学功能。近年来，人们对次生代谢产物相关的 FNTDC 的鉴定产生了越来越多的兴趣，但很少有针对包括初级代谢产物化合物在内的所有生物学功能的 FNTDC 鉴定的初步尝试。我们报告了一个广泛的 FNTDC 数据集，并对用于基因组扫描的参数及其对 FNTDC 检测的影响进行了详细评估。我们提出了 70%的身份和 70%的比对覆盖率作为排除串联重复基因的中间设置，并采用了 24 个基因的动态扫描窗口。这些设置被应用于水稻、拟南芥和葡萄基因组中，以确定 FNTDC。除了最著名的次生代谢物簇外，我们还鉴定了许多与初级代谢物相关的 FNTDC，这些 FNTDC 涉及大分子的合成/编辑、TOR 信号、泛素化、质子和电子转移复合物。使用中间 FNTDC 设置参数（在 P 值为 1e-6 时），在水稻、拟南芥和葡萄中分别调用了 130、70 和 140 个候选 FNTDC，在 3 个基因组中，与所调用的 FNTDC 相关的 20%至 30%的 GO 标签是共同的。随着这项工作的开展，数据集提供了一个丰富的框架，用于精确定位候选 FNTDC，反映了涵盖初级和次级代谢物的所有 GO-BP 标签，其中大型大分子复合物/代谢物是最具代表性的 FNTDC。值得注意的是，一些 FNTDC 被标记为细胞器靶向多酶复合物的 GO，这一发现表明，内共生体基因片段向细胞核的迁移可能是这些候选 FNTDC 类的基础。大多数 FNTDC 似乎是在基因组复制事件之前进化而来的。在调用的 FNTDC 之间散布/相邻的基因中，超过三分之一缺乏任何功能注释；然而，它们的共定位可能为候选生物学功能提供线索。
