Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.

来自200多个植物物种的基因组序列已经发表，由于测序技术的进步，预计这一数字将迅速增加。一旦组装了一个新的基因组并鉴定了基因，使用本体论对其推定的翻译产物蛋白质的功能注释就至关重要，因为它将测序数据置于生物学环境中。此外，为了跟上快速产生基因组序列的步伐，此功能注释过程必须完全自动化。在这里，我们介绍了经过重新设计和显着增强的MapMan4框架，以及相关联的在线墨卡托注释工具的修订版。与原始MapMan相比，新的本体已扩展了近三倍，并执行了更严格的分配规则。该框架随后被合并到Mercator4中，该版本已升级以反映整个陆地植物群的当前知识，从而为所有胚芽提供了相对高质量的蛋白质注释。注释过程已经过优化，可以在几分钟内对植物基因组进行注释。输出结果继续与已建立的MapMan桌面应用程序兼容。