Annotation of the genome assembly Noccaea caerulescens cira v2.3

The N. caerulescens cira genome assembly v2.3 was annotated using the OmicsBox suite v. 1.4.12 (www.biobam.com/omicsbox). Repetitive elements were masked using the Repeat Masking tool based on RepeatMasker v. 4.0.9 with the custom repetitive elements sequence library generated with RepeatModeler v. 2.0.1. Genes were then annotated using the Eukaryotic Gene Finder tool, based on AUGUSTUS v. 3.4.0 in which we used Arabidopsis thaliana as a model to predict coding sequences and UTR and use N. caerulescens Firmiensis RNA-Seq samples as RNA-Seq hints. The coding sequences of annotated genes were blasted (Blastp; E-value ≤ 10-5) to the ref seq_protein database limited to the Brassicaceae family and classified into protein families using InterProScan. Putative functions were annotated by Gene Ontology using Blast2GO. In addition, the function of predicted proteins was annotated with Mercator4 v2.0天蓝遏蓝菜（N. caerulescens）cira基因组组装版本v2.3采用OmicsBox套件v1.4.12（www.biobam.com/omicsbox）完成注释。首先，利用基于RepeatMasker v4.0.9开发的重复序列屏蔽工具，结合由RepeatModeler v2.0.1构建的自定义重复序列库，对基因组中的重复元件进行了屏蔽。随后使用真核基因预测工具，基于AUGUSTUS v3.4.0开展基因注释：以拟南芥（Arabidopsis thaliana）作为预测模型，预测编码序列与非翻译区（Untranslated Region，UTR），并以天蓝遏蓝菜Firmiensis株系的RNA测序（RNA-Seq）样本作为转录组提示信息。对注释基因的编码序列进行Blastp比对（E值≤10^-5），比对范围限定为十字花科（Brassicaceae）的RefSeq蛋白数据库；并通过InterProScan将基因划分为不同蛋白质家族。利用Blast2GO基于基因本体论（Gene Ontology，GO）对基因进行推定功能注释。此外，还使用Mercator4 v2.0对预测得到的蛋白质进行功能注释。