Supplementary materials for PMGA

Plant mitochondrial genomes (PMGs) have many unique characteristics, including highly diverse genome structure, un-conserved inter-genetic regions, extensive RNA editing, and numerous horizontally transferred sequences. PMG annotators aware of these characteristics are missing, leading to inaccurate and incomplete annotation results. Here, we built a computational pipeline, "Plant Mitogenome Annotator" (PMGA), to address these challenges. PMGA had four datasets. Dataset 1 contained the coding sequences of rRNA and protein-coding genes (PCGs) of ten species. Erroneous splicing sites were corrected with RNA-seq data. Dataset 2 contained coding and protein sequences of 329 PMG. Erroneous annotations were corrected based on multiple sequence alignment. Dataset 3 contained 423 organelle’s tRNA sequences with defined origins. Dataset 4 contained plastid sequences from CPGAVAS2. In addition to annotate PCGs, rRNA genes, tRNA genes, PMGA can annotate MTPT sequences, repetitive sequences, chimeric genes, and RNA-editing sites. In particular, we developed three algorithms: "Analysis with Upstream Extended Sequences," "Assembling Exons with Weighted Direct Graph," and " Multiple Dimension Annotation of tRNA Genes" to annotate small exons, <i>trans</i>-splicing genes, and tRNA genes, respectively. We compared PMGA with three tools using the mitogenomes of <i>Arabidopsis thaliana</i> and <i>Liriodendron tulipifera</i>, we found that PMGA performed the best. Lastly, we sequenced, assembled and annotated the mitogenomes of <i>Pueraria montana var. lobata</i> and <i>Eucommia ulmoides</i>.<i> </i><i>We used the </i>RNA-seq data, PCR, and Sanger sequencing results to determine the splicing sites. Comparison of the experimental and annotation results of the splicing sites showed 100% of accuracy. An online version of PMGA can be found at http://www.1kmpg.cn/pmga/.