TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data

Abstract

Motivation: The chloroplast is the primary site of photosynthesis in plants, converting solar energy into chemical energy. The chloroplast genome is typically a circular DNA composed of four sections: a large single copy (LSC), a small single copy (SSC), and two intervening repeats (IRs). Long-read sequencing data now allow for assembly of chloroplast genomes along with nuclear genomes, but this requires that reads originating from the chloroplast genome are distinguished from reads that represent nuclear insertions of chloroplast DNA or related sequences from the mitochondrial genomes and that chloroplast heteroplasmy, i.e., the presence of multiple distinct chloroplast genomes is taken into account. Results: We introduce TIPP_plastid, an efficient tool for the assembly of plastid genomes based on the exclusion of reads originating from the mitochondrial and the nuclear genome, followed by the construction of assembly graphs and extraction of distinct chloroplast genomes. We demonstrate the usefulness of TIPP_plastid by assembling the chloroplast genomes of 45 phylogenetically diverse species. Availability and Implementation: TIPP_plastid is available at Github (https://github.com/Wenfei-Xian/TIPP). Code to reproduce results from this paper can be found at Github (https://github.com/Wenfei-Xian/Reproducible_for_TIPP_paper). Chloroplast genomes and assembly graphs of 45 phylogenetically diverse species can be downloaded at figshare (https://doi.org/10.6084/m9.figshare.24715017.v1).