Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the mossPhyscomitrellopsis africana

Abstract

AbstractThe first reference genome assembly of the mossPhyscomitrellopsis africana, a rare narrow endemic terricolous species from southeastern coastal forests of South Africa, is presented here. Phylogenetically,Physcomitrellopsis africanabridges the major evo-devo moss modelsPhyscomitrium patensandFunaria hygrometrica, which diverged from their common ancestor 60-80 million years ago. ThePhyscomitrellopsis africanagenome was assembled with both long Nanopore reads (73x) and short Illumina reads (163x). The 440 Mb assembly comprises 2,396 contigs and 23,493 protein-coding genes (BUSCO: C:96.0%[D:13.9%]), including two unique genes of putative microbial origin absent in close relatives. While the informatic approaches to genome assembly are becoming more standardized, best practices for contamination detection are less defined. The long reads sequenced for thePhyscomitrellopsis africanagenome contained approximately 12% contamination originating from microbial sources. This study describes the informatic processes employed to distinguish contaminants from candidate horizontal gene transfer events. Following the assembly and annotation, examination of whole genome duplication, and patterns of gene family expansion and contraction, were conducted. The genome bears signatures of two whole genome duplications shared withPhyscomitrium patensandF. hygrometrica. Comparative analyses of gene family evolution revealed contractions associated with the light harvesting regulatory network inPhyscomitrellopsis africanain comparison toPhyscomitrium patensandF. hygrometrica. This first high-quality African bryophyte genome provides insights into genome evolution and HGT in an understudied moss lineage.Article SummaryThe first draft genome of the rare moss,Physcomitrellopsis africana, endemic to South Africa’s southeastern coastal forests, is presented here. The 440 Mb genome fills a critical phylogenetic gap, enabling the first comparative analysis of the genomes of three moss species that diverge over the last 60-80 million years. The analysis uncovered 23,493 genes and provides new insights into genome evolution and gene family expansion/contraction in mosses. Rigorous contaminant filtering also identified two genes uniquely acquired through horizontal gene transfer.