Phylogenetic and taxonomic insights into Betula: low-coverage whole genome sequencing and plastome analysis with focus on the rare Ukrainian endemic species Betula klokovii Zaverucha

Abstract

Betula klokovii Zaverucha is a rare endemic species of Ukraine that is still not well taxonomically studied. In the current pilot study, we performed low-coverage whole genome sequencing for B. klokovii, related species (B. pendula Roth and B. pubescens Ehrh.) and the assumed hybrid B. klokovii x B. pendula, assessed the genomic structure of taxa with different mapping settings using UMAP non-linear dimension reduction algorithm, extracted and assembled whole plastomes. Single Nucleotide Polymorphism (SNP) analysis based on low-coverage whole genome sequencing (LC-WGS) followed by UMAP visualization reveals the separation of B. klokovii from the other analysed taxa. The best taxonomic resolution was achieved with reads filtered for contamination. In contrast, the best result in obtaining complete plastome assemblies was achieved via NOVOPlasty pipeline and raw reads. The size for the eight newly assembled plastid genomes ranges between 160,535 and 160,625bp, GC content is 36,1%. We annotated 130 genes (113 unique) for all eight assemblies. In addition, we investigated B. klokoviis relationships with 20 other birch species and two intraspecific taxa by reconstructing plastome-based Bayesian inference and maximum likelihood phylogenies. Overall, plastome phylogeny provides a better resolution in comparison to phylogenies based on a few plastid or nuclear molecular markers. However, it could be affected by chloroplast capture, and some other factors like quality of sequencing and assembly, and is not suitable to detect hybrids when used alone. In particular, we found that B. klokovii is likely a separate taxon that is closely related to B. pubescens but morphologically and genetically distinct. The study shows that genome-wide SNP data and plastome phylogenies have a certain potential for addressing issues with specific taxa within the genus Betula L. However, to fully leverage the potential of this approach, we suggest collecting a much larger number of birch plastome sequences to be sequenced and assembled. For a better understanding of birch phylogeny there is a need for reference-grade chromosome scale genome assemblies for polyploid species.