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

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 15, 2025

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

Язык: Английский

Comparative plastome assembly of the yellow ironweed (Verbesina alternifolia) using Nanopore and Illumina reads

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Сен. 12, 2024

Chloroplast genomes (plastomes) represent a very important source of valuable information for phylogenetic and biogeographic reconstructions. The use short reads (as those produced from Illumina sequencing), along with

Язык: Английский

Genome sequence of the ornamental plantAquilegia vulgarisreveals the flavonoid biosynthesis gene repertoire

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 17, 2024

Abstract Aquilegia vulgaris is a widespread ornamental plant. The species well known for huge variation of different flower colors and can even be considered as model the evolution morphology. Anthocyanins are major pigment group responsible pigmentation flowers in A. many plant species. Here, we report highly continuous genome sequence European displaying purple flowers. corresponding annotation facilitates research on color morphology evolution. Candidate genes all steps core anthocyanidin biosynthesis were identified investigated with respect to their expression seedling parts. discovery flavonoid 3’5’ hydroxylase ( F3’5’H ), gene required bluish delphinidin derivatives, matches previous reports about metabolites transcripts .

Язык: Английский