Biology subjects

Wanke, S.

Publications and source records attributed to Wanke, S..

5 recordsLinked to original sources

bioRxiv2025

Evidence for plastome loss in the holoparasitic Mystropetalaceae

Plastome loss is an extremely unusual phenomenon in land plants, even for those that lose their photosynthetic ability. To date, evidence for plastome loss has only been presented for two holoparasitic angiosperm lineages: two genera (Rafflesia and Sapria) of Rafflesiaceae and one section (Subulatae) of Cuscuta (Convolvulaceae). Here we propose plastome loss in holoparasitic Mystropetalaceae (Santalales), which consists of three monotypic genera: Dactylanthus, Hachettea, and Mystropetalon. Using Illumina DNA sequencing data, we successfully assembled the complete mitochondrial genomes of all three genera; however, we failed to recover any plastome sequences from them using reference-based and de novo assembly approaches. Illumina RNA sequencing data for Hachettea revealed the absence of plastid gene transcripts and losses of many nuclear-encoded genes with plastid function, including genes involved in DNA transcription, translation and protein degradation. Convergent loss of these key genes has also been documented in other plastome-less non-photosynthetic plant lineages. Taken together, we provided compelling evidence for plastome loss in the family Mystropetalaceae.

plant biology↗

bioRxiv2025

Organellar data sets confirm overall angiosperm relationships if problematic RNA-edit sites are accounted for in mitochondrial genomes

PremisePlastid-based data sets continue to play a major role in our understanding of early flowering-plant relationships, although organellar genomes of major lineages outside the monocots and eudicots remain under-sampled. A tendency of mitochondrial RNA-edit sites to mislead phylogenetic analysis in mixed transcriptomic/genomic data sets needs attention in angiosperm-wide studies, which only rarely consider mitochondrial genomes. MethodsWe compared mitochondrial- vs. plastid-based phylogenomic inferences, examined the effect of removing putative RNA-edit sites from mitochondrial data, and performed combined organellar analysis (plastid plus filtered mitochondrial genomes). We expanded taxon sampling for multiple angiosperm lineages for phylogenomic analysis using both organellar genomes, representing several poorly sampled lineages (in particular Degeneriaceae, Trimeniaceae) with smaller (few-gene) data sets. ResultsPlastid-based inferences recover well-supported relationships that align with and build upon previous studies, and recover well-supported internal relationships for two ANA-grade families (Hydatellaceae, Trimeniaceae) sampled for nearly all species. By contrast, unfiltered mitochondrial inferences of angiosperm phylogeny are generally poorly supported, and recover anomalous relationships compared to plastid-based inferences. However, removing putative mitochondrial RNA-edit sites dramatically reduces inter-organellar conflict and improves overall branch support. ConclusionsWe accounted for phylogenomic discordance between the two organellar genomes regarding overall angiosperm-wide relationships and filled in taxonomic gaps (poorly sampled lineages). Removing RNA edit sites substantially improves congruence in interorganellar inferences by effectively correcting a systematic bias in mitochondrial data. Uncertain relationships persist among five major mesangiosperm lineages in plastid-based inferences, but a clade comprising Chloranthales, Ceratophyllales and eudicots is well supported by filtered mitochondrial data.

plant biology↗

bioRxiv2024

Diverging repeatomes in holoparasitic Hydnoraceae uncover a playground of genome evolution

O_LIThe nuclear genomes of parasitic plants have undergone unique evolutionary trajectories to adapt to the heterotrophic lifestyle. These adaptations often involve large genomic alterations, potentially driven by repetitive DNAs. Despite the recognized role of repetitive DNAs for shaping plant genomes, their contribution to parasitic plant genome evolution remains largely unexplored. This study presents the first analysis of repetitive DNAs in eleven genomes of Hydnoraceae, a holoparasitic plant family. C_LIO_LIThe repetitive DNAs were identified and annotated de novo. Patterns of abundance and presence-absence were aligned with the phylogenetic relationships, geographical distribution, and host shifts, suggesting repetitive DNAs key role in shaping Hydnoraceae genomes. C_LIO_LIThe two Hydnoraceae genera, Hydnora and Prosopanche, exhibit distinct profiles. Eight Hydnora genomes are largely populated by long terminal repeat retrotransposons, while three Prosopanche genomes vary greatly in repetitive DNA composition, including P. bonacinae with massive amplifications of a single DNA transposon and P. panguanensis with over 15% 5S rDNA, compared to <0.1% in some Hydnoraceae. Both extremely low and very high abundance of 5S rDNA challenges our current understanding on chromosomal stabilization and rDNA transcription. C_LIO_LIThese genome dynamics, while inviting for further investigations, suggest rapidly evolving repeat profiles, potentially accelerated by the adaptation to the parasitic lifestyle. C_LI

evolutionary biology↗

bioRxiv2024

Repeatome landscapes and cytogenetics of hortensias provide a framework to trace Hydrangea evolution and domestication

Background and AimsOrnamental hortensias are bred from a reservoir of over 200 species in the genus Hydrangea s.l. and are valued in gardens, households and landscapes across the globe. The phenotypic diversity of hortensia cultivars, hybrids and wild relatives is mirrored by their genomic variation, with differences in genome size, base chromosome numbers and ploidy level. We aim to understand the genomic and chromosomal basis of hortensia genome variation. Therefore, we analyze six hortensias with different origins and chromosomal setups for repeatome divergence, the genome fraction with the highest sequence turnover. This holds information from the hortensias evolutionary paths and can inform breeding initiatives. MethodsWe compiled a hortensia genotype panel representing members of the sections Macrophyllae, Hydrangea, Asperae, and Heteromallae and reconstructed a plastome-based phylogenetic hypothesis as evolutionary basis for all our analyses. We comprehensively characterized the repeatomes by whole genome sequencing and comparative repeat clustering. Major tandem repeats were localized by multi-color FISH. Key ResultsThe Hydrangea species show differing repeat profiles reflecting their separation into the two major Hydrangea clades: Diploid Hydrangea species from Japan show a conserved repeat profile, distinguishing them from Japanese polyploids as well as Chinese and American hortensias. These results are in line with plastome-based phylogenies. The presence of specific repeats indicates that H. paniculata was not polyploidized directly from the common ancestor of Japanese Hydrangea species, but evolved from a distinct progenitor. Major satellite DNAs were detected over all H. macrophylla chromosomes. ConclusionsRepeat composition among the Hydrangea species varies in congruence with their origins and phylogeny. Identified species-specific satDNAs may be used as cytogenetic markers to identify Hydrangea species and cultivars, and to infer parental species of old Hydrangea varieties. This repeatome and cytogenetics information helps to expand the genetic toolbox for tracing hortensia evolution and informing future hortensia breeding.

genomics↗

bioRxiv2016

Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic Estimates

An important goal of the angiosperm systematics community has been to develop a shared approach to molecular data collection, such that phylogenomic data sets from different focal clades can be combined for meta-studies across the entire group. Although significant progress has been made through efforts such as DNA barcoding, transcriptome sequencing, and whole-plastid sequencing, the community current lacks a cost efficient methodology for collecting nuclear phylogenomic data across all angiosperms. Here, we leverage genomic resources from 43 angiosperm species to develop enrichment probes useful for collecting ~500 loci from non-model taxa across the diversity of angiosperms. By taking an anchored phylogenomics approach, in which probes are designed to represent sequence diversity across the group, we are able to efficiently target loci with sufficient phylogenetic signal to resolve deep, intermediate, and shallow angiosperm relationships. After demonstrating the utility of this resource, we present a method that generates a heat map for each node on a phylogeny that reveals the sensitivity of support for the node across analysis conditions, as well as different locus, site, and taxon schemes. Focusing on the effect of locus and site sampling, we use this approach to statistically evaluate relative support for the alternative relationships among eudicots, monocots, and magnoliids. Although the results from supermatrix and coalescent analyses are largely consistent across the tree, we find support for this deep relationship to be more sensitive to the particular choice of sites and loci when a supermatrix approach as employed. Averaged across analysis approaches and data subsampling schemes, our data support a eudicot-monocot sister relationship, which is supported by a number of recent angiosperm studies.

evolutionary biology↗