Eric K. Wafula's research while affiliated with Pennsylvania State University and other places

... Single nucleotide polymorphism (SNP) data has also been gathered and used for 200 cacao genotypes, providing representation for ten genetic groups and a resource for population genetics research [18]. Most recently, 31 genome assemblies from wild cacao accessions across the four genetic groups were published, further increasing the wealth of cacao genomic resources [19,20]. An additional set of seven high quality de novo assembled genomes were recently developed and will be released to the public as well [19,20]. ...

... (The dataset was downloaded from the PedcBioPortal, https://pedcbioportal. kidsfirstdrc.org/study/summary?id=openpbta,pbta_all (accessed on 16 May 2023) and compiled using the Open Pediatric Brain Tumor Atlas (OpenPBTA) and Pediatric Brain Tumor Atlas (PBTA, provisional) consortiums [40] (the keywordsfor the search were "brainstem glioma, diffuse intrinsic pontine glioma, diffuse midline glioma grade 4, diffuse midline glioma H2K27M WHO grade 4, diffuse midline glioma WHO grade 4 H3K27M mutant, DMG H3 K27M mutant WHO grade 4, diffuse midline high-grade glioma, diffuse hemispheric glioma H3 G34 mutant, WHO grade 4, and infiltrating DIPG")). The PedcBio-Portal enables the acquisition of CSV-formatted files for the compiled clinical metadata and expression values of the filtered patient subsets for further analyses [41][42][43][44]. ...

... The top 45 genes identified as being predictive of texture loss from the RF regression model were selected and classified into orthogroups pre-computed with the 26Gv2.0 scaffold using PlantTribes2 [51]. Orthogroup multiple sequence alignment, phylogenetic tree estimation, homology inference, and gene model evaluation were performed using genes from 16 Rosaceae genomes (the same 15 from [52] plus Malus baccata [53]) plus the scaffolding species following methods from [52]. ...

... New Phytologist non-nodulating species in angiosperms, for example, is explained by the convergent loss or loss-of-function of NIN genes (Griesmann et al., 2018). Within mycoheterotrophic plants, progressive decreases in gene expression precede highly convergent patterns of gene loss Timilsena et al., 2023). The evolution of highly derived and reduced body plans is a feature of many aquatic plants. ...

... All phylogenomic analyses in this study showed strong support for two major clades in Asparagaceae, each consisting of at least three subfamilies (Aphyllanthoideae not sampled here): (i) an Agavoideae + Brodiaeoideae + Scilloideae clade and (ii) an Asparagoideae + Lomandroideae + Nolinoideae clade ( Figure 3; Figures S8, S9 in Appendix S8). These results support previous findings based on plastome sequences (Steele et al., 2012;Chen et al., 2013;Lu et al., 2022;Ji et al., 2023;Bentz et al., 2024) and hundreds of nuclear genes (One Thousand Plant Transcriptomes Initiative, 2019; Timilsena et al., 2022). However, in those previous plastome trees, Lomandroideae is placed sister to a Nolinoideae + Asparagoideae clade with strong support, which agrees with our plastome phylogeny ( Figure 3B) but disagrees with our ASTRAL trees inferred from 1726 nuclear genes ( Figure 3A). ...

... We summarize quality parameters of currently available genomes in Table S13. Since 2021, three more genomes have been released, two P. pyrifolia assemblies for 'Nijisseiki' and 'Cuifuan', and P. communis 'Beurré d'Anjou' (Gao et al. 2021;Shirasawa et al. 2021;Zhang et al. 2022). Further, the P. communis cv. ...

... Polyploidy and asexuality Modern genomics has revealed episodes of ancient whole-genome duplication that preceded key innovations in several eukaryotic lineages, especially in flowering plants, all of which share a polyploid common ancestor [13,28,29]. In recent polyploids, multiple gene copies allow for higher physiological and phenotypic flexibility in response to environmental conditions [30,31]. ...

... Single nucleotide polymorphism (SNP) data has also been gathered and used for 200 cacao genotypes, providing representation for ten genetic groups and a resource for population genetics research [18]. Most recently, 31 genome assemblies from wild cacao accessions across the four genetic groups were published, further increasing the wealth of cacao genomic resources [19,20]. An additional set of seven high quality de novo assembled genomes were recently developed and will be released to the public as well [19,20]. ...

... Some studies indicated that hosts have evolved the ability to detect parasitic plant-specific signals to initiate signal transduction cascades that lead to an HR and prevent the haustorium penetration process of parasitic plants [48]. For instance, a cowpea cultivar resistant to S. gesnerioides was found to trigger a downstream signalling cascade to activate the avirulence (Avr) proteins, which is a positive regulator of the HR [49]. A similar case was also reported for the interaction between sunflowers and O. cumana. ...

... Taxon sampling percentage values were calculated using recent checklists and classification literature (Söderström et al., 2016;Brinda and Atwood, 2023). The trees are rooted with the hornworts, assumed to be the sister group of the setaphytes (Renzaglia et al., 2018), i.e., liverworts and mosses (Leebens-Mack et al., 2019). ...