Search Results (8)

Moreyra and co-authors, in their recent paper published in Plants, presented a desperately needed Hyb-Seq phylogeny of the genus Cirsium sensu lato. Through their findings, they provided a critical assessment of an earlier proposal of ours to separate Cirsium sect. Eriolepis and Cirsium italicum into the genera Lophiolepis and Epitrachys, respectively. While we fully respect their right not to accept our proposal, we cannot remain silent to their arguments that not only misinterpret our findings and statements but are often in direct conflict with their own results that actually support our proposal to segregate Lophiolepis. In addition, as Moreyra and co-authors did not include Epitrachys italica (formerly Cirsium italicum) in their analyses; they have no basis for arguing in favour or against our proposal to separate it as a monotypic genus. Finally, we conclude that the genus Cirsium, as circumscribed by the above-mentioned authors (i.e., including Lophiolepis), is definitively not monophyletic. Full article

Conifers are an ecologically and economically important seed plant group that can provide significant insights into the evolution of land plants. Molecular phylogenetics has developed as an important approach in evolutionary studies, although there have been relatively few studies of conifers that employ large-scale data sourced from multiple nuclear genes. Target enrichment sequencing (target capture, exon capture, or Hyb-Seq) has developed as a key approach in modern phylogenomic studies. However, until now, there has been no bait set that specifically targets the entire conifer clade. REMcon is a target sequence capture probe set intended for family- and species-level phylogenetic studies of conifers that target c. 100 single-copy nuclear loci. We tested the REMcon probe set using 69 species, including 44 conifer genera across six families and four other gymnosperm taxa, to evaluate the efficiency of target capture to efficiently generate comparable DNA sequence data across conifers. The recovery of target loci was high, with, on average, 94% of the targeted regions recovered across samples with high read coverage. A phylogenetic analysis of these data produced a well-supported topology that is consistent with the current understanding of relationships among conifers. The REMcon bait set will be useful in generating relatively large-scale nuclear data sets consistently for any conifer lineage. Full article

The floras on the highest mountains in tropical eastern Africa are among the most unique floras in the world. Despite the exceptionally high concentration of endemic species, these floras remain understudied from an evolutionary point of view. In this study, we focus on the Carduus-Cirsium group (subtribe Carduinae) to unravel the evolutionary relationships of the species endemic to the tropical Afromontane and Afroalpine floras, aiming to improve the systematics of the group. We applied the Hyb-Seq approach using the Compositae1061 probe set on 190 samples (159 species), encompassing representatives of all genera of Carduinae. We used two recently developed pipelines that enabled the processing of raw sequence reads, identification of paralogous sequences and segregation into orthologous alignments. After the implementation of a missing data filter, we retained sequences from 986 nuclear loci and 177 plastid regions. Phylogenomic analyses were conducted using both concatenated and summary-coalescence methods. The resulting phylogenies were highly resolved and revealed three distinct evolutionary lineages consisting of the African species traditionally referred to as Carduus and Cirsium. Consequently, we propose the three new genera Afrocarduus, Afrocirsium and Nuriaea; the latter did notably not belong to the Carduus-Cirsium group. We detected some incongruences between the phylogenies based on concatenation vs. coalescence and on nuclear vs. plastid datasets, likely attributable to incomplete lineage sorting and/or hybridization. Full article

The mulberry genus, Morus L. (Moraceae), has long been taxonomically difficult, and its species circumscription has only been defined recently. This genus comprises ca. 16 species distributed across Asia and the Americas, yet its biogeographic history remains poorly understood. In this study, we reconstructed the phylogeny and explored the biogeographic history of Morus using a combination of newly generated and previously published Hyb-Seq data. Our nuclear phylogeny recovered three well-supported geographic clades of Morus and showed that M. notabilis (China) is sister to the American clade plus the Asian clade. Multiple reticulation events among species of Morus and extensive incomplete lineage sorting (ILS) likely explain the difficulties in inferring phylogenetic relationships within the genus. Divergence time estimation indicated that Morus originated at the Eocene–Oligocene boundary, and current lineages started to diverge during the early Miocene, there is ambiguity surrounding the ancestral area with the two most likely regions being Sino-Himalaya or the Americas. Biogeographic inference and the fossil record suggest that Morus might have experienced extensive local extinction events during the Tertiary. Morus has expanded its distributional range through two dispersals from the Sino-Himalayan and Sino-Japanese regions to Southeast Asia. In summary, our new phylogenetic scheme and the biogeographic history presented here provide an essential foundation for understanding species relationships and the evolutionary history of Morus. Full article

Seed size is the major yield component and a key target trait that is selected during peanut breeding. However, the mechanisms that regulate peanut seed size are unknown. Two peanut mutants with bigger seed size were isolated in this study by ⁶⁰Co treatment of a common peanut landrace, Huayu 22, and were designated as the “big seed” mutant lines (hybs). The length and weight of the seed in hybs were about 118% and 170% of those in wild-type (WT), respectively. We adopted a multi-omics approach to identify the genomic locus underlying the hybs mutants. We performed whole genome sequencing (WGS) of WT and hybs mutants and identified thousands of large-effect variants (SNPs and indels) that occurred in about four hundred genes in hybs mutants. Seeds from both WT and hybs lines were sampled 20 days after flowering (DAF) and were used for RNA-Seq analysis; the results revealed about one thousand highly differentially expressed genes (DEGs) in hybs compared to WT. Using a method that combined large-effect variants with DEGs, we identified 45 potential candidate genes that shared gene product mutations and expression level changes in hybs compared to WT. Among the genes, two candidate genes encoding cytochrome P450 superfamily protein and NAC transcription factors may be associated with the increased seed size in hybs. The present findings provide new information on the identification and functional research into candidate genes responsible for the seed size phenotype in peanut. Full article

Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies. Full article

High-throughput RNA sequencing (RNA-seq) and dedicated bioinformatics pipelines have synergized to identify an expansive repertoire of unique circular RNAs (circRNAs), exceeding 100,000 variants. While the vast majority of these circRNAs comprise canonical exonic and intronic sequences, microexons (MEs)—which occur in 30% of functional mRNA transcripts—have been entirely overlooked. CircRNAs which contain these known MEs (ME-circRNAs) could be identified with commonly utilized circRNA prediction pipelines, CIRCexplorer2 and CIRI2, but were not previously recognized as ME-circRNAs. In addition, when employing a bespoke bioinformatics pipeline for identifying RNA chimeras, called Hyb, we could also identify over 2000 ME-circRNAs which contain novel MEs at their backsplice junctions, that are uncalled by either CIRCexplorer2 or CIRI2. Analysis of circRNA-seq datasets from gliomas of varying clinical grades compared with matched control tissue has shown circRNAs have potential as prognostic markers for stratifying tumor from healthy tissue. Furthermore, the abundance of microexon-containing circRNAs (ME-circRNAs) between tumor and normal tissues is correlated with the expression of a splicing associated factor, Serine/arginine repetitive matrix 4 (SRRM4). Overexpressing SRRM4, known for regulating ME inclusion in mRNAs critical for neural differentiation, in human HEK293 cells resulted in the biogenesis of over 2000 novel ME-circRNAs, including ME-circEIF4G3, and changes in the abundance of many canonical circRNAs, including circSETDB2 and circLRBA. This shows SRRM4, in which its expression is correlated with poor prognosis in gliomas, acts as a bona fide circRNA biogenesis factor. Given the known roles of MEs and circRNAs in oncogenesis, the identification of these previously unrecognized ME-circRNAs further increases the complexity and functional purview of this non-coding RNA family. Full article