Determination of Ploidy Level and Nuclear DNA Content in the Droseraceae by Flow Cytometry

Polyploids of Brassicaceae: Genomic Insights and Assembly Strategies

The Brassicaceae family is distinguished by its inclusion of high-value crops such as cabbage, broccoli, mustard, and wasabi, all noted for their glucosinolates. In this family, many polyploidy species are distributed and shaped by numerous whole-genome duplications, independent genome doublings, and hybridization events. The evolutionary trajectory of the family is marked by enhanced diversification and lineage splitting after paleo- and meso-polyploidization, with discernible remnants of whole-genome duplications within their genomes. The recent neopolyploidization events notably increased the proportion of polyploid species within the family. Although sequencing efforts for the Brassicaceae genome have been robust, accurately distinguishing sub-genomes remains a significant challenge, frequently complicating the assembly process. Assembly strategies include comparative analyses with ancestral species and examining k-mers, long terminal repeat retrotransposons, and pollen sequencing. This review comprehensively explores the unique genomic characteristics of the Brassicaceae family, with a particular emphasis on polyploidization events and the latest strategies for sequencing and assembly. This review will significantly improve our understanding of polyploidy in the Brassicaceae family and assist in future genome assembly methods.

Molecular Phylogenomics Reveals the Deep Evolutionary History of Carnivory across Land Plants

Plastid molecular phylogenies that broadly sampled angiosperm lineages imply that carnivorous plants evolved at least 11 times independently in 13 families and 6 orders. Within and between these clades, the different prey capture strategies involving flypaper and pitfall structures arose in parallel with the subsequent evolution of snap traps and suction bladders. Attempts to discern the deep ontological history of carnivorous structures using multigene phylogenies have provided a plastid-level picture of sister relationships at the family level. Here, we present a molecular phylogeny of the angiosperms based on nuclear target sequence capture data (Angiosperms-353 probe set), assembled by the Kew Plant Trees of Life initiative, which aims to complete the tree of life for plants. This phylogeny encompasses all carnivorous and protocarnivorous families, although certain genera such as Philcoxia (Plantaginaceae) are excluded. This study offers a novel nuclear gene-based overview of relationships within and between carnivorous families and genera. Consistent with previous broadly sampled studies, we found that most carnivorous families are not affiliated with any single family. Instead, they emerge as sister groups to large clades comprising multiple non-carnivorous families. Additionally, we explore recent genomic studies across various carnivorous clades that examine the evolution of the carnivorous syndrome in relation to whole-genome duplication, subgenome dominance, small-scale gene duplication, and convergent evolution. Furthermore, we discuss insights into genome size evolution through the lens of carnivorous plant genomes.

Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory

Most plants grow and develop by taking up nutrients from the soil while continuously under threat from foraging animals. Carnivorous plants have turned the tables by capturing and consuming nutrient-rich animal prey, enabling them to thrive in nutrient-poor soil. To better understand the evolution of botanical carnivory, we compared the draft genome of the Venus flytrap (Dionaea muscipula) with that of its aquatic sister, the waterwheel plant Aldrovanda vesiculosa, and the sundew Drosera spatulata. We identified an early whole-genome duplication in the family as source for carnivory-associated genes. Recruitment of genes to the trap from the root especially was a major mechanism in the evolution of carnivory, supported by family-specific duplications. Still, these genomes belong to the gene poorest land plants sequenced thus far, suggesting reduction of selective pressure on different processes, including non-carnivorous nutrient acquisition. Our results show how non-carnivorous plants evolved into the most skillful green hunters on the planet.

Genetic diversity of Ziziphus mauritiana germplasm based on SSR markers and ploidy level estimation

A set of reliable SSR markers were developed for Ziziphus mauritiana. The genetic relationship of Z. mauritiana germplasms was generally consistent with their geographical origin, and low diversity in the maternal lineage was revealed. Ziziphus mauritiana, known as Indian jujube, is an important fruit crop that is native to southern Asia and eastern Africa. There is a variety of germplasm resources, and particularly many new cultivars were selected and introduced into wide tropical regions in recent years. However, there are few practical molecular markers for cultivar authentication and genetic analysis. In this study, we developed 55 polymorphic nuclear SSR markers based on restriction-site associated DNA sequences and transcriptome sequencing. We selected 14 robust nSSR markers for further analysis of 117 Z. mauritiana accessions from four countries (45 from China, 39 from Vietnam, 25 from Pakistan and 8 from Myanmar). In total, 137 alleles were detected and DNA fingerprints for each accession were constructed. Cluster analysis based on the unweighted pair group method with arithmetic mean displayed that most accessions clustered consistently with their geographic origin. In addition, there was common and high degree polyploidization based on nSSR and flow cytometry analyses. Only two of the 50 SSR loci in noncoding regions from the chloroplast genome had polymorphisms, and 5 haplotypes in total were identified among the 117 accessions. Haplotype C with 89 accessions was the most dominant haplotype and presented in four countries. This indicates low diversity in the maternal lineage of tested Z. mauritiana germplasm. Our research provides reliable marker resources for cultivar authentication and new insights into the genetic diversity, polyploidization and domestication of Z. mauritiana.