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PubMed2026

Development of a low-coverage whole genome sequencing screen for apomixis using a diverse set of Malus germplasm.

In the past decade, plant biologists have made several major discoveries pertaining to the genetic basis of apomixis (clonal propagation by seed) that have shown promise in preserving high-value hybrid rice and sorghum genotypes. This progress was made possible by foundational gene discovery efforts in model species and natural apomicts, but pleiotropic obstacles still limit its broad agricultural adoption, especially in eudicots. Thus, it follows that investigations of novel apomicts should lead to the development of new molecular tools for plant breeding. The two most common ways to identify clonal seed production are flow-cytometry seed screens and genome sequencing to compare the DNA sequences of the maternal parent and progeny, traditionally using low-throughput markers. While flow-cytometry has been the dominant method for more than two decades, it provides indirect information on the genetics of a resulting embryo and can be ineffective in certain species. Here we developed a method using short-read whole-genome sequencing at moderately low coverage (averaging 3X and 6X) to screen diverse Malus genotypes maintained in a USDA germplasm collection for clonal seed production. In total, we sequenced 55 genotypes, 1,216 of their embryos, and identified 17 previously undescribed apomictic genotypes. Several more were detected with the flow cytometry seed screen, which helped resolve certain types of reproduction and sources of noise in low-coverage datasets. This low-pass screening-by-sequencing method is a relatively low-cost, rapid method for detecting apomictic genotypes in diverse plant germplasm and when used thoughtfully in conjunction with flow cytometry, provides a new way to visualize the genetic outcomes of sexual and asexual reproduction in plants.

Apomixis↗

PubMed2026

Quantifying niche overlap and transgression in allopolyploid hybrids: Case study of Sorbus subgenus Aria.

BACKGROUND AND AIMS: Apomixis, the formation of seeds without recombination, facilitates adaptation and persistence under environmental change. By preserving hybrid genotypes over long time periods, apomixis may conserve adaptive trait combinations from parental niche margins. We tested whether apomictic entities occupy intermediate, marginal, or transgressive niche space relative to their parents and whether differentiation is associated with ploidy. METHODS: We studied polyploid Sorbus subgenus Aria in the Franconian Jura (Germany), comprising two progenitors Sorbus aria and S. collina, seven triploid entities, and a pool of genetically heterogenous individuals (single genotypes). Genetic structure was assessed using MIG-seq. Overall niche differentiation between parental taxa and hybrids was evaluated using Sørensen similarity of two-dimensional hypervolumes derived from principal component analysis (PCA) axes. Niche shifts were further analyzed using hypervolumes based on the three strongest PCA variables. Across 762 occurrences, observations ranged from 11 to 453 individuals per entity. KEY RESULTS: Environmental niche space was transgressive in three, significantly allocated towards the margins of parental niche space in one, while remaining intermediate in the other entities. Niche transgression occurred towards milder temperatures and drier conditions. Genetic analyses confirmed morphologically defined entities, although one morphotype was polyphyletic. Tetraploid S. collina significantly occupied warmer and wetter environments compared to other cytotypes. Triploids differed from S. aria along microtopographic gradients represented by the second PCA axis. CONCLUSIONS: Apomictic Sorbus entities show diverse strategies in niche occupation and can occupy environmental niche space at and beyond the limits of their parental taxa. Apomicts may conserve evolutionary adaptations at the edges of parental niche space that may otherwise be lost from, or fail to emerge in, the parental gene pool. Over long timescales these trait combinations may re-enter the parental gene pool through introgression, thereby reintroducing adaptations critical for survival under changing conditions.

Aria↗

PubMed2026

Resolving taxonomic complexity in the genus Boechera (Brassicaceae) using the Boechera Microsatellite Website: a case study of the rare triploid B. bodiensis.

BACKGROUND AND AIMS: The genus Boechera (rock cress) comprises ∼75 sexual diploid taxa and >355 genetically distinct hybrid lineages, many of which reproduce asexually through apomixis. This complex reproductive landscape poses substantial challenges for taxonomy, similar to those encountered in genera such as Taraxacum, Hieracium, Poa and Rubus. The Boechera Microsatellite Website (BMW) offers an extensive database and analytical tools that are proving instrumental in resolving these difficulties. Here, we demonstrate the utility of the BMW through analysis of Boechera bodiensis, a rare and poorly understood species endemic to the western Great Basin of the USA. METHODS: First described as Arabis bodiensis by Rollins in 1982, this taxon is sparsely represented in herbaria and has long been considered a candidate for protection under the Endangered Species Act. However, its taxonomic identity has remained uncertain owing to morphological similarities with other 'Arabis' (Boechera) taxa. We integrate microsatellite DNA data from the BMW with morphological analyses to provide a clearer understanding of the taxonomic status, distribution and evolutionary origins of B. bodiensis. KEY RESULTS: Pollen studies reveal that B. bodiensis is a diplosporous apomict. Microsatellite genotyping of the holotype confirms it to be triploid, containing three subgenomes derived from Boechera cobrensis, B. fernaldiana and B. sparsiflora. Expanded microsatellite surveys detect this triploid genotype at 22 additional sites, primarily in Mono County, CA, USA. Morphological analyses of genetically verified specimens identify a consistent set of characters that distinguish B. bodiensis from co-occurring congeners. CONCLUSIONS: The BMW enables high-resolution analyses of genome composition, reproductive mode and hybrid origins, making it a powerful tool for resolving taxonomic complexity in Boechera. Our case study of B. bodiensis highlights the effectiveness of combining molecular and morphological data to clarify species boundaries, inform conservation assessments and refine nomenclatural understanding in this notoriously difficult genus.

Microsatellite Repeats↗

PubMed1979

Origins of polyploids.

1. Polyploidy is a conspicuous feature of chromosomal evolution in higher plants. It is common in many genera, and numerous species are characterized by diploid and polyploid races. 2. Polyploid evolution is a process not an event. 3. Polyploid may involve somatic chromsome doubling or sexual functioning of cytologically non-reduced gametes. 4. Spontaneous chromosome doubling, either in the zygote to produce a polyploid is plant or in apical meristem to produce a polyploid chimera, is a rare event. 5. The common mode of polyploidy is through the formation and sexual functioning of cytologically non-reduced gametes. Increased in chromosome number can occur in the first or later hybrid generations. 6. Polyploid via cytologically non-reduced gametes is commonly a two step process. A diploid (2n) female gamete is fertilized by a haploid (n) male gamete to produce a triploid (3x), which in turn produces cytologically non-reduced triploid (3n) female gametes that are fertilized by haploid (n) gametes of the diploid parents and result in tetraploid (4x) offspring. 7. Fertilization of a rare diploid (2n) female gamete by an equally rare diploid (2n) male gamete to directly produce a tetraploid (4x) is extremely rare but does occur. 8. Polyploidy is successful only if the new polyploids are able to complete with their parents. Success depends on availability of suitable habitals, as well as the ability to produce successful offspring. 9. The most successful polyploids combine the diploid genomes of cytogenetically allied, but differently adapted taxa. 10. Fertility is restored in polyploids through cytological diploidization of the genomes or through gametophytic apomixis. 11. Reversible tetaploidy is part of polyploid evolution.

Biological Evolution↗

PubMed2026

The twofold cost of sex reconsidered: meiotic mechanisms protect anisogamous populations from invasion by thelytoky.

Most multicellular animals practice anisogamy (fertilization between eggs and sperm). When mothers produce sons and daughters at a 1:1 ratio, the "twofold cost of males" arises because males do not directly contribute to population growth. If thelytokous parthenogens producing only daughters invade a population, they should spread rapidly. Although thelytoky has repeatedly evolved across invertebrate and vertebrate taxa, it remains a minority. Why? The evolutionary transition from anisogamy to thelytoky requires eggs to initiate embryonic development without fertilization. However, in metazoan animals, meiotic metaphase (MM) arrest halts oogenesis midway and normally resumes only after stimulation by sperm penetration. Empirical and experimental evidences indicate that release of MM arrest without fertilization is extremely difficult, providing a strong mechanistic barrier against parthenogenesis. Even if MM arrest were released, oogenesis would proceed to produce either a haploid embryo or a diploid embryo through refusion with the second polar body (terminal fusion automixis). Outbred species typically accumulate more than one lethal equivalent of recessive deleterious alleles per genome as heterozygotes. Upon transition to haploid or automictic development, these recessive lethals normally masked in outbred diploids would be exposed simultaneously, causing embryonic death and creating the next barrier. Thus, thelytoky cannot be achieved simply by modification of the existing meiotic system; instead, other mechanisms, such as apomixis, that bypass meiosis are required. Mathematical models and simulations support this "meiotic constraint" hypothesis. Combined with recently proposed immediate benefits of anisogamy and traditional genetic benefits (e.g., Red Queen), it may largely explain the maintenance of costly anisogamy.

Animals↗

PubMed2025

Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae).

Whereas genome sequencing and assembly technologies are improving, cost can still be prohibitive for plant species with large, complex genomes. As a consequence, genomics work on some taxa in evolutionarily pivotal positions in the vascular plant tree of life has been hampered. The species-rich genus Ranunculus (Ranunculaceae) is an important angiosperm group for the study of polyploidy, apomixis, and reticulate evolution. However, neither mitochondrial nor high-quality nuclear genome sequences are available. This limits phylogenomic, functional, and taxonomic analyses thus far. Here, we tested Illumina short-read, Oxford Nanopore Technology (ONT) and PacBio (HiFi) long-read, and hybrid-read assembly strategies. We sequenced the diploid progenitor species R. cassubicifolius (R. auricomus species complex) and selected the best assemblies in terms of completeness, contiguity, and quality scores. We first assembled the plastome (156 kbp, 85 genes) and mitogenome (1.18 Mbp, 40 genes) sequences using Illumina and Illumina-PacBio-hybrid strategies, respectively. We also present an updated plastome and the first mitogenome phylogeny of Ranunculaceae, including studies of gene loss (e.g., infA, ycf15, or rps) with evolutionary implications. For the nuclear genome sequence, we favored a PacBio-based assembly polished three times with filtered short reads and subsequently scaffolded into eight pseudochromosomes by chromatin conformation data (Hi-C). We obtained a haploid genome sequence of 2.69 Gbp, with 94.1% complete BUSCO genes found and 35 482 annotated genes, and inferred ancient gene duplications compared to existing Ranunculales genomes. The genomic information presented here will enable advanced evolutionary-functional analyses for the species complex, but also for the genus and beyond Ranunculaceae.

Ranunculus↗