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PubMed2026

T2T genomes of Caenorhabditis nigoni and Caenorhabditis briggsae reveals extensive loss of satellite DNA associated with self-fertilization.

The two closely related Caenorhabditis nematode species, C. nigoni and C. briggsae , are commonly used to study the evolution of reproductive modes in animals, with the self-fertile C. briggsae and outcrossing C. nigoni sharing a common ancestor ∼3.5 million years ago. Earlier genomic analyses of these species revealed genome shrinkage associated with selfing and proposed that at least some gene loss can be adaptive. However, the incomplete C. nigoni reference genome limited most comparative analyses to genic regions. Here, we leveraged long-read sequencing to generate a telomere-to-telomere (T2T) assembly for the C. nigoni strain JU1422 and the C. briggsae strain AF16. This new 139Mb C. nigoni genome resolved 57 gaps and 149 unassigned scaffolds from the previous genome assembly. Comparison with the 107Mb T2T C. briggsae genome reveals that the major driver of genome content differences are deletions to satellite DNA arrays, reflecting a loss of 9.6Mb. Interestingly, many of the differences are on the C. nigoni X chromosome, which is >13Mb larger than in the previous assembly. The transition to selfing was thus accompanied by a 37% reduction in the size of the sex chromosome compared to 16-21% shrinkage of the autosomes. We also document a surprising degree of plasticity in the ribosomal DNA, with the X chromosome harboring a second 45S rDNA array that is absent in C. briggsae . Our analysis reveals that obligatory outcrossing may play a major role in the maintenance of satellite DNA arrays.

Journal Article↗

PubMed2025

Genomic signature and evolutionary history of completely cleistogamous lineages in the non-photosynthetic orchid Gastrodia.

Despite a long-standing interest since Darwin's time, the genomic implications of obligate self-fertilization remain elusive. Complete cleistogamy-the obligate production of closed, self-pollinating flowers-represents an extreme reproductive strategy. Here, we present the genomic profiles and evolutionary history of two lineages of the mycoheterotrophic orchid Gastrodia, both of which independently acquired complete cleistogamy, based on detailed sampling and a combination of simple sequence repeat (SSR), multiplexed ISSR genotyping by sequencing (MIG-seq) and RNA-seq data. Our analysis reveals clear species delimitation, with no evidence of introgression between the completely cleistogamous species and their co-occurring allogamous sisters. Intriguingly, all analyses indicate that both the completely cleistogamous Gastrodia species and their allogamous sisters exhibit genetic profiles typical of self-pollinating plants. This pattern suggests that their ancestors, probably bearing allogamous flowers, had already evolved mechanisms to mitigate the deleterious effects of selfing, potentially facilitating the emergence of complete cleistogamy through benefits such as reproductive assurance, enhanced colonization ability and species reinforcement. Meanwhile, further analyses suggest that complete cleistogamy evolved very recently (possibly within the last 1000-2000 years) in these two Gastrodia lineages. Combined with the scant evidence of complete cleistogamy outside Gastrodia, our findings imply a limited and ephemeral role for complete cleistogamy in plant speciation.

Biological Evolution↗

PubMed2025

Inbreeding load in finite populations from dominant and overdominant mutations.

Inbreeding depression is a widespread phenomenon that reflects the burden of deleterious effects hidden in heterozygosis in non-inbred populations but exposed in homozygosis in inbred individuals, known as inbreeding load (B). This load can be due to partially or fully recessive deleterious mutations (dominance model) or to heterozygote advantage (overdominance model, where both homozygotes are deleterious relative to the heterozygote). There are many studies addressing the changes in inbreeding load in finite populations assuming the dominance model. However, the contribution of overdominance to inbreeding depression has been focused on infinite-size populations. We carried out computer simulations to investigate the joint impact of dominant and pure overdominant mutations on inbreeding load, both for self-fertilizing populations and for panmictic populations suffering from a drastic bottleneck. We found that the overdominant inbreeding load can be substantially reduced by drift even for symmetrical overdominance, at least when considering mutations of small effect. For panmictic bottlenecked populations, the reduction in inbreeding load under dominance and overdominance loci cannot be easily distinguished. However, while purging depletes inbreeding load from dominant loci, slowing inbreeding depression and leading to partial fitness recovery, for overdominant loci fitness declines monotonically.

Inbreeding↗

PubMed2026

T2T genomes of Caenorhabditis nigoni and Caenorhabditis briggsae reveal divergence in satellite DNA abundance.

The two closely related nematode species, Caenorhabditis nigoni and Caenorhabditis briggsae, are commonly used to study the evolution of reproductive modes in animals, with the self-fertile C. briggsae and outcrossing C. nigoni sharing a common ancestor ∼3.5 million years ago. Earlier genomic analyses revealed that selfing Caenorhabditis species have smaller genomes and proposed that at least some gene loss in C. briggsae is adaptive. However, the incomplete C. nigoni reference genome has limited most comparative analyses to genic regions. Here, we leverage long-read sequencing to generate and annotate telomere-to-telomere (T2T) assemblies for the C. nigoni strain JU1422 and the C. briggsae strain AF16. This new 139 Mb C. nigoni genome resolves 57 gaps and 149 unassigned scaffolds from the previous genome assembly. A major driver of the size difference with the 107 Mb T2T C. briggsae genome is the abundance of satellite DNA, which accounts for 12.8 Mb (9.2%) in C. nigoni and only 3.2 Mb (3.0%) in C. briggsae Notably, the C. nigoni X Chromosome is 13.4 Mb larger than in the previous assembly, making it 60% larger than the C. briggsae X Chromosome compared with 18%-26% difference for the autosomes. We also document a surprising degree of plasticity in the ribosomal DNA, with the C. nigoni X Chromosome harboring a second 45S rDNA array that is absent in C. briggsae The hitherto undocumented divergence in the abundance of repetitive DNA elements makes the new genomes an invaluable resource for genomic analysis.

Journal Article↗

PubMed2025

Alternative splice acceptor site in MSH4 gene is responsible for male sterility conferred by ms5 in soybean.

In soybean breeding, using the recessive male-sterile ms5 gene, derived from fast neutron mutagenesis, for recurrent selection is advantageous because of the d2 locus, which controls cotyledon color in mature seeds and can be used as a phenotypic selection marker for ms5 male sterility. However, occasional self-fertilization occurs because of the elimination of d2 linkage and instability of male sterility. Elucidating the mechanism and the gene responsible for ms5 male sterility may resolve these problems. Using fine mapping with 15 simple sequence repeat (SSR) markers, we narrowed down the candidate ms5 locus to a 54-kbp region. Bulked-DNA analysis using next-generation sequencing revealed a deletion as a candidate variation in the region. This 15-bp deletion and a nucleotide substitution were identified in intron 1 of MutS homolog (GmMSH4), which modulates chromosomal recombination in meiosis. The ms5 transcript contained a novel exon with a premature termination codon. This exon originated from an alternative splice acceptor site caused by the deletion and nucleotide substitution, disrupting gene function. Co-segregation of male sterility with five independent mutations in GmMSH4 was confirmed using progeny of mutant lines. Mutations in GmMSH4 led to biased DNA partitioning during meiosis, resulting in collapsed or enlarged pollen and suggesting that ms5 male sterility is caused by the failure of pollen formation during meiosis due to the loss of function of GmMSH4. These findings could help explain the mechanism of instability of ms5 male sterility and improve the efficiency of recurrent selection using DNA markers in soybean breeding.

Glycine max↗

PubMed2026

REVIEW: CAUSES AND CONSEQUENCES OF DOING IT WITH ONESELF-SYNTHESIS AND META-ANALYSIS OF NEODERMATAN HERMAPHRODITIC MATING SYSTEMS.

Hermaphroditic mating systems profoundly influence evolution, yet in parasitic flatworms (Neodermata) they remain strikingly understudied. For decades, sweeping claims have oscillated between pervasive selfing and near-universal outcrossing, reflecting a lack of comprehensive synthesis. This review, the first in more than 40 yr, integrates nearly a century of research, from early observational studies to modern genetic analyses, to reveal a far more nuanced picture. Our meta-analysis of population-genetic data shows a sharp departure from the bimodal selfing patterns typical of plants and other hermaphroditic animals: neodermatan parasites are strongly skewed toward outcrossing. We link variation in mating systems to parasite demography and life-history traits, especially in species exhibiting mixed mating or elevated selfing. Current evidence suggests outcrossing is common, but taxonomic and life-history gaps preclude definitive conclusions. Beyond patterns and causes, we explore evolutionary consequences ranging from fitness costs such as inbreeding depression to trait evolution, including delayed selfing, sex allocation, and complex life cycles. Evidence for inbreeding depression is mixed and limited, yet emerging approaches using selfing-rate comparisons offer promising avenues for future research. Notably, demographic constraints, such as infection intensity and life-cycle architecture, often explain mixed mating without invoking selection, challenging classical models. Similarly limited in number, studies on sex allocation indicate that hermaphroditic mating systems can shape reproductive investment, with patterns consistent with local sperm competition in some taxa. By consolidating historical observations with modern genetic insights, this review provides the most comprehensive synthesis of hermaphroditic mating systems in the Neodermata to date. We highlight critical gaps in taxonomic coverage and experimental data and point to future opportunities for integrating genomic approaches with ecological and demographic frameworks. Such integration will be essential to illuminate how mating systems shape parasite evolution and to resolve long-standing questions about the persistence of mixed mating despite theoretical expectations.

Animals↗