bims-plasge 2025-08-03 papers

Issue of 2025–08–03
four papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Proc Natl Acad Sci U S A. 2025 Aug 05. 122(31): e2410943122

A trans-species cytoplasmic polymorphism is associated with seed shape and aridity across multiple species of sunflowers.

Gregory L Owens, Zhe Cai, Natalia Bercovich, Marco Todesco, Julie A Lee-Yaw, Loren H Rieseberg.

The cytoplasmic genomes of plants and animals often fail to track species boundaries. However, the mechanisms responsible for such patterns are poorly understood, in part because few studies have linked cytoplasmic variation to phenotypic traits or environmental differences. Here, we use 1,554 previously published and 185 new whole genome sequences representing 14 taxa from the sunflower genus Helianthus, 91 phenotypic traits measured in common gardens, and 39 environmental variables to test for environmental and phenotypic effects of cytoplasmic genome variation. In agreement with previous work, two distinct chloroplast clades were found across multiple species and the sharing of chloroplast clades between species was mainly due to repeated introgression rather than incomplete lineage sorting. Two mitochondrial clades were also found that matched the chloroplast clades for 98% of individuals, implying predominantly maternal inheritance of both genomes. Cytoplasmic clade was associated with differences in seed shape across several species, and likely with aridity, suggestive of a role in local adaptation. Conversely, we failed to find any credible cytonuclear interactions based on associations between chloroplast and nuclear variation. Taken together, this work suggests that cytoplasmic genomes in annual sunflowers represent a trans-species balanced polymorphism that is likely maintained by adaptation to different environments. More broadly, our results corroborate the syngameon concept, showing how introgression across even very strong reproductive barriers can facilitate environmental adaptation across a species complex.

Keywords: cytoplasmic genomes; introgression; local adaptation; sunflower; trans-species polymorphism

DOI: https://doi.org/10.1073/pnas.2410943122

Plant Physiol Biochem. 2025 Jul 18. pii: S0981-9428(25)00796-X. [Epub ahead of print]228 110268

Transcriptome mapping of unfertilized pea flowers under high temperature: insights into gene regulatory networks genomics resources.

Chanderkant Chaudhary, Meenakshi Kanwar, Parul Sirohi, Kumar Ankit Anand, Sohini Barua, Jaswinder Singh, Harsh Chauhan.

Heat stress is the most significant environmental constraint on pea production, and heat tolerance mechanisms are mediated through a variety of pathways. Pea (Pisum sativum L.) cultivar Arka Chaitra (AC) is considered a heat tolerant variety, whereas cultivar Matar Ageta (MA) is heat sensitive. Transcriptome profiling of two pea cultivars, AC and MA, was conducted under control and heat stress (HS) conditions to elucidate the molecular mechanisms and identify genes associated with heat tolerance. In this study, we initially reported the repertoire of morpho-physiological traits namely pod number (PNP), weight of pods (PW), seed number/pod (SNP) and weight of seed/pod (SW) during HS conditions in AC and MA. Subsequently, Pollen viability assay was performed to further examine the pollen behavior under HS. Morpho-physiological analysis revealed that cultivar AC exhibited greater number of pods and seeds, as well as higher pod and seed weights, compared to MA under HS. Furthermore, pollen viability in cultivar AC was reduced by 23 %, whereas in cultivar MA, it was reduced by 41 %, indicating that AC exhibits robust tolerance mechanisms under HS conditions. Based on these observations, we delve deeper to investigate the regulatory mechanisms by profiling the transcriptomes of cultivars AC and MA using RNA Sequencing (RNA-Seq) under HS. We selected a subset of genes, including heat shock transcription factors, and heat shock proteins involved in heat resilience, to validate the RNA-Seq expression patterns using quantitative RT-PCR, which revealed higher expression levels in AC compared to MA. Furthermore, gene ontology (GO) analysis of the identified DEGs revealed significant enrichment of GO terms associated with pollen and flower development, heat stress proteins, and plastid development in the tolerant variety, whereas, the susceptible variety was enriched with GO terms related to cell morphogenesis, cell growth, and cell wall biogenesis. These findings provide in-depth analysis of genes and pathways contributing to thermotolerance in pea cultivars AC and MA.

Keywords: Gene regulatory networks; Pea pollen development; RNA-Sequencing; Thermotolerance

DOI: https://doi.org/10.1016/j.plaphy.2025.110268

Heredity (Edinb). 2025 Aug;134(8): 512-518

Both maternal and paternal genotypes modulate Wolbachia-induced cytoplasmic incompatibility in graham bean beetles.

Yuko Numajiri, Natsuko I Kondo, Yukihiko Toquenaga, Daisuke Kageyama.

Cytoplasmic incompatibility (CI) is a phenomenon where embryonic development is disrupted-often leading to complete failure-when the female parent lacks the symbiont strain carried by the male parent. This mechanism, employed by maternally transmitted symbionts such as Wolbachia, facilitates their rapid spread within a host population. CI has significant potential as a tool for achieving population replacement or suppression, particularly targeting disease vectors and agricultural pests. While complete expression of CI is ideal for such applications, its intensity can vary. Despite extensive research on the symbiont genotypes, the influence of host genetic background on CI expression remains poorly understood. Here, we found that in the bean beetle Callosobruchus analis, the Wolbachia strain wCana2 induces weak CI in its native nuclear background but strong CI in a previously unassociated nuclear background. Crossing experiments reveal that the nuclear backgrounds of both male and female parents can significantly affect CI expression independent of Wolbachia titres in C. analis. These findings uncover novel perspectives on the host-symbiont interactions underlying CI and highlight the complexities to be addressed for its practical application.

DOI: https://doi.org/10.1038/s41437-025-00787-5

Nat Genet. 2025 Jul 30.

Pangenome analysis provides insights into legume evolution and breeding.

Longfei Wang, Xinyu Jiang, Wu Jiao, Junrong Mao, Wenxue Ye, Yangrong Cao, Qingshan Chen, Qingxin Song.

Grain legumes hold great promise for advancing sustainable agriculture. Although the evolutionary history of legume species has been investigated, the conserved mechanisms that drive adaptive evolution and govern agronomic improvement remain elusive. Here we present high-quality genome assemblies for nine widely consumed pulses, including common bean, chickpea, pea, lentil, faba bean, pigeon pea, cowpea, mung bean and hyacinth bean. Pangenome analysis reveals the expansion of distinct gene sets in cool-season and warm-season legumes, highlighting the role of gene birth and duplication in the autoregulation of nodulation. Notably, hundreds of genes undergo convergent selection during the evolution of legumes, affecting agronomic traits such as seed weight. In addition, we demonstrate that tandem amplification of transposable elements in gene-depleted regions has a crucial role in driving genome enlargement and the formation of regulatory elements in cool-season legumes. Our results provide insights into the molecular mechanisms underlying the diversification of legumes and represent a valuable resource for facilitating legume breeding.

DOI: https://doi.org/10.1038/s41588-025-02280-5