bims-plasge 2025-03-23 papers

Issue of 2025–03–23
two papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

BMC Plant Biol. 2025 Mar 18. 25(1): 353

Genomic variation and evolutionary patterns in organelle genomes between annual and perennial Glycine species.

Xuchen Yang, Jiaxian He, Minghui Zhou, Changwei Bi, Jiali Kong, Jie Wang, Fanjiang Kong, Zhiqiang Wu, Zefu Wang, Meina Li.

BACKGROUND: The complexity of structural variations and long stretches of repetitive DNA make the analysis of plant mitochondrial genomes (mitogenomes) exceptionally challenging. A thorough investigation of plant mitogenomes is essential for uncovering the evolutionary processes of plant organelles and optimizing traits related to plant cellular metabolism. The genus Glycine includes groups with both perennial and annual life strategies, making it an ideal subject for studying the complexity and variations of plant mitogenomes during evolution across different life strategies.
RESULTS: Here, we assembled 20 complete mitochondrial and plastid genomes of Glycine accessions, including both annual and perennial species using the latest organelle genome assembly tool. Significant structural variations and differences in tRNA content were observed in the mitogenomes between the two life-history strategy subgenera, while protein-coding genes and rRNAs content were highly conserved. Distinct patterns of nuclear plastid DNAs and nuclear mitochondrial DNAs (NUPTs/NUMTs) were uncovered among annual and perennial species. Genes residing in NUMTs (NUMGs) showed a substantial presence in Glycine accessions, with annual soybeans exhibiting a higher proportion of protein-coding genes fully integrated into the nuclear genome. Phylogenetic analysis indicated a closely related evolutionary trajectory between mitochondrial and nuclear genomes in Glycine, providing supplementary evidence relevant to the evolutionary history of Glycine.
CONCLUSIONS: This study showed the structural variations and evolutionary patterns of mitochondrial genomes between annual and perennial Glycine species. These findings contribute to our understanding of plant organelle complexity, variation and history of intracellular genomic integration.

Keywords: Glycine ; Intracellular transfer; Mitochondrion; Plastid

DOI: https://doi.org/10.1186/s12870-025-06312-4

Nat Commun. 2025 Mar 18. 16(1): 2655

Genomic structural variation in an alpha/beta hydrolase triggers hybrid necrosis in wheat.

Hybrid necrosis, a century-old mystery in wheat, is caused by complementary genes Ne1 and Ne2. Ne2, encoding a nucleotide-binding leucine-rich repeat (NLR) immune receptor, has been cloned, yet Ne1 remains elusive. Here, we report that Ne1, which encodes an alpha/beta hydrolase (ABH) protein generated by structural variation, triggers hybrid necrosis with Ne2 by activating autoimmune responses. We further verify that not only allelic variation but also copy number variation (CNV) of Ne1 are pivotal for hybrid necrosis diversity in wheat. Ne1 likely originates from wild emmer wheat, potentially through duplication and ectopic recombination events. Unlike Ne2, which is frequently selected for rust resistance in wheat breeding, the lower prevalence of Ne1 in modern wheat cultivars is attributed to its association with hybrid necrosis. Altogether, these findings illuminate the co-evolution of the NLR/ABH gene pair in plant development and innate immunity, offering potential benefits for wheat breeding.

DOI: https://doi.org/10.1038/s41467-025-57750-5