Adaptation in Unstable Environments and Global Gene Losses: Small but Stable Gene Networks by the May-Wigner Theory

Conserved genome structure and phylogenetic insights for the heterogeneous subfamily of Convallarioideae (Asparagaceae) revealed from plastome data

BACKGROUND

Convallarioideae, a subfamily of Asparagaceae, encompasses a wide range of morphologically diverse lineages previously classified under different traditional families and holds significant economic value. Despite its importance, chloroplast genome data for Convallarioideae remain limited, hindering a comprehensive understanding of their genome structural evolution and phylogenetic relationships. This study aims to provide a detailed characterization of chloroplast genome features and to conduct robust phylogenetic analyses of this subfamily using an expanded dataset of chloroplast genomes.

RESULTS

The plastomes of the subfamily exhibit a typical circular quadripartite structure with conserved genomic organization and gene content. However, variations were observed in genome size, SSRs, and codon usage across the subfamily. Nine highly variable regions and positive selection genes were identified. Phylogenetic analyses based on complete plastid genomes resolved the non-monophyly of Polygonateae. Compared to Eriospermum mackenii, the chloroplast genomes of tribe Rusceae, tribe Dracaeneae, and the Polygonatum-Disporopsis lineage showed significant size reduction.

CONCLUSIONS

Chloroplast genomes across Convallarioideae exhibit remarkable structural conservation. The phylogenetic analyses revealed weakly resolved backbone relationships among core members of this subfamily. Indels in the LSC region and gene loss were identified as key drivers of structural divergence in plastome size. These results clarify the interplay between genomic architecture and phylogenetic discordance, advancing our understanding of genomic evolution within Convallarioideae.

Chromosomal-Level Genome Suggests Adaptive Constraints Leading to the Historical Population Decline in an Extremely Endangered Plant

Increased human activity and climate change have significantly impacted wild habitats and increased the number of endangered species. Exploring evolutionary history and predicting adaptive potential using genomic data will facilitate species conservation and biodiversity recovery. Here, we examined the genome evolution of a critically endangered tree Pellacalyx yunnanensis, a plant species with extremely small populations (PSESP) that is narrowly distributed in Xishuangbanna, China. The species has neared extinction due to economic exploitation in recent decades. We assembled a chromosome-level genome of 334 Mb, with the N50 length of 20.5 Mb. Using the genome, we discovered that P. yunnanensis has undergone several population size reductions, leading to excess deleterious mutations. The species may possess low adaptive potential due to reduced genetic diversity and the loss of stress-responsive genes. We estimate that P. yunnanensis is the basal species of its genus and diverged from its relatives during global cooling, suggesting it was stranded in unsuitable environments during periods of dramatic climate change. In particular, the loss of seed dormancy leads to germination under unfavourable conditions and reproduction challenges. This dormancy loss may have occurred through genetic changes that suppress ABA signalling and the loss of genes involved in seed maturation. The high-quality genome has also enabled us to reveal phenotypic trait evolution in Rhizophoraceae and identify divergent adaptation to intertidal and inland habitats. In summary, our study elucidates mechanisms underlying the decline and evaluates the adaptive potential of P. yunnanensis to future climate change, informing future conservation efforts.

Genome-Wide Investigation of MADS-Box Genes in Flower Development and Environmental Acclimation of Lumnitzera littorea (Jack) Voigt

Lumnitzera littorea (Jack) Voigt is an endangered mangrove species in China. Low fecundity and environmental pressure are supposed to be key factors limiting the population expansion of L. littorea. Transcription factors with the MADS-box domain are crucial regulators of plant flower development, reproduction, and stress response. In this study, we performed a comprehensive investigation into the features and functions of MADS-box genes of L. littorea. Sixty-three LlMADS genes with similar structure and motif composition were identified in the L. littorea genome, and these genes were unevenly distributed on the 11 chromosomes. Segmental duplication was suggested to make a main contribution to the expansion of the LlMADS gene family. Some LIMADS genes exhibited differential expression in different flower types or in response to cold stress. Overexpression of the B-class gene LlMADS37 had substantial effects on the flower morphology and flowering time of transgenic Arabidopsis plants, demonstrating its key role in regulating flower morphogenesis and inflorescence. These findings largely enrich our understanding of the functional importance of MADS-box genes in the inflorescence and stress acclimation of L. littorea and provide valuable resources for future genetic research to improve the conservation of this species.

Plant reproduction: Mangroves use 'child-care' in extreme environments

Using population genomics and molecular biological methods, a recent study reveals the molecular mechanisms of vivipary in mangroves, a term designating all woody plants of the tropical intertidal zones.