Terrestrial plants benefit from many well-understood mutualistic relationships with root- and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the seagrasses Zostera marina and Zostera japonica collected from mixed beds in Netarts Bay, OR, United States. The phylogenetic composition of leaf-, root-, and water column-associated bacterial communities were strikingly different, but these communities were not significantly different between plant species. Many taxa present on leaves were related to organisms capable of consuming the common plant metabolic waste product methanol, and of producing agarases, which can limit the growth of epiphytic algae. Taxa present on roots were related to organisms capable of oxidizing toxic sulfur compounds and of fixing nitrogen. Metatranscriptomic sequencing identified expression of genes involved in all of these microbial metabolic processes at levels greater than typical water column bacterioplankton, and also identified expression of genes involved in denitrification and in bacterial synthesis of the plant growth hormone indole-3-acetate. These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe–plant mutualisms support the health and growth of aquatic plants.

Severe drought conditions and extreme weather events are increasing worldwide with climate change, threatening the persistence of native plant communities and ecosystems. Many studies have investigated the genomic basis of plant responses to drought. However, the extent of this research throughout the plant kingdom is unclear, particularly among species critical for the sustainability of natural ecosystems. This study aimed to broaden our understanding of genome-to-phenome (G2P) connections in drought-stressed plants and identify focal taxa for future research. Bioinformatics pipelines were developed to mine and link information from databases and abstracts from 7730 publications. This approach identified 1634 genes involved in drought responses among 497 plant taxa. Most (83.30%) of these species have been classified for human use, and most G2P interactions have been described within model organisms or crop species. Our analysis identifies several gaps in G2P research literature and database connectivity, with 21% of abstracts being linked to gene and taxonomy data in NCBI. Abstract text mining was more successful at identifying potential G2P pathways, with 34% of abstracts containing gene, taxa, and phenotype information. Expanding G2P studies to include non-model plants, especially those that are adapted to drought stress, will help advance our understanding of drought responsive G2P pathways.

There is a gap in the conceptual framework linking genes to phenotypes (G2P) for non-model organisms, as most non-model organisms do not yet have genomic resources readily available. To address this, researchers often perform literature reviews to understand G2P linkages by curating a list of likely gene candidates, hinging upon other studies already conducted in closely related systems. Sifting through hundreds to thousands of articles is a cumbersome task that slows down the scientific process and may introduce bias into a study. To fill this gap, we created G2PMineR, a free and open source literature mining tool developed specifically for G2P research. This R package uses automation to make the G2P review process efficient and unbiased, while also generating hypothesized associations between genes and phenotypes within a taxonomical framework. We applied the package to a literature review for drought-tolerance in plants. The analysis provides biologically meaningful results within the known framework of drought tolerance in plants. Overall, the package is useful for conducting literature reviews for genome to phenome projects, and also has broad appeal to scientists investigating a wide range of study systems as it can conduct analyses under the auspices of three different kingdoms (Plantae, Animalia, and Fungi).

Hybridization and adaptive introgression are increasingly recognized as important components of how natural selection shapes plant speciation and ecological diversification, yet their roles in tropical clades remain poorly understood. We investigated these processes in Pandanus Parkinson (Pandanaceae), a palaeotropical tree genus of high ecological significance and the tenth-most diverse tree genus worldwide. Although morphological evidence suggested hybridization across the Indian Ocean, its genomic basis remained untested. Using 398 total samples (331 nuclear ones for Pandanus), we assessed hybridization and adaptive phenotypes by: (i) testing for broad and morphology-specific transoceanic gene flow through genome-wide conflict, gene conflict, and admixture analyses from Angiosperms353 data; (ii) evaluating whether gene flow occurred via long-distance dispersal or through a bridge clade; and (iii) testing directly and indirectly for adaptive introgression. We found strong, statistically significant evidence of bidirectional transoceanic gene flow, with nuclear clade Ba acting as a critical genetic and biogeographical bridge between Asian and Afro-Malagasy lineages. Contrary to predictions, the striking morphological similarity between geographically disjunct "swamp" lineages reflects convergent evolution rather than shared introgressive history, likely shaped by distinct macroclimatic regimes. Support for adaptive introgression in the bridge clade rested on a consilience of independent evidence: inferred chloroplast capture, differential purifying selection on plastome clades, correlated distribution of a novel foliar water-storage trait, and ecological niche overlap, all coinciding with Miocene forest contraction, Tethys Sea closure, and increasing climatic seasonality. These results highlight hybridization's central role in shaping tropical tree diversity and facilitating ecological adaptation under environmental change.