Phenotypic diversity assessment within a major ex situ collection of wild endemic coffees in Madagascar

Reprogramming of Metabolome and Transcriptome Shaped the Elevational Adaptation of Quercus variabilis by Regulating Leaf Functional Traits

Exploring how plants adapt to environmental changes is key to plant survive and protection under accelerating climate change. Quercus variabilis is widely distributed in China with high economic and ecological value, yet its elevational adaptation mechanism remains unclear. Here, we investigated the leaf functional traits, metabolome and transcriptome of Q. variabilis along an elevational gradient (800-1400 m) in Mt. Li, China. Results showed that leaves at higher elevations became smaller, narrower, thicker, with smaller and denser stomata, and maintained higher levels of nitrogen, soluble sugar, total phenol, lignin and soluble sugar-to-starch ratio. With increasing elevation, Q. variabilis underwent a metabolic shift from being dominated by primary metabolism to secondary metabolism, and 1300 m could be identified as the transition point. Particularly, phenylpropanoid metabolism and its metabolites (flavonoids and phenolic acids) played crucial roles in its adaptation to elevations. Moreover, 24 hub transcription factors (TFs) were screened through WGCNA and verified by RT-qPCR. Environmental factors not only directly influenced leaf functional traits, but also affected metabolite accumulation through TF-mediated gene expression, which in turn influenced leaf functional traits. This study highlights that integrating plant functional traits, metabolome and transcriptome simultaneously provides novel insights into the mechanisms for shaping plants' adaptability.

The evolutionary history of three Baracoffea species from western Madagascar revealed by chloroplast and nuclear genomes

The wild species of the Coffea genus present a very wide morphological, genetic, and biochemical diversity. Wild species are recognized more resistant to diseases, pests, and environmental variations than the two species currently cultivated worldwide: C. arabica (Arabica) and C. canephora (Robusta). Consequently, wild species are now considered as a crucial resource for adapting cultivated coffee trees to climate change. Within the Coffea genus, 79 wild species are native to the Indian Ocean islands of Comoros, Mayotte, Mauritius, Réunion and Madagascar, out of a total of 141 taxa worldwide. Among them, a group of 9 species called "Baracoffea" are particularly atypical in their morphology and adaptation to the sandy soils of the dry deciduous forests of western Madagascar. Here, we have attempted to shed light on the evolutionary history of three Baracoffea species: C. ambongensis, C. boinensis and C. bissetiae by analyzing their chloroplast and nuclear genomes. We assembled the complete chloroplast genomes de novo and extracted 28,800 SNP (Single Nucleotide Polymorphism) markers from the nuclear genomes. These data were used for phylogenetic analysis of Baracoffea with Coffea species from Madagascar and Africa. Our new data support the monophyletic origin of Baracoffea within the Coffea of Madagascar, but also reveal a divergence with a sister clade of four species: C. augagneurii, C. ratsimamangae, C. pervilleana and C. Mcphersonii (also called C. vohemarensis), belonging to the Subterminal botanical series and living in dry or humid forests of northern Madagascar. Based on a bioclimatic analysis, our work suggests that Baracoffea may have diverged from a group of Malagasy Coffea from northern Madagascar and adapted to the specific dry climate and low rainfall of western Madagascar. The genomic data generated in the course of this work will contribute to the understanding of the adaptation mechanisms of these particularly singular species.