Exploring the Influence of Date Palm Cultivars on Soil Microbiota.

Plants thrive in diverse environments, where root-microbe interactions play a pivotal role. Date palm (Phoenix dactylifera L.), with its genetic diversity and resilience, is an ideal model for studying microbial adaptation to different genotypes and stresses. This study aimed to analyze the bacterial and fungal communities associated with traditional date palm cultivars and the widely cultivated "Deglet Nour" were explored using metabarcoding approaches. The microbial diversity analysis identified a rich community with 13,189 bacterial and 6442 fungal Amplicon Sequence Variants (ASVs). Actinobacteriota, Proteobacteria, and Bacteroidota dominated bacterial communities, while Ascomycota dominated fungal communities. Analysis of the microbial community revealed the emergence of two distinct clusters correlating with specific date palm cultivars, but fungal communities showed higher sensitivity to date palm genotype variations compared to bacterial communities. The commercial cultivar "Deglet Nour" exhibited a unique microbial composition enriched in pathogenic fungal taxa, which was correlated with its genetic distance. Overall, our study contributes to understanding the complex interactions between date palm genotypes and soil microbiota, highlighting the genotype role in microbial community structure, particularly among fungi. These findings suggest correlations between date palm genotype, stress tolerance, and microbial assembly, with implications for plant health and resilience. Further research is needed to elucidate genotype-specific microbial interactions and their role in enhancing plant resilience to environmental stresses.

The de novo, chromosome-level genome assembly of the sweet chestnut (Castanea sativa Mill.) Cv. Marrone Di Chiusa Pesio.

OBJECTIVES: The sweet chestnut Castanea sativa Mill. is the only native Castanea species in Europe, and it is a tree of high economic value that provides appreciated fruits and valuable wood. In this study, we assembled a high-quality nuclear genome of the ancient Italian chestnut variety 'Marrone di Chiusa Pesio' using a combination of Oxford Nanopore Technologies long reads, whole-genome and Omni-C Illumina short reads. DATA DESCRIPTION: The genome was assembled into 238 scaffolds with an N50 size of 21.8 Mb and an N80 size of 7.1 Mb for a total assembled sequence of 750 Mb. The BUSCO assessment revealed that 98.6% of the genome matched the embryophyte dataset, highlighting good completeness of the genetic space. After chromosome-level scaffolding, 12 chromosomes with a total length of 715.8 and 713.0 Mb were constructed for haplotype 1 and haplotype 2, respectively. The repetitive elements represented 37.3% and 37.4% of the total assembled genome in haplotype 1 and haplotype 2, respectively. A total of 57,653 and 58,146 genes were predicted in the two haplotypes, and approximately 73% of the genes were functionally annotated using the EggNOG-mapper. The assembled genome will be a valuable resource and reference for future chestnut breeding and genetic improvement.

Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships.

BACKGROUND: Date palm (Phoenix dactylifera L.) is the most widespread crop in arid and semi-arid regions and has great traditional and socioeconomic importance, with its fruit well-known for its high nutritional and health value. However, the genetic variation of date palm cultivars is often neglected. The advent of high-throughput sequencing has made possible the resequencing of whole organelle (mitochondria and chloroplast) genomes to explore the genetic diversity and phylogenetic relationships of cultivated plants with unprecedented detail. RESULTS: Whole organelle genomes of 171 Tunisian accessions (135 females and 36 males) were sequenced. Targeted bioinformatics pipelines were used to identify date palm haplotypes and genome variants, aiming to provide variant annotation and investigate patterns of evolutionary relationship. Our results revealed the existence of unique haplotypes, identified by 45 chloroplastic and 156 mitochondrial SNPs. Estimation of the effect of these SNPs on genes functions was predicted in silico. CONCLUSIONS: The results of this study have important implications, in the light of ongoing environmental changes, for the conservation and sustainable use of the genetic resources of date palm cultivars in Tunisia, where monoculture threatens biodiversity leading to genetic erosion. These data will be useful for breeding and genetic improvement programs of the date palm through selective cross-breeding.

Mock community experiments can inform on the reliability of eDNA metabarcoding data: a case study on marine phytoplankton.

Environmental DNA metabarcoding is increasingly implemented in biodiversity monitoring, including phytoplankton studies. Using 21 mock communities composed of seven unicellular diatom and dinoflagellate algae, assembled with different composition and abundance by controlling the number of cells, we tested the accuracy of an eDNA metabarcoding protocol in reconstructing patterns of alpha and beta diversity. This approach allowed us to directly evaluate both qualitative and quantitative metabarcoding estimates. Our results showed non-negligible rates (17-25%) of false negatives (i.e., failure to detect a taxon in a community where it was included), for three taxa. This led to a statistically significant underestimation of metabarcoding-derived alpha diversity (Wilcoxon p = 0.02), with the detected species richness being lower than expected (based on cell numbers) in 8/21 mock communities. Considering beta diversity, the correlation between metabarcoding-derived and expected community dissimilarities was significant but not strong (R2 = 0.41), indicating suboptimal accuracy of metabarcoding results. Average biovolume and rDNA gene copy number were estimated for the seven taxa, highlighting a potential, though not exhaustive, role of the latter in explaining the recorded biases. Our findings highlight the importance of mock communities for assessing the reliability of phytoplankton eDNA metabarcoding studies and identifying their limitations.

First genome-wide data from Italian European beech (Fagus sylvatica L.): Strong and ancient differentiation between Alps and Apennines.

The European beech (Fagus sylvatica L.) is one of the most widespread forest trees in Europe whose distribution and intraspecific diversity has been largely shaped by repeated glacial cycles. Previous studies, mainly based on palaeobotanical evidence and a limited set of chloroplast and nuclear genetic markers, highlighted a complex phylogeographic scenario, with southern and western Europe characterized by a rather heterogeneous genetic structure, as a result of recolonization from different glacial refugia. Despite its ecological and economic importance, the genome of this broad-leaved tree has only recently been assembled, and its intra-species genomic diversity is still largely unexplored. Here, we performed whole-genome resequencing of nine Italian beech individuals sampled from two stands located in the Alpine and Apennine mountain ranges. We investigated patterns of genetic diversity at chloroplast, mitochondrial and nuclear genomes and we used chloroplast genomes to reconstruct a temporally-resolved phylogeny. Results allowed us to test European beech differentiation on a whole-genome level and to accurately date their divergence time. Our results showed comparable, relatively high levels of genomic diversity in the two populations and highlighted a clear differentiation at chloroplast, mitochondrial and nuclear genomes. The molecular clock analysis indicated an ancient split between the Alpine and Apennine populations, occurred between the Günz and the Riss glaciations (approximately 660 kyrs ago), suggesting a long history of separation for the two gene pools. This information has important conservation implications in the context of adaptation to ongoing climate changes.

A validated protocol for eDNA-based monitoring of within-species genetic diversity in a pond-breeding amphibian.

In light of the dramatic decline in amphibian biodiversity, new cost-efficient tools to rapidly monitor species abundance and population genetic diversity in space and time are urgently needed. It has been amply demonstrated that the use of environmental DNA (eDNA) for single-species detection and characterization of community composition can increase the precision of amphibian monitoring compared to traditional (observational) approaches. However, it has been suggested that the efficiency and accuracy of the eDNA approach could be further improved by more timely sampling; in addition, the quality of genetic diversity data derived from the same DNA has been confirmed in other vertebrate taxa, but not amphibians. Given the availability of previous tissue-based genetic data, here we use the common frog Rana temporaria Linnaeus, 1758 as our target species and an improved eDNA protocol to: (i) investigate differences in species detection between three developmental stages in various freshwater environments; and (ii) study the diversity of mitochondrial DNA (mtDNA) haplotypes detected in eDNA (water) samples, by amplifying a specific fragment of the COI gene (331 base pairs, bp) commonly used as a barcode. Our protocol proved to be a reliable tool for monitoring population genetic diversity of this species, and could be a valuable addition to amphibian conservation and wetland management.

Deciphering the drivers of negative species-genetic diversity correlation in Alpine amphibians.

The evolutionary and ecological importance of neutral and adaptive genetic diversity is widely recognized. Nevertheless, genetic diversity is rarely assessed for conservation planning, which often implicitly assumes a positive correlation between species and genetic diversity. Multiple drivers can cause the co-variation between the genetic diversity of one species and the richness of the whole communities, and explicit tests are needed to identify the processes that can determine species-genetic diversity correlations (SGDCs). Here, we tested whether intrapopulation genetic diversity (at neutral loci) and species richness co-vary in the amphibian communities of a southern Alpine region (Trentino, Italy), using the common frog (Rana temporaria) as focal species for the study of genetic diversity. We also analysed ecological similarity, niche overlap and interspecific interactions between the species, to unravel the processes determining SGDC. The neutral genetic diversity of common frogs was negatively related to species richness. The negative SGDC was probably due to an opposite influence of environmental gradients on the two levels of biodiversity, since the focal species and the other amphibians differ in ecological preferences, particularly in terms of thermal optimum. Conversely, we did not find evidence for a role of interspecific interactions in the negative SGDC. Our findings stress that species richness cannot be used as a universal proxy for genetic diversity, and only combining SGDC with analyses on the determinants of biodiversity can allow to identify the processes determining the relationships between genetic and species diversity.