Phylogenetic utility of the nuclear genes AGAMOUS 1 and PHYTOCHROME B in palms (Arecaceae): an example within Bactridinae

Agro-morphological traits assessment of Tunisian male date palms (Phœnix dactylifera L.) for preservation and sustainable utilization of local germplasm

Date palm (Phœnix dactylifera L.) like other crop species in the arid Mediterranean region is being threatened by genetic erosion and climate change. Therefore, the understanding and assessment of the diversity extent of this species is a primary requisite for preserving these crop resources. This study was designed to quantify the potential of Tunisian male date palms using a set of agro-morphological characteristics i.e. flowering traits, inflorescence morphology and pollen quality. The flowering time traits exhibited a trend of precocious phenotype at emergence spathe trait and the dominance of the full-season phenotype at the opening date. At inflorescence morphology, all observed traits expressed wide ranges which reflected the broad variability of the evaluated male genotypes. Significant difference was recorded for the majority of the examined traits with a high significant variation in the tree quantitative traits: Spathe Total Length, Spathe Maximum Width and Length to the brunched part. Pollen viability ranged from 51.10% to 98.75% while the germination rate was between 0.90% and 70.50%. Our phenotypic investigation has allowed the identification of males with desirable agronomic traits which have been genotyped using 18 nuclear SSR markers and a chloroplast minisatellite for preservation and effective utilization purposes.

The plastomes of Astrocaryum aculeatum G. Mey. and A. murumuru Mart. show a flip-flop recombination between two short inverted repeats

The plastomes of Astrocaryum murumuru and A. aculeatum revealed a lineage-specific structural feature originated by flip-flop recombination, non-synonymous substitutions in conserved genes and several molecular markers. Astrocaryum murumuru Mart. and A. aculeatum G.Mey. are two palm species of Amazon forest that are economically important as source of food, oil and raw material for several applications. Genetic studies aiming to establish strategies for conservation and domestication of both species are still in the beginning given that the exploitation is mostly by extractive activity. The identification and characterization of molecular markers are essential to assess the genetic diversity of natural populations of both species. Therefore, we sequenced and characterized in detail the plastome of both species. We compared both species and identified 32 polymorphic SSR loci, 150 SNPs, 46 indels and eight hotspots of nucleotide diversity. Additionally, we reported a specific RNA editing site found in the ccsA gene, which is exclusive to A. murumuru. Moreover, the structural analysis in the plastomes of both species revealed a 4.6-kb inversion encompassing a set of genes involved in chlororespiration and plastid translation. This 4.6-kb inversion is a lineage-specific structural feature of the genus Astrocaryum originated by flip-flop recombination between two short inverted repeats. Furthermore, our phylogenetic analysis using whole plastomes of 39 Arecaceae species placed the Astrocaryum species sister to Acrocomia within the tribe Cocoseae. Finally, our data indicated substantial changes in the plastome structure and sequence of both species of the genus Astrocaryum, bringing new molecular markers, several structural and evolving features, which can be applied in several areas such as genetic, evolution, breeding, phylogeny and conservation strategies for both species.

Phylogeny, historical biogeography and diversification rates in an economically important group of Neotropical palms: Tribe Euterpeae

Tribe Euterpeae is an economically and ecologically important group of Neotropical palms (Arecaceae). Some species are hyperdominant in the Neotropics, and many constitute a good source of revenue. To reconstruct the biogeographical history and diversification of the Euterpeae, we inferred a robust dated molecular phylogenetic hypothesis including 82% of the species sequenced for five DNA regions (trnD-trnT, CISP4, WRKY6, RPB2, and PHYB). Ancestral range was estimated using all models available in BioGeoBEARS and Binary State Speciation and Extinction analysis was used to evaluate the association of biome and inflorescence type with diversification rates. All intergeneric relationships were resolved providing insight on the taxonomic controversy of Jessenia, Euterpe and Prestoea. Three widely distributed Neotropical species were non-monophyletic, inviting a revision of species circumscriptions. The Euterpeae started its diversification in the mid Eocene (40 Mya), with most species-level divergence events occurring in the last 10 million years. Four colonization events from Central to South America were inferred. Different diversification rates were associated with biomes. Lowland rainforest was inferred as the ancestral biome of Euterpeae, attesting to the importance of lowland adapted lineages on the assembly of the montane flora. The two-fold higher speciation rate for montane taxa (compared with lowland rainforest taxa) was contemporaneous to the Andean orogenic uplift. The specialized beetle pollination of Oenocarpus with its hippuriform (horsetail shape) inflorescence was not associated with diversification rates in Euterpeae.

Genetic structuring in a Neotropical palm analyzed through an Andean orogenesis-scenario

Andean orogenesis has driven the development of very high plant diversity in the Neotropics through its impact on landscape evolution and climate. The analysis of the intraspecific patterns of genetic structure in plants would permit inferring the effects of Andean uplift on the evolution and diversification of Neotropical flora. In this study, using microsatellite markers and Bayesian clustering analyses, we report the presence of four genetic clusters for the palm Oenocarpus bataua var. bataua which are located within four biogeographic regions in northwestern South America: (a) Chocó rain forest, (b) Amotape-Huancabamba Zone, (c) northwestern Amazonian rain forest, and (d) southwestern Amazonian rain forest. We hypothesize that these clusters developed following three genetic diversification events mainly promoted by Andean orogenic events. Additionally, the distinct current climate dynamics among northwestern and southwestern Amazonia may maintain the genetic diversification detected in the western Amazon basin. Genetic exchange was identified between the clusters, including across the Andes region, discarding the possibility of any cluster to diversify as a distinct intraspecific variety. We identified a hot spot of genetic diversity in the northern Peruvian Amazon around the locality of Iquitos. We also detected a decrease in diversity with distance from this area in westward and southward direction within the Amazon basin and the eastern Andean foothills. Additionally, we confirmed the existence and divergence of O. bataua var. bataua from var. oligocarpus in northern South America, possibly expanding the distributional range of the latter variety beyond eastern Venezuela, to the central and eastern Andean cordilleras of Colombia. Based on our results, we suggest that Andean orogenesis is the main driver of genetic structuring and diversification in O. bataua within northwestern South America.

Diversity of Algerian oases date palm (Phoenix dactylifera L., Arecaceae): Heterozygote excess and cryptic structure suggest farmer management had a major impact on diversity

Date palm (Phoenix dactyliferaL.) is the mainstay of oasis agriculture in the Saharan region. It is cultivated in a large part of the Mediterranean coastal area of the Sahara and in most isolated oases in the Algerian desert. We sampled 10 oases in Algeria to understand the structure of date palm diversity from the coastal area to a very isolated desert location. We used 18 microsatellite markers and a chloroplast minisatellite to characterize 414 individual palm trees corresponding to 114 named varieties. We found a significant negative inbreeding coefficient, suggesting active farmer selection for heterozygous individuals. Three distinct genetic clusters were identified, a ubiquitous set of varieties found across the different oases, and two clusters, one of which was specific to the northern area, and the other to the drier southern area of the Algerian Sahara. The ubiquitous cluster presented very striking chloroplast diversity, signing the frequency of haplotypes found in Saudi Arabia, the most eastern part of the date palm range. Exchanges of Middle Eastern and Algerian date palms are known to have occurred and could have led to the introduction of this particular chlorotype. However, Algerian nuclear diversity was not of eastern origin. Our study strongly suggests that the peculiar chloroplastic diversity of date palm is maintained by farmers and could originate from date palms introduced from the Middle East a long time ago, which since then, hasbeen strongly introgressed. This study illustrates the complex structure of date palm diversity in Algerian oases and the role of farmers in shaping such cryptic diversity.

Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan (Daemonorops jenkinsiana)

Rattan is an important group of regenerating non-wood climbing palm in tropical forests. The cirrus is an essential climbing organ and provides morphological evidence for evolutionary and taxonomic studies. However, limited data are available on the molecular mechanisms underlying the development of the cirrus. Thus, we performed in-depth transcriptomic sequencing analyses to characterize the cirrus development at different developmental stages of Daemonorops jenkinsiana. The result showed 404,875 transcripts were assembled, including 61,569 high-quality unigenes were identified, of which approximately 76.16% were annotated and classified by seven authorized databases. Moreover, a comprehensive analysis of the gene expression profiles identified differentially expressed genes (DEGs) concentrated in developmental pathways, cell wall metabolism, and hook formation between the different stages of the cirri. Among them, 37 DEGs were validated by qRT-PCR. Furthermore, 14,693 transcriptome-based microsatellites were identified. Of the 168 designed SSR primer pairs, 153 were validated and 16 pairs were utilized for the polymorphic analysis of 25 rattan accessions. These findings can be used to interpret the molecular mechanisms of cirrus development, and the developed microsatellites markers provide valuable data for assisting rattan taxonomy and expanding the understanding of genomic study in rattan.

Endemic insular and coastal Tunisian date palm genetic diversity

The breeding of crop species relies on the valorisation of ancestral or wild varieties to enrich the cultivated germplasm. The Tunisian date palm genetic patrimony is being threatened by diversity loss and global climate change. We have conducted a genetic study to evaluate the potential of spontaneous coastal resources to improve the currently exploited Tunisian date palm genetic pool. Eighteen microsatellite loci of Phoenix dactylifera L. were used to compare the genetic diversity of coastal accessions from Kerkennah, Djerba, Gabès and continental date palm accessions from Tozeur. A collection of 105 date palms from the four regions was analysed. This study has provided us with an extensive understanding of the local genetic diversity and its distribution. The coastal date palm genotypes exhibit a high and specific genetic diversity. These genotypes are certainly an untapped reservoir of agronomically important genes to improve cultivated germplasm in continental date palm.

Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations

BACKGROUND AND AIMS

Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species.

METHODS

Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite.

KEY RESULTS

Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species.

CONCLUSIONS

This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool.

Reprint of: using nuclear gene data for plant phylogenetics: progress and prospects

The paper reviews the current state of low and single copy nuclear markers that have been applied successfully in plant phylogenetics to date, and discusses case studies highlighting the potential of massively parallel high throughput or next-generation sequencing (NGS) approaches for molecular phylogenetic and evolutionary investigations. The current state, prospects and challenges of specific single- or low-copy plant nuclear markers as well as phylogenomic case studies are presented and evaluated.

A continental-wide perspective: the genepool of nuclear encoded ribosomal DNA and single-copy gene sequences in North American Boechera (Brassicaceae)

74 of the currently accepted 111 taxa of the North American genus Boechera (Brassicaceae) were subject to pyhlogenetic reconstruction and network analysis. The dataset comprised 911 accessions for which ITS sequences were analyzed. Phylogenetic analyses yielded largely unresolved trees. Together with the network analysis confirming this result this can be interpreted as an indication for multiple, independent, and rapid diversification events. Network analyses were superimposed with datasets describing i) geographical distribution, ii) taxonomy, iii) reproductive mode, and iv) distribution history based on phylogeographic evidence. Our results provide first direct evidence for enormous reticulate evolution in the entire genus and give further insights into the evolutionary history of this complex genus on a continental scale. In addition two novel single-copy gene markers, orthologues of the Arabidopsis thaliana genes At2g25920 and At3g18900, were analyzed for subsets of taxa and confirmed the findings obtained through the ITS data.