Search

Marupa (Simarouba amara Aublet 1775) is a tropical tree of the family Simaroubaceae. It is commonly used for its wood in the Amazonian forest, and it is an important species for restoring degraded environments. Yet, very little genetic resources are available to study this plant. In this paper, we sequenced for the first time the complete chloroplast genome of Marupa, using Oxford Nanopore long‐read technology. The genome is 159,838 bp, includes 131 genes in total and presents a classic quadripartite structure. Its length and structure are similar to those of sister species of the Simaroubaceae family. A maximum likelihood phylogeny of the order Sapindale reveals that Simarouba amara is well positioned in its family. This complete plastome is a first step towards a better analysis of Marupa future evolution. [ABSTRACT FROM AUTHOR]

Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programmes. To this end, landscape genomics is a useful approach for assessing putative adaptations to future climatic conditions, especially in long‐lived species such as trees. We conducted a population genomics study of 207 Coffea canephora trees from seven forests along different climate gradients in Uganda. For this, we sequenced 323 candidate genes involved in key metabolic and defence pathways in coffee. Seventy‐one single nucleotide polymorphisms (SNPs) were found to be significantly associated with bioclimatic variables, and were thereby considered as putatively adaptive loci. These SNPs were linked to key candidate genes, including transcription factors, like DREB‐like and MYB family genes controlling plant responses to abiotic stresses, as well as other genes of organoleptic interest, such as the DXMT gene involved in caffeine biosynthesis and a putative pest repellent. These climate‐associated genetic markers were used to compute genetic offsets, predicting population responses to future climatic conditions based on local climate change forecasts. Using these measures of maladaptation to future conditions, substantial levels of genetic differentiation between present and future diversity were estimated for all populations and scenarios considered. The populations from the forests Zoka and Budongo, in the northernmost zone of Uganda, appeared to have the lowest genetic offsets under all predicted climate change patterns, while populations from Kalangala and Mabira, in the Lake Victoria region, exhibited the highest genetic offsets. The potential of these findings in terms of ex situ conservation strategies are discussed. [ABSTRACT FROM AUTHOR]

Local people's perceptions of cultivated and wild agrobiodiversity, as well as their management of hybridization are still understudied in Amazonia. Here we analyze domesticated treegourd ( Crescentia cujete), whose versatile fruits have technological, symbolic, and medicinal uses. A wild relative ( C. amazonica) of the cultivated species grows spontaneously in Amazonian flooded forests. We demonstrated, using whole chloroplast sequences and nuclear microsatellites, that the two species are strongly differentiated. Nonetheless, they hybridize readily throughout Amazonia and the proportions of admixture correlate with fruit size variation of cultivated trees. New morphotypes arise from hybridization, which are recognized by people and named as local varieties. Small hybrid fruits are used to make the important symbolic rattle ( maracá), suggesting that management of hybrid trees is an ancient human practice in Amazonia. Effective conservation of Amazonian agrobiodiversity needs to incorporate this interaction between wild and cultivated populations that is managed by smallholder families. Beyond treegourd, our study clearly shows that hybridization plays an important role in tree crop phenotypic diversification and that the integration of molecular analyses and farmers' perceptions of diversity help disentangle crop domestication history. [ABSTRACT FROM AUTHOR]

Uncovering genomic regions involved in adaption is a major goal in evolutionary biology. High-throughput sequencing now makes it possible to tackle this challenge in nonmodel species. Yet, despite the increasing number of methods targeted to specifically detect genomic footprints of selection, the complex demography of natural populations often causes high rates of false positive in gene discoveries. The aim of this study was to identify climate adaptations in wild pearl millet populations, Cenchrus americanus ssp. monodii. We focused on two climate gradients, one in Mali and one in Niger. We used a two-step strategy to limit false-positive outliers. First, we considered gradients as biological replicates and performed RNA sequencing of four populations at the extremities. We combined four methods-three based on differentiation among populations and one based on diversity patterns within populations-to identify outlier SNPs from a set of 87 218 high-quality SNPs. Among 11 155 contigs of pearl millet reference transcriptome, 540 exhibited selection signals as evidenced by at least one of the four methods. In a second step, we genotyped 762 samples in 11 additional populations distributed along the gradients using SNPs from the detected contigs and random SNPs as control. We further assessed selection on this large data set using a differentiation-based method and a method based on correlations with environmental variables based. Four contigs displayed consistent signatures between the four extreme and 11 additional populations, two of which were linked to abiotic and biotic stress responses. [ABSTRACT FROM AUTHOR]

Aim The subduction of the Nazca Plate and the eastward propagation of the Andean orogenic wedge in western Amazonia caused the formation of arches or ridges that have influenced the modern configuration of the upper Amazon drainage and the diversification of biota. We used a lineage of 15 palm species ( Astrocaryum sect. Huicungo, Arecaceae) to test two biogeographical hypotheses for lowland plants: (1) that vicariance resulted from tectonically mediated geographical barriers (population contraction), and (2) that recurrent dispersal events (population expansion) produced geographical isolation and subsequent speciation. Location Rain forests of South America. Methods A total of 78 palm individuals were collected in the field, from which five chloroplast and two nuclear DNA fragments were sequenced. We reconstructed a Bayesian dated phylogeny and inferred the demographic history. We used a Bayesian phylogeographical spatial diffusion approach to propose a model of colonization. Results We found a phylogeographical break at c. 5° S between two main clades with crown ages of c. 6.7 and 7.3 Ma located in the Fitzcarrald Arch ( FA) and the subsiding northern Amazonian foreland basin ( NAFB), respectively. These diversification times were close to the emergence of the FA in the late Miocene, and the coeval development of the transcontinental modern drainage and sedimentation plain of the NAFB. As expected for the recurrent-dispersal hypothesis, lineage delimitations were spatially inconsistent with the location of rivers or ridges, and we found some evidence of past ancestral population expansion supported particularly by the chloroplast sequences. Main conclusions Our results support the biogeographical scenario whereby recurrent dispersal into western Amazonia produced spatial isolation of populations, followed by speciation within two areas of contrasting geological activity: tectonic uplift in the FA versus subsidence in the NAFB. We did not test and cannot rule out ecological speciation within western Amazonia or at finer spatial scales. [ABSTRACT FROM AUTHOR]

Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living member of the sister group to all other extant angiosperms, is endemic to New Caledonia. We addressed the intraspecific phylogeography of Amborella by investigating whether its present population genetic structure could be related to its current and past habitats. We found moderate range-wide genetic diversity based on nuclear microsatellite data and detected four well-differentiated, geographically distinct genetic groups using Bayesian clustering analyses. We modelled the ecological niche of Amborella based on the current climatic and environmental conditions. The predictive ability of the model was very good throughout the Central East mainland zone, but Amborella was predicted in the northern part of the island where this plant has not been reported. Furthermore, no significant barrier was detected based on habitat suitability that could explain the genetic differentiation across the area. Conversely, we found that the main genetic clusters could be related to the distribution of the suitable habitat at the last glacial maximum ( LGM, c. 21 000 years BP), when Amborella experienced a dramatic 96.5% reduction in suitable area. At least two lineages survived in distinct putative refugia located in the Massif des Lèvres and in the vicinity of Mount Aoupinié. Our findings finally confirmed the importance of LGM rainforest refugia in shaping the current intra- and interspecific diversity in New Caledonian plants and revealed the possibility of an as yet unreported refugium. The combination of niche modelling and population genetics thereby offered novel insight into the biogeographical history of an emblematic taxon. [ABSTRACT FROM AUTHOR]

* Premise of the study: Informative markers are required for assessing the diversity of Amborella trichopoda, the only species of its order, endemic to New Caledonia and considered to be the sister species to all flowering plants. Therefore, expressed sequence tag (EST)-based microsatellite markers were developed. * Methods and Results: Fifty-five microsatellite loci were characterized in 14896 putative unigenes, which were generated by assembling A. trichopoda ESTs from the public sequence database. Seventeen markers revealed polymorphism in 80 adult shrubs from three populations. The number of alleles per locus ranged from two to 12, with a total of 132 alleles scored. The mean expected heterozygosity per population ranged from 0.336 to 0.567. * Conclusions: These markers offer an appropriate amount of variation to investigate genetic diversity structure, gene flow, and other conservation issues. [ABSTRACT FROM AUTHOR]

Identifying the molecular bases of adaptation is a key issue in evolutionary biology. Genome scan is an efficient approach for identifying important molecular variation involved in adaptation. Association mapping also offers an opportunity to gain insight into genotype-phenotype relationships. Using these two approaches coupled with environmental data should help to come up with a refined picture of the evolutionary process underlying adaptation. In this study, we first conducted a selection scan analysis on a transcription factor gene family. We focused on the MADS-box gene family, a gene family which plays a crucial role in vegetative and flower development. Twenty-one pearl millet populations were sampled along an environmental gradient in West Africa. We identified one gene, i.e. PgMADS11, using Bayesian analysis to detect selection signatures. Polymorphism at this gene was also associated with flowering time variation in an association mapping framework. Finally, we found that PgMADS11 allele frequencies were closely associated with annual rainfall. Overall, we determined an efficient way to detect functional polymorphisms associated with climate variation in non-model plants by combining genome scan and association mapping. These results should help monitor the impact of recent climatic changes on plant adaptation. [ABSTRACT FROM AUTHOR]

Premise: Third‐generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities for the study of biodiversity, phylogeography, and population genetics. We developed a protocol for in‐solution enrichment hybridization capture of long DNA fragments applicable to complete plastid genomes. Methods and Results: The protocol uses cost‐effective in‐house probes developed via long‐range PCR and was used in six non‐model monocot species (Poaceae: African rice, pearl millet, fonio; and three palm species). DNA was extracted from fresh and silica gel–dried leaves. Our protocol successfully captured long‐read plastome fragments (3151 bp median on average), with an enrichment rate ranging from 15% to 98%. DNA extracted from silica gel–dried leaves led to low‐quality plastome assemblies when compared to DNA extracted from fresh tissue. Conclusions: Our protocol could also be generalized to capture long sequences from specific nuclear fragments. [ABSTRACT FROM AUTHOR]

Social Impact Statement The use of neglected and underutilized species (NUS) in agrosystems is a potential solution to the challenges arising from global change. These species could contribute to the equitable diversification of agricultural systems. Providing knowledge on their genetic diversity and fostering access to data and results is essential for the development of strong collaborative future research. The study addressed these issues by assessing the diversity of the largest fonio (Digitaria exilis) collection existing to date. Associated with a user‐friendly Shiny application (https://shinyapps.southgreen.fr/app/foniodiv), our results reinforce research efficiency and broaden the prospects for all actors involved in enhancing fonio and indigenous crops as valuable resources for the future. [ABSTRACT FROM AUTHOR]