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.

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

BACKGROUND AND AIMS

Like other clades, the Coffea genus is highly diversified on the island of Madagascar. The 66 endemic species have colonized various environments and consequently exhibit a wide diversity of morphological, functional and phenological features and reproductive strategies. The trends of interspecific trait variation, which stems from interactions between genetically defined species and their environment, still needed to be addressed for Malagasy coffee trees.

METHODS

Data acquisition was done in the most comprehensive ex situ collection of Madagascan wild Coffea. The structure of endemic wild coffees maintained in an ex situ collection was explored in terms of morphological, phenological and functional traits. The environmental (natural habitat) effect was assessed on traits in species from distinct natural habitats. Phylogenetic signal (Pagel's λ, Blomberg's K) was used to quantify trait proximities among species according to their phylogenetic relatedness.

KEY RESULTS

Despite the lack of environmental difference in the ex situ collection, widely diverging phenotypes were observed. Phylogenetic signal was found to vary greatly across and even within trait categories. The highest values were exhibited by the ratio of internode mass to leaf mass, the length of the maturation phase and leaf dry matter content (ratio of dry leaf mass to fresh leaf mass). By contrast, traits weakly linked to phylogeny were either constrained by the original natural environment (leaf size) or under selective pressures (phenological traits).

CONCLUSIONS

This study gives insight into complex patterns of trait variability found in an ex situ collection, and underlines the opportunities offered by living ex situ collections for research characterizing phenotypic variation.

Internal trophic pressure, a regulator of plant development? Insights from a stochastic functional-structural plant growth model applied to Coffea trees

BACKGROUND AND AIMS

Using internal trophic pressure as a regulating variable to model the complex interaction loops between organogenesis, production of assimilates and partitioning in functional-structural models of plant growth has attracted increasing interest in recent years. However, this approach is hampered by the fact that internal trophic pressure is a non-measurable quantity that can be assessed only through model parametric estimation, for which the methodology is not straightforward, especially when the model is stochastic.

METHODS

A stochastic GreenLab model of plant growth (called 'GL4') is developed with a feedback effect of internal trophic competition, represented by the ratio of biomass supply to demand (Q/D), on organogenesis. A methodology for its parameter estimation is presented and applied to a dataset of 15 two-year-old Coffea canephora trees. Based on the fitting results, variations in Q/D are reconstructed and analysed in relation to the estimated variations in organogenesis parameters.

KEY RESULTS

Our stochastic retroactive model was able to simulate realistically the progressive set-up of young plant architecture and the branch pruning effect. Parameter estimation using real data for Coffea trees provided access to the internal trophic dynamics. These dynamics correlated with the organogenesis probabilities during the establishment phase.

CONCLUSIONS

The model can satisfactorily reproduce the measured data, thus opening up promising avenues for further applying this original procedure to other experimental data. The framework developed can serve as a model-based toolkit to reconstruct the hidden internal trophic dynamics of plant growth.

WCSdb: a database of wild Coffea species

Coffee is a beverage enjoyed by millions of people worldwide and an important commodity for millions of people. Beside the two cultivated species (Coffea arabica and Coffea canephora), the 139 wild coffee species/taxa belonging to the Coffea genus are largely unknown to coffee scientists and breeders although these species may be crucial for future coffee crop development to face climate changes. Here we present the Wild Coffee Species database (WCSdb) hosted by Pl@ntNet platform (http://publish.plantnet-project.org/project/wildcofdb_en), providing information for 141 coffee species/taxa, for which 84 contain a photo gallery and 82 contain sequencing data (genotyping-by-sequencing, chloroplast or whole genome sequences). The objective of this database is to better understand and characterize the species (identification, morphology, biochemical compounds, genetic diversity and sequence data) in order to better protect and promote them.

DATABASE URL

http://publish.plantnet-project.org/project/wildcofdb_en.

Potential use of biochar, compost and iron grit associated with Trifolium repens to stabilize Pb and As on a multi-contaminated technosol

Vegetation cover can be used in the phytomanagement of polluted areas by adding value to abandoned sites and reducing the dispersion of pollutants by erosion. Appropriate amendments, that allow both efficient plant growth and the immobilization of contaminants in the soil must be chosen in order to optimize the efficiency of this process. We used a mining technosol mainly contaminated by arsenic (1068 mg kg^-1) and lead (23387 mg kg^-1) to study the effect of three amendments (biochar, compost and iron grit) on (i) physico-chemical properties of the soil and soil pore water, (ii) metal(loid) mobility, bioavailability and bioaccessibility (CaCl₂ and Simple Bioaccessibility Extraction Test (SBET)), and (iii) the capability of Trifolium repens to germinate and grow. All the amendments used increased the pH and electrical conductivity of the SPW, resulting in a 90% decrease in the concentration of lead in the soil pore water (SPW). We also demonstrated a decrease in Pb phytoavailability. The amendments allowed the establishment of a plant cover, although the addition of iron grit alone did not allow any clover germination. For the Pontgibaud technosol, the combination of the three amendments resulted in a significant decrease in As and Pb concentrations in clover tissues, mainly in the aerial organs. The amendments also made it possible for some of them to halve the phytoavailable fraction of arsenic. However, for compost, both the As concentrations in the SPW, and the bioavailable fraction of As increased. All the amendments used had contrasting effects on the bioaccessible fractions of metal(loid)s. The most efficient amendment combination was the addition of 5% biochar and 5% compost.

Capability of amendments (biochar, compost and garden soil) added to a mining technosol contaminated by Pb and As to allow poplar seed (Populus nigra L.) germination

The germination capacity of poplar seeds has never been studied in the context of metal(loid)-contaminated soils, even though poplars are present over a vast geographical area. In this study, black poplar seeds from the Loire Valley (France) were grown for 28 days in mesocosm on a heavily polluted soil that was subjected to different amendments. This phytomanagement process aimed to allow the revegetation of an As and Pb-contaminated mining soil by adding appropriate amendments, resulting in metal(loid) soil stabilisation and efficient plant growth. The objectives were to evaluate the effect of three amendments (garden soil, compost and biochar) when added alone or combined to a technosol on (i) the soil physicochemical properties, (ii) the mobility of As and Pb in the soil pore water (SPW), (iii) the capacity of poplar seeds to germinate and to grow and (iv) the metal(loid) distribution within the plant organs. The addition of amendments alone or combined allowed a 90% decrease in SPW Pb concentrations, while the arsenic concentrations were between 18 and 416 times higher. However, we were only able to obtain seed germination and plant growth on amended soils. These promising results will allow us to explore the use of such amendments in rehabilitating areas that are sources of significant metal(loid) dissemination, as well as allowing a natural plant recolonisation of these sites by seeds from the surrounding environment.

Stochastic modelling of tree architecture and biomass allocation: application to teak (Tectona grandis L. f.), a tree species with polycyclic growth and leaf neoformation

Background and aims

For a given genotype, the observed variability of tree forms results from the stochasticity of meristem functioning and from changing and heterogeneous environmental factors affecting biomass formation and allocation. In response to climate change, trees adapt their architecture by adjusting growth processes such as pre- and neoformation, as well as polycyclic growth. This is the case for the teak tree. The aim of this work was to adapt the plant model, GreenLab, in order to take into consideration both these processes using existing data on this tree species.

Methods

This work adopted GreenLab formalism based on source-sink relationships at organ level that drive biomass production and partitioning within the whole plant over time. The stochastic aspect of phytomer production can be modelled by a Bernoulli process. The teak model was designed, parameterized and analysed using the architectural data from 2- to 5-year-old teak trees in open field stands.

Key results

Growth and development parameters were identified, fitting the observed compound organic series with the theoretical series, using generalized least squares methods. Phytomer distributions of growth units and branching pattern varied depending on their axis category, i.e. their physiological age. These emerging properties were in accordance with the observed growth patterns and biomass allocation dynamics during a growing season marked by a short dry season.

Conclusions

Annual growth patterns observed on teak, including shoot pre- and neoformation and polycyclism, were reproduced by the new version of the GreenLab model. However, further updating is discussed in order to ensure better consideration of radial variation in basic specific gravity of wood. Such upgrading of the model will enable teak ideotypes to be defined for improving wood production in terms of both volume and quality.

Deciphering the developmental plasticity of walnut saplings in relation to climatic factors and light environment

Developmental plasticity, the acclimation of plants to their local environment, is known to be crucial for the fitness of perennial organisms such as trees. However, deciphering the many possible developmental and environmental influences involved in such plasticity in natural conditions requires dedicated statistical models integrating developmental phases, environmental factors, and interindividual heterogeneity. These models should be able to analyse retrospective data (number of leaves or length of annual shoots along the main stem in the present case). In this study Markov switching linear mixed models were applied to the analysis of the developmental plasticity of walnut saplings during the establishment phase in a mixed Mediterranean forest. In the Markov switching linear mixed models estimated from walnut data sets, the underlying Markov chain represents both the succession and lengths of growth phases, while the linear mixed models represent both the influence of climatic factors and interindividual heterogeneity within each growth phase. On the basis of these integrative statistical models, it is shown that walnut saplings have an opportunistic mode of development that is primarily driven by the changing light environment. In particular, light availability explains the ability of a tree to reach a phase of strong growth where the first branches can appear. It is also shown that growth fluctuation amplitudes in response to climatic factors increased while interindividual heterogeneity decreased during tree development.

Periods of organogenesis in mono- and bicyclic annual shoots of Juglans regia L. (Juglandaceae)

The organogenetic cycle of shoots on main branches of 4-year-old Juglans regia trees was studied. Mono- and bicyclic floriferous and vegetative annual shoots were analysed. Five parent annual shoot types were sampled between October 1992 and August 1993. Organogenesis of summer growth units was monitored between 16 Jun. and 3 Aug. 1993. Variations over time in the number of nodes, cataphylls and embryonic green leaves of terminal buds were studied. The number of nodes of parent shoot buds was compared with the number of nodes of shoots derived from parent shoot buds. The spring growth units of mono- and bicyclic shoots consist exclusively of preformed leaves which were differentiated, respectively, during the spring flush of growth (mid-April until mid-May) or the summer flush of growth (mid-June until early August) in the previous growing season. Thus, winter buds may consist of flower and leaf primordia differentiated in two different periods during annual shoot extension. The summer growth units of bicyclic shoots consist of preformed leaves that were differentiated in spring buds during the spring flush of growth in the current growing season. Bud morphology is compared between spring and summer shoots.

Recipients in need of ancillary services and their receipt of HIV medical care in California

For many individuals with access to quality medical care, HIV disease is no longer a critical short term illness but a chronic condition giving rise to more clients requiring ongoing medical care. Programs funded by the federal Ryan White Comprehensive AIDS Resources Emergency Act not only provide essential medical care for these individuals but also facilitate access to medical care services. These programmes fund services, including case management, transportation, and translation assistance, that feature ongoing assistance and enable individuals to remain in the health care system. Because of the importance of maintaining the strict drug regimen, retention in care is also an important part of the overall HIV care component. This study analyzed the relationship of ancillary services and a federal health programme client's receipt of medical care and retention in the health care system. We defined a cohort in need of ancillary services in part by a questionnaire designed to identify factors relating to need. These factors included education, language, and substance use. By merging client level data files we were able to identify medical service utilization trends among the individuals in the cohort who received a high number of ancillary services (more than 11 ancillary service visits in the two-year study period, n = 138) and those who received few services (fewer than six ancillary service visits in the two-year study period, n = 132). Results suggest that the receipt of ancillary services is associated with receipt of and retention in primary medical care. We found that for federal health programme clients in need of ancillary services, a positive relationship existed between their receipt of ancillary services and their access to primary medical care (p </= 0.001). This observation held constant when age, race, gender, and insurance coverage were controlled for. Also, these clients were more likely to be seen by a medical doctor at least once in three consecutive six-month periods when they received needed ancillary services (p </= 0.01).

Non-erythroid genes inserted on either side of human HS-40 impair the activation of its natural alpha -globin gene targets without being themselves preferentially activated

The human alpha-globin gene complex includes three functional globin genes (5'-zeta2-alpha2-alpha1-3') regulated by a common positive regulatory element named HS-40 displaying strong erythroid-specific enhancer activity. How this enhancer activity can be shared between different promoters present at different positions in the same complex is poorly understood. To address this question, we used homologous recombination to target the insertion of marker genes driven by cytomegalovirus or long terminal repeat promoters in both possible orientations either upstream or downstream from the HS-40 region into the single human alpha-globin gene locus present in hybrid mouse erythroleukemia cells. We also used CRE recombinase-mediated cassette exchange to target the insertion of a tagged alpha-globin gene at the same position downstream from HS-40. All these insertions led to a similar decrease in the HS-40-dependent transcription of downstream human alpha-globin genes in differentiated cells. Interestingly, this decrease is associated with the strong activation of the proximal newly inserted alpha-globin gene, whereas in marked contrast, the transcription of the non-erythroid marker genes remains insensitive to HS-40. Taken together, these results indicate that the enhancer activity of HS-40 can be trapped by non-erythroid promoters in both upstream and downstream directions without necessarily leading to their own activation.

Targeted inactivation of the major positive regulatory element (HS-40) of the human alpha-globin gene locus

We have examined the role of the major positive upstream regulatory element of the human alpha-globin gene locus (HS-40) in its natural chromosomal context. Using homologous recombination, HS-40 was replaced by a neo marker gene in a mouse erythroleukemia hybrid cell line containing a single copy of human chromosome 16. In clones from which HS-40 had been deleted, human alpha-globin gene expression was severely reduced, although basal levels of alpha 1 and alpha 2-globin mRNA expression representing less than 3% of the level in control cell lines were detected. Deletion of the neo marker gene, by using FLP recombinase/FLP recombinase target system, proved that the phenotype observed was not caused by the regulatory elements of this marker gene. In the targeted clones, deletion of HS-40 apparently does not affect long-range or local chromatin structure at the alpha promoters. Therefore, these results indicate that, in the experimental system used, HS-40 behaves as a strong inducible enhancer of human alpha-globin gene expression.