Complete chloroplast genome sequences of Myristicaceae species with the comparative chloroplast genomics and phylogenetic relationships among them.

BACKGROUND: Myristicaceae was widly distributed from tropical Asia to Oceania, Africa, and tropical America. There are 3 genera and 10 species of Myristicaceae present in China, mainly distributed in the south of Yunnan Province. Most research on this family focuses on fatty acids, medicine, and morphology. Based on the morphology, fatty acid chemotaxonomy, and a few of molecular data, the phylogenetic position of Horsfieldia pandurifolia Hu was controversial. RESULTS: In this study, the chloroplast genomes of two Knema species, Knema globularia (Lam.) Warb. and Knema cinerea (Poir.) Warb., were characterized. Comparing the genome structure of these two species with those of other eight published species, including three Horsfieldia species, four Knema species, and one Myristica species, it was found that the chloroplast genomes of these species were relatively conserved, retaining the same gene order. Through sequence divergence analysis, there were 11 genes and 18 intergenic spacers were subject to positive selection, which can be used to analyze the population genetic structure of this family. Phylogenetic analysis showed that all Knema species were clustered in the same group and formed a sister clade with Myristica species support by both high maximum likelihood bootstrap values and Bayesian posterior probabilities; among Horsfieldia species, Horsfieldia amygdalina (Wall.) Warb., Horsfieldia kingii (Hook.f.) Warb., Horsfieldia hainanensis Merr. and Horsfieldia tetratepala C.Y.Wu. were grouped together, but H. pandurifolia formed a single group and formed a sister clade with genus Myristica and Knema. Through the phylogenetic analysis, we support de Wilde' view that the H. pandurifolia should be separated from Horsfieldia and placed in the genus Endocomia, namely Endocomia macrocoma subsp. prainii (King) W.J.de Wilde. CONCLUSION: The findings of this study provide a novel genetic resources for future research in Myristicaceae and provide a molecular evidence for the taxonomic classification of Myristicaceae.

Microsatellite markers development for Indonesian nutmeg (Myristica fragrans Houtt.) and transferability to other Myristicaceae spp.

Myristica fragrans (Myristicaceae) is a tropical evergreen tree that yields the two famous spices: nutmeg and mace. Despite its socio-economic importance, the spatial distribution of its genetic diversity is barely documented. In this aim, 48 nuclear microsatellite markers were isolated of which 14 were polymorphic in M. fragrans. Number of alleles per locus ranged from 2 to 6. The level of observed heterozygosity ranged from 0.038 to 0.929 across loci. Transferability of these microsatellites in other Myristica species (M. fatua, M. argentea, and M. crassipes) and Myristicaceae species (Horsfieldia palauensis) was tested and successful. These new microsatellites will be useful for future investigation on genetic diversity and population structure of M. fragrans and phylogenetically-related species.

Evidence of within-species specialization by soil microbes and the implications for plant community diversity.

Microbes are thought to maintain diversity in plant communities by specializing on particular species, but it is not known whether microbes that specialize within species (i.e., on genotypes) affect diversity or dynamics in plant communities. Here we show that soil microbes can specialize at the within-population level in a wild plant species, and that such specialization could promote species diversity and seed dispersal in plant communities. In a shadehouse experiment in Panama, we found that seedlings of the native tree species, Virola surinamensis (Myristicaceae), had reduced performance in the soil microbial community of their maternal tree compared with in the soil microbial community of a nonmaternal tree from the same population. Performance differences were unrelated to soil nutrients or to colonization by mycorrhizal fungi, suggesting that highly specialized pathogens were the mechanism reducing seedling performance in maternal soils. We then constructed a simulation model to explore the ecological and evolutionary consequences of genotype-specific pathogens in multispecies plant communities. Model results indicated that genotype-specific pathogens promote plant species coexistence-albeit less strongly than species-specific pathogens-and are most effective at maintaining species richness when genetic diversity is relatively low. Simulations also revealed that genotype-specific pathogens select for increased seed dispersal relative to species-specific pathogens, potentially helping to create seed dispersal landscapes that allow pathogens to more effectively promote diversity. Combined, our results reveal that soil microbes can specialize within wild plant populations, affecting seedling performance near conspecific adults and influencing plant community dynamics on ecological and evolutionary time scales.

Isolation of microsatellite loci in the African tree species Staudtia kamerunensis (Myristicaceae) using high-throughput sequencing.

Staudtia kamerunensis (Myristicaceae) or 'Niové' is an evergreen tree widespread in Central African moist forests. The bark and seeds are used in traditional medicine, yet the tree is mainly harvested for its high quality, multi-purpose timber. To facilitate sustainable harvesting and conservation of the species, we aim to develop microsatellite markers that can be used to study the mating system, gene flow, genetic diversity and population structure. Genomic DNA of S. kamerunensis was sequenced on an Illumina MiSeq platform, generating 195,720 paired-end reads with 3671 sequences containing microsatellites. Amplification tests resulted in the development of 16 highly polymorphic microsatellite loci of which 14 were tested in 183 individuals of S. kamerunensis from three populations. The number of detected alleles per locus ranged from 15 to 39 and the average observed and expected heterozygosity across loci and populations were Ho = 0.713 (0.14-0.97) and He = 0.879 (0.19-0.95) respectively. The high levels of polymorphism observed in the newly developed microsatellite markers demonstrate their usefulness to study gene flow, population structure and spatial distribution of genetic diversity in S. kamerunensis.

Female fruit production depends on female flower production and crown size rather than male density in a continuous population of a tropical dioecious tree (Virola surinamensis).

PREMISE OF THE STUDY: Factors related to pollen and resource limitation were evaluated to predict female fruit production in a tropical dioecious tree. Pollen limitation via variation in the male density at local scales is expected to limit female reproduction success in dioecious plants. METHODOLOGY: We modeled the roles of local male density, female crown size, crown illumination, and female flower production on female fruit initiation and mature fruit production in a continuous population (62 ha plot) of a tropical dioecious tree (Virola surinamensis). In addition, we used microsatellites to describe the scale of effective pollen flow, the male effective population size, and the spatial genetic structure within/between progenies and males. KEY RESULTS: The local male density was not related to female fruit initiation or mature fruit production. Female floral production had a positive effect on fruit initiation. The female crown size was positively related to fruit maturation. Seeds from the same female and seeds from different but spatially proximal females were generally half-siblings; however, proximal females showed greater variation. Proximal male-female adult pairs were not significantly more genetically related than distant pairs. The probability of paternity was negatively affected by the distance between seeds and males; most effective pollen dispersal events (∼85%) occurred from males located less than 150 m from females. The number of males siring progenies was greater than the number of males found at local scales. CONCLUSIONS: Female fecundity in this continuous population of Virola surinamensis is not limited by the availability of pollen from proximal males. Rather, resource allocation to floral production may ultimately determine female reproductive success.

High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species.

BACKGROUND: The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources. RESULTS: In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs. CONCLUSION: The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.

Do ecological niche model predictions reflect the adaptive landscape of species?: a test using Myristica malabarica Lam., an endemic tree in the Western Ghats, India.

Ecological niche models (ENM) have become a popular tool to define and predict the "ecological niche" of a species. An implicit assumption of the ENMs is that the predicted ecological niche of a species actually reflects the adaptive landscape of the species. Thus in sites predicted to be highly suitable, species would have maximum fitness compared to in sites predicted to be poorly suitable. As yet there are very few attempts to address this assumption. Here we evaluate this assumption. We used Bioclim (DIVA GIS version 7.3) and Maxent (version 3.3.2) to predict the habitat suitability of Myristica malabarica Lam., an economically important tree occurring in the Western Ghats, India. We located populations of the trees naturally occurring in different habitat suitability regimes (from highly suitable to poorly suitable) and evaluated them for their regeneration ability and genetic diversity. We also evaluated them for two plant functional traits, fluctuating asymmetry--an index of genetic homeostasis, and specific leaf weight--an index of primary productivity, often assumed to be good surrogates of fitness. We show a significant positive correlation between the predicted habitat quality and plant functional traits, regeneration index and genetic diversity of populations. Populations at sites predicted to be highly suitable had a higher regeneration and gene diversity compared to populations in sites predicted to be poor or unsuitable. Further, individuals in the highly suitable sites exhibited significantly less fluctuating asymmetry and significantly higher specific leaf weight compared to individuals in the poorly suitable habitats. These results for the first time provide an explicit test of the ENM with respect to the plant functional traits, regeneration ability and genetic diversity of populations along a habitat suitability gradient. We discuss the implication of these results for designing viable species conservation and restoration programs.