Three complete chloroplast genomes from two north American Rhus species and phylogenomics of Anacardiaceae

BACKGROUND

The suamc genus Rhus (sensu stricto) includes two subgenera, Lobadium (ca. 25 spp.) and Rhus (ca. 10 spp.). Their members, R. glabra and R. typhina (Rosanae: Sapindales: Anacardiaceae), are two economic important species. Chloroplast genome information is of great significance for the study of plant phylogeny and taxonomy.

RESULTS

The three complete chloroplast genomes from two Rhus glabra and one R. typhina accessions were obtained with a total of each about 159k bp in length including a large single-copy region (LSC, about 88k bp), a small single-copy regions (SSC, about 19k bp) and a pair of inverted repeats regions (IRa/IRb, about 26k bp), to form a canonical quadripartite structure. Each genome contained 88 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes. The overall GC content of the three genomes all were same (37.8%), and RSCU values showed that they all had the same codon prefers, i.e., to use codon ended with A/U (93%) except termination codon. Three variable hotspots, i.e., ycf4-cemA, ndhF-rpl32-trnL and ccsA-ndhD, and a total of 152-156 simple sequence repeats (SSR) were identified. The nonsynonymous (Ka)/synonymous (Ks) ratio was calculated, and cemA and ycf2 genes are important indicators of gene evolution. The phylogenetic analyses of the family Anacardiaceae showed that the eight genera were grouped into three clusters, and supported the monophyly of the subfamilies and all the genera. The accessions of five Rhus species formed four clusters, while, one individual of R. typhina grouped with the R. glabra accessions instead of clustering into the two other individuals of R. typhina in the subgenus Rhus, which showed a paraphyletic relationship.

CONCLUSIONS

Comparing the complete chloroplast genomes of the Rhus species, it was found that most SSRs were A/T rich and located in the intergenic spacer, and the nucleotide divergence exhibited higher levels in the non-coding region than in the coding region. The Ka/Ks ratio of cemA gene was > 1 for species collected in America, while it was < 1 for other species in China, which dedicated that the Rhus species from North America and East Asia have different evolutionary pressure. The phylogenetic analysis of the complete chloroplast genome clarified the Rhus placement and relationship. The results obtained in this study are expected to provide valuable genetic resources to perform species identification, molecular breeding, and intraspecific diversity of the Rhus species.

Sequence diversity and differential expression of major phenylpropanoid-flavonoid biosynthetic genes among three mango varieties

BACKGROUND

Mango fruits contain a broad spectrum of phenolic compounds which impart potential health benefits; their biosynthesis is catalysed by enzymes in the phenylpropanoid-flavonoid (PF) pathway. The aim of this study was to reveal the variability in genes involved in the PF pathway in three different mango varieties Mangifera indica L., a member of the family Anacardiaceae: Kensington Pride (KP), Irwin (IW) and Nam Doc Mai (NDM) and to determine associations with gene expression and mango flavonoid profiles.

RESULTS

A close evolutionary relationship between mango genes and those from the woody species poplar of the Salicaceae family (Populus trichocarpa) and grape of the Vitaceae family (Vitis vinifera), was revealed through phylogenetic analysis of PF pathway genes. We discovered 145 SNPs in total within coding sequences with an average frequency of one SNP every 316 bp. Variety IW had the highest SNP frequency (one SNP every 258 bp) while KP and NDM had similar frequencies (one SNP every 369 bp and 360 bp, respectively). The position in the PF pathway appeared to influence the extent of genetic diversity of the encoded enzymes. The entry point enzymes phenylalanine lyase (PAL), cinnamate 4-mono-oxygenase (C4H) and chalcone synthase (CHS) had low levels of SNP diversity in their coding sequences, whereas anthocyanidin reductase (ANR) showed the highest SNP frequency followed by flavonoid 3'-hydroxylase (F3'H). Quantitative PCR revealed characteristic patterns of gene expression that differed between mango peel and flesh, and between varieties.

CONCLUSIONS

The combination of mango expressed sequence tags and availability of well-established reference PF biosynthetic genes from other plant species allowed the identification of coding sequences of genes that may lead to the formation of important flavonoid compounds in mango fruits and facilitated characterisation of single nucleotide polymorphisms between varieties. We discovered an association between the extent of sequence variation and position in the pathway for up-stream genes. The high expression of PAL, C4H and CHS genes in mango peel compared to flesh is associated with high amounts of total phenolic contents in peels, which suggest that these genes have an influence on total flavonoid levels in mango fruit peel and flesh. In addition, the particularly high expression levels of ANR in KP and NDM peels compared to IW peel and the significant accumulation of its product epicatechin gallate (ECG) in those extracts reflects the rate-limiting role of ANR on ECG biosynthesis in mango.

Molecular data and ecological niche modelling reveal the phylogeographic pattern of Cotinus coggygria (Anacardiaceae) in China's warm-temperate zone

The phylogeography of common and widespread species helps to elucidate the history of local flora and vegetation. In this study, we selected Cotinus coggygria, a species widely distributed in China's warm-temperate zone. One chloroplast DNA (cpDNA) region and ecological niche modelling were used to examine the phylogeographic pattern of C. coggygria. The cpDNA data revealed two phylogeographic groups (Southern and Northern) corresponding to the geographic regions. Divergence time analyses revealed that divergence of the two groups occurred at approximately 147,000 years before the present (BP), which coincided with the formation of the downstream area of the Yellow River, indicating that the Yellow River was a weak phylogeographic divide for C. coggygria. The molecular data and ecological niche modelling also indicated that C. coggyria did not experience population expansion after glaciations. This study thus supports the fact that Pleistocene glacial cycles only slightly affected C. coggygria, which survived in situ and occupied multiple localised glacial refugia during glaciations. This finding is contrary to the hypothesis of large-scale range habitat contraction and retreat into a few main refugia.

Analysis of umbu (Spondias tuberosa Arruda (Anacardiaceae)) in different landscape management regimes: a process of incipient domestication?

Plant domestication is an evolutionary process guided by human groups who modify the landscape for their needs. The objective of this study was to evaluate the phenotypic variations between populations of Spondias tuberosa Arruda (umbuzeiro) when subjected to different local landscape management strategies. The influence of the landscape management system on these populations was evaluated in five identified regional units (mountains, base of mountains, pastures, cultivated areas and home gardens). Ten individuals were randomly selected from each region and subjected to morphological and chemical fruit analysis. The diversity index, based on Simpson's index, was determined for the different populations. We then evaluated the morphological differences between the individual fruits from the distinct landscape areas. We observed no significant differences in morphological diversity between the areas studied. Our data suggest that the umbuzeiro specimens in this region may be in the process of incipient domestication.

Colonization patterns of the invasive Brazilian peppertree, Schinus terebinthifolius, in Florida

Invasive species are believed to spread through a process of stratified dispersal consisting of short-distance diffusive spread around established foci and human mediated long-distance jumps. Brazilian peppertree (Schinus terebinthifolius), native to South America, was introduced twice as an ornamental plant into Florida, USA, just over 100 years ago. A previous study indicated that these two introductions were from genetically differentiated source populations in the native range. In this study, we took advantage of these contrasting genetic signatures to study the spatial spread of Brazilian peppertree across its entire range in Florida. A combination of spatial genetic and geostatistical analyses using chloroplast and nuclear microsatellite markers revealed evidence for both diffusive dispersal and long-distance jumps. Chloroplast DNA haplotype distributions and extensive bands of intra-specific hybridization revealed extensive dispersal by both introduced populations across the state. The strong genetic signature around the original introduction points, the presence of a general southeast to northwest genetic cline, and evidence for short-distance genetic spatial autocorrelation provided evidence of diffusive dispersal from an advancing front, probably by birds and small mammals. In the northernmost part of the range, there were patches having a high degree of ancestry from each introduction, suggesting long-distance jump dispersal, probably by the movement of humans. The evidence for extensive movement throughout the state suggests that Brazilian peppertree will be capable of rapidly recolonizing areas from which it has been eradicated. Concerted eradication efforts over large areas or the successful establishment of effective biocontrol agents over a wide area will be needed to suppress this species.

Domestication and the distribution of genetic variation in wild and cultivated populations of the Mesoamerican fruit tree Spondias purpurea L. (Anacardiaceae)

Domestication occurs as humans select and cultivate wild plants in agricultural habitats. The amount and structure of variation in contemporary cultivated populations has been shaped, in part, by how genetic material was transferred from one cultivated generation to the next. In some cultivated tree species, domestication involved a shift from sexually reproducing wild populations to vegetatively propagated cultivated populations; however, little is known about how domestication has impacted variation in these species. We employed AFLP data to explore the amount, structure, and distribution of variation in clonally propagated domesticated populations and sexually reproducing wild populations of the Neotropical fruit tree, Spondias purpurea (Anacardiaceae). Cultivated populations from three different agricultural habitats were included: living fences, backyards, and orchards. AFLP data were analysed using measures of genetic diversity (% polymorphic loci, Shannon's diversity index, Nei's gene diversity, panmictic heterozygosity), population structure (F(ST) analogues), and principal components analyses. Levels of genetic variation in cultivated S. purpurea populations are significantly less than variation found in wild populations, although the amount of diversity varies in different agricultural habitats. Cultivated populations have a greater proportion of their genetic variability distributed among populations than wild populations. The genetic structure of backyard populations resembles that of wild populations, but living fence and orchard populations have 1/3 more variability distributed among populations, most likely a reflection of relative levels of vegetative reproduction. Finally, these results suggest that S. purpurea was domesticated in two distinct regions within Mesoamerica.

Domestication of a Mesoamerican cultivated fruit tree, Spondias purpurea

Contemporary patterns of genetic variation in crops reflect historical processes associated with domestication, such as the geographic origin(s) of cultivated populations. Although significant progress has been made in identifying several global centers of domestication, few studies have addressed the issue of multiple origins of cultivated plant populations from different geographic regions within a domestication center. This study investigates the domestication history of jocote (Spondias purpurea), a Mesoamerican cultivated fruit tree. Sequences of the chloroplast spacer trnG-trnS were obtained for cultivated and wild S. purpurea trees, two sympatric taxa (Spondias mombin var. mombin and Spondias radlkoferi), and two outgroups (S. mombin var. globosa and Spondias testudinus). A phylogeographic approach was used and statistically significant associations of clades and geographical location were tested with a nested clade analysis. The sequences confirm that wild populations of S. purpurea are the likely progenitors of cultivated jocote trees. This study provides phylogeographic evidence of multiple domestications of this Mesoamerican cultivated fruit tree. Haplotypes detected in S. purpurea trees form two clusters, each of which includes alleles recovered in both cultivated and wild populations from distinct geographic regions. Cultivated S. purpurea populations have fewer unique trnG-trnS alleles than wild populations; however, five haplotypes were absent in the wild. The presence of unique alleles in cultivation may reflect contemporary extinction of the tropical dry forests of Mesoamerica. These data indicate that some agricultural habitats may be functioning as reservoirs of genetic variation in S. purpurea.

Chloroplast and microsatellite DNA diversities reveal the introduction history of Brazilian peppertree (Schinus terebinthifolius) in Florida

Brazilian peppertree (Schinus terebinthifolius) is a woody perennial that has invaded much of Florida. This native of northeastern Argentina, Paraguay, and Brazil was brought as an ornamental to both the west and east coasts of Florida at the end of the 19th century. It was recorded as an invader of natural areas in the 1950s, and has since extended its range to cover over 280 000 ha. Our goals were to understand the history of this invasion, as one step toward understanding why this exotic was so successful, and ultimately to improve development of biological control agents. We sampled plants from the native and exotic ranges, particularly Florida, and genotyped these individuals at nuclear and chloroplast loci. Nuclear microsatellite and cpDNA loci reveal strong genetic population structure consistent with limited dispersal in the introduced and native ranges. Bayesian clustering of microsatellite data separates the east and west coast plants in Florida into distinct populations. The two chloroplast haplotypes found in Florida are also concordant with this separation: one predominates on the east coast, the other on the west coast. Analysis of samples collected in South America shows that haplotypes as distinct as the two in Florida are unlikely to have come from a single source population. We conclude that the genetic evidence supports two introductions of Brazilian peppertree into Florida and extensive hybridization between them. The west coast genotype likely came from coastal Brazil at about 27 degrees south, whereas the east coast genotype probably originated from another, as yet unidentified site. As a result of hybridization, the Florida population does not exhibit low genetic variation compared to populations in the native range, possibly increasing its ability to adapt to novel environments. Hybridization also has important consequences for the selection of biocontrol agents since it will not be possible to identify closely co-adapted natural enemies in the native range, necessitating more extensive host testing.

[The function of leaf meristematic cells in Cotinus coggygria Scop]

Proliferation of leaf meristem cells and formation of multicellular glands and unicellular hairs in Cotinus coggygria were studied under conditions of complex stressors exerting influence on this species when introduced and grown in such a big industrial city as Voronezh. Variability in the length of dividing meristematic cells (from 7.5 to 30.0 microns) was detected. The chromosome number was calculated, and the mean length of chromosomes (1 micron) was determined. The modal chromosome number in the leaf meristem cells in 2 n = 30. However, along with these cells, aneuploid (2.7%), uninucleate polypoid (1.9%), binuclear (10%), and polynuclear (3%) cells were also observed. The length of trichomes initials, formed in the epidermis, was near 40 microns. These have a large nucleus and may have, presumably, a polyploid nature. It is assumed that a heterogeneous meristematic cell population, at the expense of selection into such a population, is able to provide an optimum combination of cells with different level ploidy and aneuploidy for more effective realization of gene function in the extremal environment conditions.