An integrative approach reveals five new species of highland papayas (Caricaceae, Vasconcellea) from northern Peru

The assignment of accurate species names is crucial, especially for those with confirmed agronomic potential such as highland papayas. The use of additional methodologies and data sets is recommended to establish well-supported boundaries among species of Vasconcellea. Accordingly, six chloroplast (trnL-trnF, rpl20-rps12, psbA-trnH intergenic spacers, matK and rbcL genes) and nuclear (ITS) markers were used to delimit species in the genus Vasconcellea using phylogeny and four DNA-based methods. Our results demonstrated congruence among different methodologies applied in this integrative study (i.e., morphology, multilocus phylogeny, genetic distance, coalescence methods). Genetic distance (ABGD, SPN), a coalescence method (BPP), and the multilocus phylogeny supported 22–25 different species of Vasconcellea, including the following five new species from northern Peru: V. badilloi sp. nov., V. carvalhoae sp. nov., V. chachapoyensis sp. nov., V. pentalobis sp. nov., and V. peruviensis sp. nov. Genetic markers that gave better resolution for distinguishing species were ITS and trnL-trnF. Phylogenetic diversity and DNA-species delimitation methods could be used to discover taxa within traditionally defined species.

The Production and Quality of Different Varieties of Papaya Grown under Greenhouse in Short Cycle in Continental Europe

In Europe, papaya consumption is growing due to its nutritional properties. The proximity of consumer markets to Southeast Spain allows fruits to be harvested at a more advanced stage of maturity compared to exporting countries from outside Europe, a timeline which improves the quality of the papaya. Experiments have been carried out to assess the adaptation of papaya to protected cropping systems (under greenhouse) in the region. In this paper, we showed the results obtained in an experiment with five varieties, taking the most cultivated variety as control, which was grafted on its own female rootstock, in addition to another four new varieties that were introduced. Transplanting was made with early sex-identified plants in the nursery. Cultivation was developed in a 446-day cycle, almost 15 months and fruits were always harvested from the soil, due to the height that the plant reached in that period. The best yield parameters and fruit characteristics were obtained from hermaphrodite Intenzza papaya grafted on female papaya rootstock, although there were also other varieties which gave results that made possible its cultivation under this production system.

A wild origin of the loss-of-function lycopene beta cyclase (CYC-b) allele in cultivated, red-fleshed papaya (Carica papaya)

PREMISE OF THE STUDY

The red flesh of some papaya cultivars is caused by a recessive loss-of-function mutation in the coding region of the chromoplast-specific lycopene beta cyclase gene (CYC-b). We performed an evolutionary genetic analysis of the CYC-b locus in wild and cultivated papaya to uncover the origin of this loss-of-function allele in cultivated papaya.

METHODS

We analyzed the levels and patterns of genetic diversity at the CYC-b locus and six loci in a 100-kb region flanking CYC-b and compared these to genetic diversity levels at neutral autosomal loci. The evolutionary relationships of CYC-b haplotypes were assessed using haplotype network analysis of the CYC-b locus and the 100-kb CYC-b region.

KEY RESULTS

Genetic diversity at the recessive CYC-b allele (y) was much lower relative to the dominant Y allele found in yellow-fleshed wild and cultivated papaya due to a strong selective sweep. Haplotype network analyses suggest the y allele most likely arose in the wild and was introduced into domesticated varieties after the first papaya domestication event. The shared haplotype structure between some wild, feral, and cultivated haplotypes around the y allele supports subsequent escape of this allele from red cultivars back into wild populations through feral intermediates.

CONCLUSIONS

Our study supports a protracted domestication process of papaya through the introgression of wild-derived traits and gene flow from cultivars to wild populations. Evidence of gene flow from cultivars to wild populations through feral intermediates has implications for the introduction of transgenic papaya into Central American countries.

Evolutionary relationship and structural characterization of the EPF/EPFL gene family

EPF1-EPF2 and EPFL9/Stomagen act antagonistically in regulating leaf stomatal density. The aim of this study was to elucidate the evolutionary functional divergence of EPF/EPFL family genes. Phylogenetic analyses showed that AtEPFL9/Stomagen-like genes are conserved only in vascular plants and are closely related to AtEPF1/EPF2-like genes. Modeling showed that EPF/EPFL peptides share a common 3D structure that is constituted of a scaffold and loop. Molecular dynamics simulation suggested that AtEPF1/EPF2-like peptides form an additional disulfide bond in their loop regions and show greater flexibility in these regions than AtEPFL9/Stomagen-like peptides. This study uncovered the evolutionary relationship and the conformational divergence of proteins encoded by the EPF/EPFL family genes.

Hybrid 'Sinta' papaya exhibits unique ACC synthase 1 cDNA isoforms

Five ripening-related ACC synthase cDNA isoforms were cloned from 80% ripe papaya cv. 'Sinta' by reverse transcription-PCR using gene-specific primers. Clone 2 had the longest transcript and contained all common exons and three alternative exons. Clones 3 and 4 contained common exons and one alternative exon each, while clone 1, the most common transcript, contained only the common exons. Clone 5 could be due to cloning artifacts and might not be a unique cDNA fragment. Thus, there are only four isoforms of ACC synthase mRNA. Southern blot analysis indicates that all five clones came from only one gene existing as a single copy in the 'Sinta' papaya genome. Multiple sequence alignment indicates that the four isoforms arise from a single gene, possibly through alternative splicing mechanisms. All the putative alternative exons were present at the 5'-end of the gene comprising the N-terminal region of the protein. 'Sinta' ACC synthase cDNAs were of the capacs 1 type and are most closely related to a 1.4 kb capacs 1-type DNA (AJ277160) from Eksotika papaya. No capacs 2-type cDNAs were cloned from 'Sinta' by RT-PCR. This is the first report of possible alternative splicing mechanism in ripening-related ACC synthase genes in hybrid papaya, possibly to modulate or fine-tune gene expression relevant to fruit ripening.

Detection of genetically modified organisms by electrochemiluminescence PCR method

With the development of biotechnology, more and more genetically modified organisms (GMOs) have entered commercial market. Because of the safety concerns, detection and characterization of GMOs have attracted much attention recently. In this study, electrochemiluminescence polymerase chain reaction (ECL-PCR) combined with hybridization technique was applied to detect the GMOs in genetically modified (GM) soybeans and papayas for the first time. Whether the soybeans and the papayas contain GM components was discriminated by detecting the Cauliflower mosaic virus 35S (CaMV35S) promoter. The experiment results show that the detection limit for CaMV35S promoter is 100 fmol, and the GM components can be clearly identified in GM soybeans and papayas. The technique may provide a new means in GMOs detection due to its simplicity and high efficiency.

Phylogenetic analysis of the highland papayas ( Vasconcellea) and allied genera (Caricaceae) using PCR-RFLP

The chloroplast and mitochondrial DNA diversity of 61 genotypes belonging to 18 Vasconcellea species, the so-called highland papayas, was studied by PCR-RFLP analysis of two non-coding cpDNA regions ( trnM- rbcL and trnK1- trnK2) and one non-coding mtDNA region ( nad4/1- nad4/2). This sample set was supplemented with six genotypes belonging to three other Caricaceae genera: the monotypic genus Carica, including only the cultivated papaya, and the genera Jacaratia and Cylicomorpha. Moringa ovalifolia was added as an outgroup species. The PCR-amplified cpDNA regions were digested with 18 restriction endonucleases, the mtDNA region with 11. A total of 22 point mutations and four insertion/deletions were scored in the sample. A higher level of interspecific variation was detected in the two cpDNA regions in comparison to the analysis of the mtDNA. Wagner parsimony and Neighbor-Joining analysis resulted in dendrograms with similar topologies. PCR-RFLP analysis supported the monophyly of Caricaceae, but among the 26 mutations scored, an insufficient number of markers discriminated between the different Caricaceae genera included in this study. Hence the inference of the intergeneric relationships within Caricaceae was impossible. However, some conclusions can be noted at a lower taxonomic level. The Caricaceae species were divided into two lineages. One group included only Vasconcellea spp., whereas the second included the remaining Vasconcellea spp., together with the papaya genotypes and those from the other Caricaceae genera. This may indicate a higher level of inter-fertility for the Vasconcellea species from the latter clade in interspecific crossings with papaya. The putative progenitors of the natural sterile hybrid V. x heilbornii, i.e. V. stipulata and V. cundinamarcensis, were only distantly related to V. x heilbornii. This indicates that probably none of these species was involved as the maternal progenitor in the origin of V. x heilbornii. Surprisingly, V. x heilbornii had organellar genome patterns identical with V. weberbaueri, suggesting a possible involvement of this species in the origin of V. x heilbornii. On the basis of discrepancy between morphological traits and the cpDNA profiles of some pairs of Vasconcellea species, we believe that besides V. x heilbornii, some other species have originated through interspecific hybridization. A reticulate evolution for Vasconcellea has therefore been suggested. Finally, intraspecific cpDNA variation was detected in V. microcarpa, thus providing molecular evidence for the high diversity previously indicated by morphological observations.