Diversity and Cytogenomic Characterization of Wild Carrots in the Macaronesian Islands.
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ABSTRACT:
SUBMITTER: Roxo G
PROVIDER: S-EPMC8473144 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:In eukaryotes, centromeres are the assembly sites for the kinetochore, a multi-protein complex to which spindle microtubules are attached at mitosis and meiosis, thereby ensuring segregation of chromosomes during cell division. They are specified by incorporation of CENH3, a centromere specific histone H3 variant which replaces canonical histone H3 in the nucleosomes of functional centromeres. To lay a first foundation of a putative alternative haploidization strategy based on centromere-mediated genome elimination in cultivated carrots, in the presented research we aimed at the identification and cloning of functional CENH3 genes in Daucus carota and three distantly related wild species of genus Daucus varying in basic chromosome numbers. Based on mining the carrot transcriptome followed by a subsequent PCR-based cloning, homologous coding sequences for CENH3s of the four Daucus species were identified. The ORFs of the CENH3 variants were very similar, and an amino acid sequence length of 146 aa was found in three out of the four species. Comparison of Daucus CENH3 amino acid sequences with those of other plant CENH3s as well as their phylogenetic arrangement among other dicot CENH3s suggest that the identified genes are authentic CENH3 homologs. To verify the location of the CENH3 protein in the kinetochore regions of the Daucus chromosomes, a polyclonal antibody based on a peptide corresponding to the N-terminus of DcCENH3 was developed and used for anti-CENH3 immunostaining of mitotic root cells. The chromosomal location of CENH3 proteins in the centromere regions of the chromosomes could be confirmed. For genetic localization of the CENH3 gene in the carrot genome, a previously constructed linkage map for carrot was used for mapping a CENH3-specific simple sequence repeat (SSR) marker, and the CENH3 locus was mapped on the carrot chromosome 9.
| S-EPMC4041860 | biostudies-literature
Project description:BackgroundCarrot is a crop with a wide range of phenotypic and molecular diversity. Within cultivated carrots, the western gene pool comprises types characterized by different storage root morphology. First western carrot cultivars originated from broad-based populations. It was followed by intercrosses among plants representing early open-pollinated cultivars, combined with mass phenotypic selection for traits of interest. Selective breeding improved root uniformity and led to the development of a range of cultivars differing in root shape and size. Based on the root shape and the market use of cultivars, a dozen of market types have been distinguished. Despite their apparent phenotypic variability, several studies have suggested that western cultivated carrot germplasm was genetically non-structured.ResultsNinety-three DcS-ILP markers and 2354 SNP markers were used to evaluate the structure of genetic diversity in the collection of 78 western type open-pollinated carrot cultivars, each represented by five plants. The mean percentage of polymorphic loci segregating within a cultivar varied from 31.18 to 89.25% for DcS-ILP markers and from 45.11 to 91.29% for SNP markers, revealing high levels of intra-cultivar heterogeneity, in contrast to its apparent phenotypic stability. Average inbreeding coefficient for all cultivars was negative for both DcS-ILP and SNP, whereas the overall genetic differentiation across all market classes, as measured by FST, was comparable for both marker systems. For DcS-ILPs 90-92% of total genetic variation could be attributed to the differences within the inferred clusters, whereas for SNPs the values ranged between 91 to 93%. Discriminant Analysis of Principal Components enabled the separation of eight groups cultivars depending mostly on their market type affiliation. Three groups of cultivars, i.e. Amsterdam, Chantenay and Imperator, were characterized by high homogeneity regardless of the marker system used for genotyping.ConclusionsBoth marker systems used in the study enabled detection of substantial variation among carrot plants of different market types, therefore can be used in germplasm characterization and analysis of genome relationships. The presented results likely reveal the actual genetic diversity structure within the western carrot gene pool and point at possible discrepancies within the cultivars' passport data.
| S-EPMC8077844 | biostudies-literature
Project description:Pollinator shifts are considered to drive floral trait evolution, yet little is still known about the modifications of petal epidermal surface at a biogeographic region scale. Here we investigated how independent shifts from insects to passerine birds in the Macaronesian Islands consistently modified this floral trait (i.e. absence of papillate cells). Using current phylogenies and extensive evidence from field observations, we selected a total of 81 plant species and subspecies for petal microscopy and comparative analysis, including 19 of the 23 insular species pollinated by opportunistic passerine birds (Macaronesian bird-flowered element). Species relying on passerine birds as the most effective pollinators (bird-pollinated) independently evolved at least five times and in all instances associated with a loss of papillate cells, whereas species with a mixed pollination system (birds plus insects and/or other vertebrates) evolved at least five times in Macaronesia and papillate cells were lost in only 25% of these transitions. Our findings suggest that petal micromorphology is a labile trait during pollinator shifts and that papillate cells tend to be absent on those species where pollinators have limited mechanical interaction with flowers, including opportunistic passerine birds that forage by hovering or from the ground.
| S-EPMC4881347 | biostudies-literature
Project description:Species richness on oceanic islands has been related to a series of ecological factors including island size and isolation (i.e. the Equilibrium Model of Island Biogeography, EMIB), habitat diversity, climate (i.e., temperature and precipitation) and more recently island ontogeny (i.e. the General Dynamic Model of oceanic island biogeography, GDM). Here we evaluate the relationship of these factors with the diversity of bryophytes in the Macaronesian region (Azores, Madeira, Canary Islands and Cape Verde). The predictive power of EMIB, habitat diversity, climate and the GDM on total bryophyte richness, as well as moss and liverwort richness (the two dominant bryophyte groups), was evaluated through ordinary least squares regressions. After choosing the best subset of variables using inference statistics, we used partial regression analyses to identify the independent and shared effects of each model. The variables included within each model were similar for mosses and liverworts, with orographic mist layer being one of the most important predictors of richness. Models combining climate with either the GDM or habitat diversity explained most of richness variation (up to 91%). There was a high portion of shared variance between all pairwise combinations of factors in mosses, while in liverworts around half of the variability in species richness was accounted for exclusively by climate. Our results suggest that the effects of climate and habitat are strong and prevalent in this region, while geographical factors have limited influence on Macaronesian bryophyte diversity. Although climate is of great importance for liverwort richness, in mosses its effect is similar to or, at least, indiscernible from the effect of habitat diversity and, strikingly, the effect of island ontogeny. These results indicate that for highly vagile taxa on oceanic islands, the dispersal process may be less important for successful colonization than the availability of suitable ecological conditions during the establishment phase.
| S-EPMC4086965 | biostudies-literature
Project description:The Mediterranean region, comprising the Mediterranean Basin and the Macaronesian Islands, represents a center of diversification for many organisms. The genetic structure and connectivity of mainland and island microbial populations has been poorly explored, in particular in the case of symbiotic fungi. Here we investigated genetic diversity and spatial structure of the obligate outcrossing lichen-forming fungus Parmelina carporrhizans in the Mediterranean region. Using eight microsatellite and mating-type markers we showed that fungal populations are highly diverse but lack spatial structure. This is likely due to high connectivity and long distance dispersal of fungal spores. Consistent with low levels of linkage disequilibrium and lack of clonality, we detected both mating-type idiomorphs in all populations. Furthermore we showed that the Macaronesian Islands are the result of colonization from the Mediterranean Basin. The unidirectional gene flow, though, seemed not to be sufficient to counterbalance the effects of drift, resulting in comparatively allelic poor peripheral populations. Our study is the first to shed light on the high connectivity and lack of population structure in natural populations of a strictly sexual lichen fungus. Our data further support the view of the Macaronesian Islands as the end of the colonization road for this symbiotic ascomycete.
| S-EPMC5244402 | biostudies-literature
Project description:The carrot is the most popular root vegetable worldwide. The genetic makeup underlying the development of the edible storage root are fragmentary. Here, we report the first comparative transcriptome analysis between wild and cultivated carrot roots at multiple developmental stages. Overall, 3285, 4637, and 570 genes were differentially expressed in the cultivated carrot in comparisons made for young plants versus developing roots, young plants versus mature roots, and developing roots versus mature roots, respectively. Of those, 1916, 2645, and 475, respectively, were retained after filtering out genes showing similar profiles of expression in the wild carrot. They were assumed to be of special interest with respect to the development of the storage root. Among them, transcription factors and genes encoding proteins involved in post-translational modifications (signal transduction and ubiquitination) were mostly upregulated, while those involved in redox signaling were mostly downregulated. Also, genes encoding proteins regulating cell cycle, involved in cell divisions, development of vascular tissue, water transport, and sugar metabolism were enriched in the upregulated clusters. Genes encoding components of photosystem I and II, together with genes involved in carotenoid biosynthesis, were upregulated in the cultivated roots, as opposed to the wild roots; however, they were largely downregulated in the mature storage root, as compared with the young and developing root. The experiment produced robust resources for future investigations on the regulation of storage root formation in carrot and Apiaceae.
| S-EPMC6162504 | biostudies-literature
Project description:BackgroundCryptosporidium spp. are worldwide protozoan parasites which include species that can lead to cryptosporidiosis in humans. Different animal species can serve as reservoirs and sources of dissemination of the disease, such as rodent species due their potential in transmitting zoonotic pathogens to humans and other animals. In the Canary Islands (Spain), Cryptosporidium parvum and Cryptosporidium hominis have been identified in patients with diarrhea. However, the occurrence of Cryptosporidium spp. in possible reservoirs in this archipelago remains unclear. Considering the zoonotic potential of these protozoans, the aim of the present study was to determine the presence of Cryptosporidium spp. in peridomestic wild rodents and the possible role of these mammals as a source of transmission of these protozoans in Canary Islands.MethodsA total of 179 rodents belonging to Rattus rattus and Mus musculus domesticus from four Canary Islands, La Palma, El Hierro, Tenerife and Lanzarote, were analyzed. Feces were screened for Cryptosporidium spp. by nested PCR of the 18S ribosomal RNA fragment and the sequences used for phylogenetic analyses.ResultsCryptosporidium spp. were found widely distributed with an overall prevalence of 12.30% in rodents (13.86% for R. rattus and 10.25% for M. m. domesticus). The overall prevalence by island was 19.60% for Tenerife, 7.14% for La Palma, 5.71% for El Hierro and 0% for Lanzarote. Cryptosporidium tyzzeri, Cryptosporidium meleagridis, Cryptosporidium muris and Cryptosporidium sp. rat genotype I and II/III were successfully identified, in addition to two unidentified Cryptosporidium genotypes.ConclusionsThis study contributes to the knowledge of the biodiversity and distribution of Cryptosporidium spp. in wild rodents from the Canary Islands, highlighting the presence of three zoonotic species, C. tyzzeri, C. meleagridis and C. muris, being the first detection of these three species in wild rodents in the Canary Islands and the first report of C. meleagridis in R. rattus. Given the results obtained in our study, future studies in non-sampled areas are required to better understand the epidemiology of these protozoans in wild rodents in the archipelago.
| S-EPMC7472698 | biostudies-literature
Project description:In sub-Saharan Africa, grain legumes (pulses) are essential food sources and play an important role in sustainable agriculture. Among the major pulse crops, the native cowpea (Vigna unguiculata) and introduced common bean (Phaseolus vulgaris) stand out. This paper has two main goals. First, we provide a comprehensive view of the available genetic resources of these genera in Africa, including data on germplasm collections and mapping biodiversity-rich areas. Second, we investigate patterns of physicochemical and cytogenomic variation across Africa to explore the geographical structuring of variation between native and introduced beans. Our results revealed that 73 Vigna and 5 Phaseolus species occur in tropical regions of Africa, with 8 countries accounting for more than 20 native species. Conversely, germplasm collections are poorly represented when compared to the worldwide collections. Regarding the nuclear DNA content, on average, V. unguiculata presents significantly higher values than P. vulgaris. Also, V. unguiculata is enriched in B, Mg, S, and Zn, while P. vulgaris has more Fe, Ca, and Cu. Overall, our study suggests that the physicochemical and cytogenomic diversity of native Vigna species is higher than previously thought, representing valuable food resources to reduce food insecurity and hunger, particularly of people living in African developing countries.
| S-EPMC8213759 | biostudies-literature
Project description:Background:Malignant mesothelioma (MM) is a rare aggressive cancer primary located in pleura and lung. MMs can be divided into biphasic, epithelioid and sarcomatoid subtypes. In majority of cases MMs are induced by asbestos fiber exposure. As latency period after asbestos exposure ranges between?~?10 and 60 years MMs are mainly observed in elder people. Human MM, being a rare tumor type, lacks detailed cytogenetic data, while molecular genetic studies have been undertaken more frequently. However, murine MM cell lines are also regularly applied to get more insight into MM biology and to test new therapy strategies. Results:Here the murine MM cell lines AB1, AB22 and AC29 were studied by molecular cytogenetics and molecular karyotyping. Interestingly, yet there were no genetic or genomic studies undertaken for these already in 1992 established cell lines. The obtained data on genomic imbalances in these murine cell lines was translated into the human genome as previously reported based on human and murine genomic browsers. Conclusions:It turned out that all three cell lines showed high similarities in copy number variants as observed typically in human MM. Also, all three cell lines were most similar to human epithelioid MMs, and should be used as models therefore.
| S-EPMC7488062 | biostudies-literature
Project description:The islands of Madeira and Selvagens are less than 300 km apart but offer a clear contrast between a densely populated and highly developed island (Madeira), and a largely uninhabited and remote archipelago (Selvagens) within Macaronesia in the eastern Atlantic. The Madeira Archipelago has ~260,000 inhabitants and receives over six million visitor days annually. The Selvagens Islands Reserve is one of the oldest nature reserves in Portugal and comprises two islands and several islets, including the surrounding shelf to a depth of 200 m. Only reserve rangers and a small unit of the maritime police inhabit these islands. The benthic community around Selvagens was dominated by erect and turf algae, while the community at Madeira was comprised of crustose coralline and turf algae, sessile invertebrates, and sea urchin barrens. The sea urchin Diadema africanum was 65% more abundant at Madeira than at Selvagens. Total fish biomass was 3.2 times larger at Selvagens than at Madeira, and biomass of top predators was more than 10 times larger at Selvagens. Several commercially important species (e.g., groupers, jacks), which have been overfished throughout the region, were more common and of larger size at Selvagens than at Madeira. Important sea urchin predators (e.g., hogfishes, triggerfishes) were also in higher abundance at Selvagens compared to Madeira. The effects of fishing and other anthropogenic influences are evident around Madeira. This is in stark contrast to Selvagens, which harbors healthy benthic communities with diverse algal assemblages and high fish biomass, including an abundance of large commercially important species. The clear differences between these two island groups highlights the importance of expanding and strengthening the protection around Selvagens, which harbors one of the last intact marine ecosystems in the North Atlantic, and the need to increase management and protection around Madeira.
| S-EPMC5685627 | biostudies-literature