Common Gene Pool Research Articles

Indirect Fitness Benefits Enable the Spread of Host Genes Promoting Costly Transfer of Beneficial Plasmids.

Bacterial genes that confer crucial phenotypes, such as antibiotic resistance, can spread horizontally by residing on mobile genetic elements (MGEs). Although many mobile genes provide strong benefits to their hosts, the fitness consequences of the process of transfer itself are less clear. In previous studies, transfer has been interpreted as a parasitic trait of the MGEs because of its costs to the host but also as a trait benefiting host populations through the sharing of a common gene pool. Here, we show that costly donation is an altruistic act when it spreads beneficial MGEs favoured when it increases the inclusive fitness of donor ability alleles. We show mathematically that donor ability can be selected when relatedness at the locus modulating transfer is sufficiently high between donor and recipients, ensuring high frequency of transfer between cells sharing donor alleles. We further experimentally demonstrate that either population structure or discrimination in transfer can increase relatedness to a level selecting for chromosomal transfer alleles. Both mechanisms are likely to occur in natural environments. The simple process of strong dilution can create sufficient population structure to select for donor ability. Another mechanism observed in natural isolates, discrimination in transfer, can emerge through coselection of transfer and discrimination alleles. Our work shows that horizontal gene transfer in bacteria can be promoted by bacterial hosts themselves and not only by MGEs. In the longer term, the success of cells bearing beneficial MGEs combined with biased transfer leads to an association between high donor ability, discrimination, and mobile beneficial genes. However, in conditions that do not select for altruism, host bacteria promoting transfer are outcompeted by hosts with lower transfer rate, an aspect that could be relevant in the fight against the spread of antibiotic resistance.

Beneficial role of D allele in controlling ACE levels: a study among Brahmins of north India.

India being a country with vast diversity is expected to have different dietary and life style patterns which in turn may lead to population-specific environmental risk factors. Further, the interaction of these risk factors with the genetic makeup of population makes it either susceptible or resistant to cardiovascular disease. One such candidate gene is angiotensin converting enzyme (ACE) for various cardiovascular mechanisms. ACE is the key enzyme of the renin angiotensin aldosterone system pathway which maintains homeostasis blood pressure in the body and any variation in the levels is reported to be associated with various complex diseases. The DD genotype is found to increase ACE levels, which is associated with cardiovascular diseases and decrease in ACE levels are associated with kidney diseases. The aim of this study was to understand the distribution of ACE I/D polymorphism and ACE levels among Brahmins of National Capital Region (NCR) north India, with respect to age and sex ratio distribution. In this study, 136 subjects of which 50 males and 86 females, who were unrelated up to first cousin, aged 25 to70 years were studied. ACE gene was found to be polymorphic with high frequency of heterozygote (ID) followed by II and DD genotypes. The studied population was found to be in Hardy-Weinberg equilibrium with respect to ACE I/D polymorphism (P = 0.55). I allele frequency was found to be higher (0.560) than the D allele (0.44). The median level of ACE was found to be 65.96 ng/mL (48.12-86.24) which is towards lower side of the normal range. ACE levels were found to be increased among individual having either of the homozygotes that is II or DD and higher frequency of heterozygote (ID) is indicative of advantage in the population by maintaining lower ACE levels. The limitation of the present study is low sample size, however, the merit is that the subjects belonged to a Mendalian population with a common gene pool.

Mitochondrial Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species.

Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. O. minuta has the potential to resist against various pathogenic diseases such as bacterial blight (BB), white backed planthopper (WBPH) and brown plant hopper (BPH). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. The mtDNA genome is 515,022 bp, containing 60 protein coding genes, 31 tRNA genes and two rRNA genes. The mitochondrial genome organization and the gene content at the nucleotide level are highly similar (89%) to that of O. rufipogon. Comparison with other related species revealed that most of the genes with known function are conserved among the Poaceae members. Similarly, O. minuta mt genome shared 24 protein-coding genes, 15 tRNA genes and 1 ribosomal RNA gene with other rice species (indica and japonica). The evolutionary relationship and phylogenetic analysis revealed that O. minuta is more closely related to O. rufipogon than to any other related species. Such studies are essential to understand the evolutionary divergence among species and analyze common gene pools to combat risks in the current scenario of a changing environment.

Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana.

The effects of the direct interaction between hybridization and speciation-two major contrasting evolutionary processes--are poorly understood. We present here the evolutionary history of the Galápagos marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient within--island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, the Galápagos land iguanas, around 4.5 million years ago (Ma), but divergence among extant populations is exceedingly young (less than 50,000 years). Despite Amblyrhynchus appearing as a single long-branch species phylogenetically, we find strong population structure between islands, and one case of incipient speciation of sister lineages within the same island--ostensibly initiated by volcanic events. Hybridization between both lineages is exceedingly rare, yet frequent hybridization with migrants from nearby islands is evident. The contemporary snapshot provided by highly variable markers indicates that speciation events may have occurred throughout the evolutionary history of marine iguanas, though these events are not visible in the deeper phylogenetic trees. We hypothesize that the observed interplay of speciation and hybridization might be a mechanism by which local adaptations, generated by incipient speciation, can be absorbed into a common gene pool, thereby enhancing the evolutionary potential of the species as a whole.

New microsatellite markers for Campanula scheuchzeri (Campanulaceae), with cross-amplification in C. rotundifolia.

Premise of the study:We developed new microsatellite primers for the alpine bellflower Campanula scheuchzeri. Allelic polymorphisms will be used to study differentiation along elevation gradients of C. scheuchzeri populations and in the co-occurring sister-species C. rotundifolia in the Alps.Methods and Results:We analyzed C. scheuchzeri from three high-elevation sites and C. rotundifolia from two low-elevation sites in Switzerland. Campanula scheuchzeri was found to be tetraploid (2n = 68 = 4x), and up to 22 alleles were found per locus and population. Of the 15 polymorphic loci developed for C. scheuchzeri, 10 loci were tested, all of which amplified in C. rotundifolia, with similar amplicon length. Campanula rotundifolia individuals also showed tetraploid signals.Conclusions:We speculate that C. scheuchzeri and C. rotundifolia share a common gene pool and evolve under vicariance. This presents a testable hypothesis that will be evaluated through future work. Our developed primers might also amplify in other related Campanula taxa.

The congruence between matrilineal genetic (mtDNA) and geographic diversity of Iranians and the territorial populations.

From the ancient era, emergence of Agriculture in the connecting region of Mesopotamia and the Iranian plateau at the foothills of the Zagros Mountains, made Iranian gene pool as an important source of populating the region. It has differentiated the population spread and different language groups. In order to trace the maternal genetic affinity between Iranians and other populations of the area and to establish the place of Iranians in a broad framework of ethnically and linguistically diverse groups of Middle Eastern and South Asian populations, a comparative study of territorial groups was designed and used in the population statistical analysis. Mix of 616 samples was sequenced for complete mtDNA or hyper variable regions in this study. A published dataset of neighboring populations was used as a comparison in the Iranian matrilineal lineage study based on mtDNA haplogroups. Statistical analyses data, demonstrate a close genetic structure of all Iranian populations, thus suggesting their origin from a common maternal ancestral gene pool and show that the diverse maternal genetic structure does not reflect population differentiation in the region in their language. In the aggregate of the eastward spreads of proto-Elamo-Dravidian language from the Southwest region of Iran, the Elam province, a reasonable degree of homogeneity has been observed among Iranians in this study. The approach will facilitate our perception of the more detailed relationship of the ethnic groups living in Iran with the other ancient peoples of the area, testing linguistic hypothesis and population movements.

Comparison among recognized and non-recognized Phaseolus vulgaris L. landraces as traditional agro-food products of the Campania region (Italy)

Efforts to safeguard and promote the on-farm maintenance of common bean (Phaseolus vulgaris L.) landraces should take seed quality into high consideration. Seed quality, in addition to suitable agronomic performances, is a good criterion to identify the most interesting materials among those traditionally cultivated. Ten landraces, still cultivated in the Campania region (southern Italy), were investigated. Five of these landraces, recognized as regional traditional agro-food products, are included in the list of the Italian typical products. Landraces belonging to both Mesoamerican and Andean common bean gene pools were present in the ten studied materials. The harvests of two subsequent growing seasons were analysed in order to compare the physico-chemical, culinary and nutritional seed quality of, recognised or not, landraces. Eighteen agronomic and nutritional traits were scored. When individually considered, none of the scored traits was able to discriminate the two groups of landraces. Conversely, submitting all traits to cluster analysis, two sub-clusters corresponding to recognised or not traditional products were obtained. Two landraces, one for each group, remained isolated. On the bases of these results, it can be inferred that the landraces recognized as traditional agro-food products have different culinary and nutritional characteristics in respect to the non-recognized ones.

Plasmids from Euryarchaeota.

Many plasmids have been described in Euryarchaeota, one of the three major archaeal phyla, most of them in salt-loving haloarchaea and hyperthermophilic Thermococcales. These plasmids resemble bacterial plasmids in terms of size (from small plasmids encoding only one gene up to large megaplasmids) and replication mechanisms (rolling circle or theta). Some of them are related to viral genomes and form a more or less continuous sequence space including many integrated elements. Plasmids from Euryarchaeota have been useful for designing efficient genetic tools for these microorganisms. In addition, they have also been used to probe the topological state of plasmids in species with or without DNA gyrase and/or reverse gyrase. Plasmids from Euryarchaeota encode both DNA replication proteins recruited from their hosts and novel families of DNA replication proteins. Euryarchaeota form an interesting playground to test evolutionary hypotheses on the origin and evolution of viruses and plasmids, since a robust phylogeny is available for this phylum. Preliminary studies have shown that for different plasmid families, plasmids share a common gene pool and coevolve with their hosts. They are involved in gene transfer, mostly between plasmids and viruses present in closely related species, but rarely between cells from distantly related archaeal lineages. With few exceptions (e.g., plasmids carrying gas vesicle genes), most archaeal plasmids seem to be cryptic. Interestingly, plasmids and viral genomes have been detected in extracellular membrane vesicles produced by Thermococcales, suggesting that these vesicles could be involved in the transfer of viruses and plasmids between cells.

Divergence of protein-coding capacity and regulation in the Bacillus cereus sensu lato group.

BackgroundThe Bacillus cereus sensu lato group contains ubiquitous facultative anaerobic soil-borne Gram-positive spore-forming bacilli. Molecular phylogeny and comparative genome sequencing have suggested that these organisms should be classified as a single species. While clonal in nature, there do not appear to be species-specific clonal lineages, excepting B. anthracis, in spite of the wide array of phenotypes displayed by these organisms.ResultsWe compared the protein-coding content of 201 B. cereus sensu lato genomes to characterize differences and understand the consequences of these differences on biological function. From this larger group we selected a subset consisting of 25 whole genomes for deeper analysis. Cluster analysis of orthologous proteins grouped these genomes into five distinct clades. Each clade could be characterized by unique genes shared among the group, with consequences for the phenotype of each clade. Surprisingly, this population structure recapitulates our recent observations on the divergence of the generalized stress response (SigB) regulons in these organisms. Divergence of the SigB regulon among these organisms is primarily due to the placement of SigB-dependent promoters that bring genes from a common gene pool into/out of the SigB regulon.ConclusionsCollectively, our observations suggest the hypothesis that the evolution of these closely related bacteria is a consequence of two distinct processes. Horizontal gene transfer, gene duplication/divergence and deletion dictate the underlying coding capacity in these genomes. Regulatory divergence overlays this protein coding reservoir and shapes the expression of both the unique and shared coding capacity of these organisms, resulting in phenotypic divergence. Data from other organisms suggests that this is likely a common pattern in prokaryotic evolution.

English

Willow (Salix spp.) includes closely related dioecious polyploid species, which are obligate outcrossers. Natural populations of willows and their hybrids are represented by a mixture of highly heterozygous genotypes sharing a common gene pool. Random amplified polymorphism DNAs (RAPD) and microsatellites (simple sequence repeats, SSRs) are useful methods for studying genetic diversity of willow (Salix spp.). RAPD delivers a large number of data points from a single experiment and is a useful method for distinguishing between closely related individuals. SSR markers are very robust tools, and we have identified several markers that show high levels of polymorphism in willow. Genetic characterization of 94 genotypes (four female, ten male, and 80 half sibs) of Salix collected from Naganji Nursery of University of Horticulture and Forestry, Solan, Himachal Pradesh, India were analyzed using 10 SSRs and 15 RAPDs PCR-based molecular markers. RAPD analysis yielded 87 polymorphic fragments (98.9%), with an average of 5.8 polymorphic fragments per primer. Similarly, SSR analysis produced 33 bands, out of which 26 were polymorphic (78.8%) with an average of 2.6 polymorphic fragments per primer. The genetic diversity was high among the genotypes (Nei’s genetic diversity = 0.354 and Shannon’s information index = 0.536) as measured by combination of both RAPD and SSR markers. The mean coefficient of gene differentiation (Gst) was 0.037, indicating 96.6% of the genetic diversity resided within the genotypes. It was found that the genetic diversity among genotypes was broader, suggesting the importance and feasibility of introducing elite genotypes from different hybrids for willows germplasm conservation and breeding programs.   Key words: Salix sp., female, male, half sibs, molecular markers, genetic diversity, Random amplified polymorphism DNAs (RAPD), simple sequence repeats (SSRs).

Genetic studies on morpho-phenological traits in lentil (Lens culinaris Medikus) wide crosses.

Genetic studies were undertaken in nine intersubspecific and interspecific crosses of lentil to understand the inheritance pattern of morphological characters viz., growth habit, flower colour, cotyledon colour and pod dehiscence. The F1 and F2 generations of these wide crosses were assessed and suggested monogenic inheritance of these traits. The segregation pattern of these qualitative traits will also help in the identification of true to type F1 plants from the interspecific crosses. All nine intersubspecific and interspecific crosses exhibited a wide variability for days to flowering, maturity and duration from flowering to maturity. The results indicated that these characters are governed by independent sets of genes during the growth and development phases. Heritability of both characters has been reported to be high in all wide crosses. In India, cultivated lentil species have an intrinsically narrow genetic base and that situation limits our plant breeder’s progress today (Earskine et al. 1998). To attain further breakthrough in increasing yield and improving stability in future crop cultivars, new sources of variation need to be incorporated into the cultivated gene pool. Therefore, some efforts for broadening the genetic base of lentil cultivars using wild Lens taxa have been initiated by the National Bureau of Plant Genetic Resources, Pusa, New Delhi, India (Singh et al. 2013), and also in some other research organizations (Ahmad et al. 1995; Fratini and Ruiz 2006; Gupta and Sharma 2007). Incorporation of different traits of interest in the background of cultivated varieties has helped in the flow of useful genes with increased allelic frequency from wild Lens taxa in the common gene pool of cultivated varieties (Ladizinsky et al. 1988).

No reduction in genetic diversity of Swiss stone pine (Pinus cembra L.) in Tatra Mountains despite high fragmentation and small population size

In Europe, most of the alpine timberline ecotone has been altered by human activities and climate change. Hence, mountain forests are of the highest conservation interest. Here, we screened 25 populations of Swiss stone pine (Pinus cembra L.) from the Carpathians and the Alps, using a set of ten microsatellite primers to assess the relative conservation value of populations sampled in Polish and Slovak Tatra National Parks, where potential extinction risk is the highest within the Carpathian range. Although endangered, with small and fragmented populations, P. cembra in the Tatra Mts. shows high levels of allelic richness (AR = 5.0) and observed heterozygosity (H o = 0.554). Our results suggest that anthropogenic habitat fragmentation has had little impact on DNA variation of Swiss stone pine in the Tatra Mts. However, the effects of changing conditions on the genetic structure may occur with a substantial time delay due to the long life span of P. cembra. Moreover, inbreeding depression may occur in the next generations, since we found inbreeding (F IS = 0.063) and elevated coancestry coefficient (θ = 0.062) in all populations. Also a shallow pattern of genetic differentiation between populations was found, indicating recent fragmentation of a common gene pool that formerly occupied a larger range. Therefore, the Tatra Mts. can be considered as a single conservation unit. Based on our results, we suggest possible conservation activities for Swiss stone pine both in Poland and Slovakia.

Pyramiding white mould resistance between and within common bean gene pools

Singh, S. P., Schwartz, H. F., Terán, H., Viteri, D. and Otto, K. 2014. Pyramiding white mould resistance between and within common bean gene pools. Can. J. Plant Sci. 94: 947–954. White mould caused by Sclerotinia sclerotiorum (Lib.) de Bary is a severe disease of common bean (Phaseolus vulgaris L.) in North America and similar production regions. Low to high levels of white mould resistance exist in cultivated and wild common bean and the secondary gene pool. But, cultivars with high levels of resistance are not yet available. The objectives of this study were: (1) to combine or pyramid high levels of resistance from multiple-parent populations between and within gene pools, and (2) to compare the response of pyramided breeding lines (PBL) to four isolates of the white mould pathogen with that of known sources of resistance. Two Andean PBL each derived from an Andean intra-gene pool and inter-gene pool, four Middle American pinto bean PBL from one inter-gene pool multiple-parent population, their seven resistant parents, and susceptible pinto, Othello, were inoculated in the greenhouse with pathogen isolates ARS12D and ND710 at University of Idaho, Kimberly in 2012, and isolates CO467 and NY133 at Colorado State University, Fort Collins in 2013. The percentage of resistant plants for the PBL ranged from 62.5 to 81.9, and mean white mould score from 4.0 to 4.6. The respective values for the white mould resistant parents ranged from 3.1 to 57.0 for the percentage of resistant plants and from 4.8 to 7.5 for the mean white mould score. Furthermore, PBL SE154-1 inoculated with isolate ARS12D, and SE152-6 with isolates ARS12D and ND710 had 100% resistant plants. But, only SE153-1 and SE155-9 inoculated with isolates CO467 and NY133 had significantly (P ≤0.05) higher levels of resistance than the most resistant parents A 195 and VA 19. The pinto bean PBL SE153-1, SE153-6, and SE153-7, and Andean types SE152-6 and SE155-9 were the most resistant among all genotypes inoculated with the four isolates of the white mould pathogen in both greenhouses.

Evidence supporting panmixia in Greenland halibut (Reinhardtius hippoglossoides) in the Northwest Atlantic

Assessment of population structure is critical to the design and implementation of sound management and conservation strategies. However, population structure must be assessed using markers attuned to population genetic processes such as genetic drift and gene flow, which reflect actual levels of reproductive isolation among putative genetic clusters. This is critical for highly exploited, commercial species that form the backbone of regional and local economies. Here, we show extremely low levels of population genetic differentiation among Greenland halibut (Reinhardtius hippoglossoides) collected from throughout the Northwest Atlantic, which cannot be statistically differentiated from panmixia using 12 species-specific polymorphic microsatellite markers. In contrast, some previous studies have demonstrated significant differences among individuals collected from various parts of the species’ range using a variety of both genetic and nongenetic techniques. In accordance with other reports and consistent with the species’ life history, we demonstrate that the most parsimonious explanation reconciling observed patterns is a repeated high degree of local differentiation of new recruits and colonizers originating from a common gene pool. Such a scenario has important conservation implications in terms of devising more appropriate strategies balancing species persistence and replenishment with sustainable resource use.

Bears in Pakistan: Distribution, Population Biology and Human Conflicts

We conducted questionnaire based interviews (n = 1873) of respondents coming from 258 localities about bear tracts in northern parts of Pakistan in 2012-2014 to study Himalyan brown (U. arctos isalbellinus) and Himalayan black (U. t. laniger) bears. Brown bears were more frequent in northern latitudes (northern Chitral, Ghizer, Gilgit and Skardu), while black bears were widely distributed in southern latitudes (Battagram). Both brown and black bears are present in central latitudes (Astor, Diamir, Kohistan and Mansehra). We identified 34 populations of brown bears; a large population in the Deosai Plateau and small to very small populations in other localities. We identified 9 isolated meta-populations sharing common gene pools; 7 (Bomborat, Gias, Chowgram, Laspur-Malkov, Koshi-Palas, Phunder-Yasin, Khunjerab) very small with serious inbreeding and threat of extinction, while Deosai and Diamir-Astor populations were large but were expected to have a high level inbreeding. Black bears were present in 45 localities; larger populations in three localities of Battagram (Nagram, Rahing and Shamli). We identified 6 meta-populations of black bears; Kohistan-Batagram-Mansehra, Diamir-Astor and south Chitral meta-populations were large; but 3 other populations (Thack, Hisper-Minipin and Chasma) were small/very small, possibly having high inbreeding. Bears raid standing maize crops (regular and severe in 2 localities and irregular and severe in 6) and fruit (apricot, grape, mulberry and walnut). Average annual bears depredation of 54 cattle, 188 goat/sheep, 4 yaks, and 9 horses/donkeys/mules were reported, inflicting an economic loss of Pak Rs. 2,840,000 (US$ 28,400) to the livestock farming community. Respondents reported 4 incidences of bear attack (1 killed, 3 injured) and 2 cases of cub poaching during 2013.

Mitochondrial DNA Variability among Six South American Amerindian Villages from the Pano Linguistic Group

Mitochondrial DNA Variability among Six South American Amerindian Villages from the Pano Linguistic Group Celso T. Mendes-Junior and Aguinaldo L. Simoes abstract Although scattered throughout a large geographic area, the members of the Pano linguistic group present strong ethnic, linguistic, and cultural homogeneity, a feature that causes them to be considered components of a same “Pano” tribe. Nevertheless, the genetic homogeneity between Pano villages has not yet been examined. To study the genetic structure of the Pano linguistic group, four major Native American mitochondrial DNA (mtDNA) founder haplogroups were analyzed in 77 Amerindians from six villages of four Pano tribes (Katukina, Kaxináwa, Marúbo, and Yaminawa) located in the Brazilian Amazon. The central position of these tribes in the continent makes them relevant for attempts to reconstruct population movements in South America. Except for a single individual that presented an African haplogroup L, all remaining individuals presented one of the four Native American haplogroups. Significant heterogeneity was observed across the six Pano villages. Although Amerindian populations are usually characterized by considerable interpopulational diversity, the high heterogeneity level observed is unexpected if the strong ethnic, linguistic, and cultural homogeneity of the Pano linguistic group is taken into account. The present findings indicate that the ethnic, linguistic, and cultural homogeneity does not imply genetic homogeneity. Even though the genetic heterogeneity uncovered may be a female-specific process, the most probable explanation for that is the joint action of isolation and genetic drift as major factors influencing the genetic structure of the Pano linguistic group. keywords Mtdna, Genetic Diversity, Amerindians, South America The central west region of the Brazilian Amazon attracts attention because of its central position in South America, which makes it relevant for attempts to reconstruct the population movements and biological relationships of South American indigenous populations. Many tribes inhabit the western part of the northern region of Brazil, including several that are classified as Pano. They descend from populations that used to inhabit the eastern Andean slopes of Ecuador. At the end of the seventeenth century, they experienced some migrational events that culminated in their distribution along the Juruá and Purus Rivers in the Brazilian territory and in adjacent portions of Peru (Mohrenweiser et al. 1979; Salzano and Jacques 1979). At that time, they suffered a series of fissions that gave rise to the current tribes (Salzano and Jacques 1979). In spite of their large geographic distribution, the Pano group attracts attention for its remarkable ethnic homogeneity, reinforced by outstanding cultural and linguistic cohesion [End Page 93] (Erikson 1998). For instance, a linguistic analysis based on the cognate density disclosed a high degree of mutual intelligibility (Mohrenweiser et al. 1979), even greater than that encountered among the various subdivisions of the Yanomami (Spielman et al. 1974). Therefore, the several Pano groups are sometimes considered as members of a single Pano tribe (Mohrenweiser et al. 1979; Salzano and Jacques 1979). The genetic structure of the Pano group has not been comprehensively studied. So far, analyses of classical genetic markers, including both blood groups and erythrocyte and serum proteins (ABO, Kell, MNSs, P, Rh, Duffy, Kidd, Diego, haptoglobin, GC, transferrin, albumin, Lewis, ceruloplasmin, Gm, Km, phosphoglucomutase, acid phosphatase, galactose-1-phosphate uridyltransferase, and esterase D), revealed that the Brazilian and Peruvian Kaxináwa (one of the Pano tribes) can be grouped in a common gene pool, while Kaxináwa and Katukina (another Pano tribe) are somewhat more heterogeneous (Salzano and Jacques 1979). The only DNA markers that were exhaustively studied in Pano populations were two HLA-G polymorphisms: a cytosine deletion (ΔC) at codon 130 in exon 3 that determines a premature stop codon (Mendes-Junior et al. 2007a) and a 14-bp insertion/ deletion polymorphism at exon 8 of the HLA-G gene (Mendes-Junior et al. 2007b). While the ΔC was not observed in the four Pano tribes, the 14-bp insertion/deletion polymorphism revealed heterogeneous insertion frequencies that ranged from 36.11% (Marúbo) to 77.78% (Kaxináwa) (Mendes-Junior et al. 2007a, 2007b). Mitochondrial DNA (mtDNA) haplogroups, which present a matrilineal pattern of inheritance, have yet to be extensively analyzed among the Pano Indians. Although mtDNA markers have already been analyzed in many South American...

Identification of resistance to rust (Uromyces appendiculatus) and powdery mildew (Erysiphe diffusa) in Portuguese common bean germplasm

AbstractPortugal has a diverse common bean germplasm, which is still grown in farmers' fields. In this work, we searched for resistance to rust (Uromyces appendiculatus) and powdery mildew (Erysiphe diffusa) in a representative collection of the Portuguese common bean germplasm. Despite many accessions depicting intermediate levels of resistance when compared to the susceptible check, 24 and 13 accessions showed low levels of infection, in spite of a compatible interaction (disease severity (DS) values lower than 5% and infection type (IT) of 4), to rust and powdery mildew, respectively, indicative of partial resistance. Moreover, a resistant reaction was observed in 11 accessions when inoculated with powdery mildew (IT = 0–1) and in additional 11 accessions (one in common) when inoculated with rust (IT = 0–2). The levels of resistance found in this report anticipate great potential of the Portuguese national germplasm, recently reported as genetically closer to the Andean common bean gene pool, for disease resistance breeding of this important crop.

Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits

Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.

Genetic and phenoptypic differentiation of zebra mussel populations colonizing Spanish river basins

Zebra mussel populations in Ebro and Mijares Rivers (northern Spain) were analyzed to study the mechanisms by which this aquatic species deals with pollution. Variability analyses of mitochondrial cytochrome oxidase I gene and of one nuclear microsatellite were performed for ten populations from the Ebro River and one from the Mijares River. Comparison of these results with those from five additional European populations indicated that the Spanish populations constitute a homogeneous gene pool. Transcriptome analyses of gill samples from a subset of the Spanish populations showed changes on expression levels that correlated with variations in general fitness and loads of heavy metals. The less polluted upstream Ebro populations showed overexpression of mitochondrial and cell proliferation-related genes compared to the more polluted, downstream Ebro populations. Our data indicate that heavy metals were the main factors explaining these transcriptomic patterns, and that zebra mussel is resilient to pollutants (like mercury and organochlorine compounds) proved to be extremely toxic to vertebrates. We propose that zebra mussel populations sharing a common gene pool may acclimate to different levels and forms of pollution through modulations in their transcriptomic profile, although direct selection on genes showing differential expression patterns cannot be ruled out.

Human races

Human races