Genetics and Molecular Biology
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Open Access journal
ISSN (Print) 1415-4757
Published by SciELO [714 journals]
- The complete mitochondrial genome of the threatened Neotropical catfish
Lophiosilurus alexandri (Silurifomes: Pseudopimelodidae) and phylogenomic
analysis indicate monophyly of Pimelodoidea
Abstract: Lophiosilurus alexandri is an endemic catfish from the São Francisco River Basin (Brazil) popularly known as pacamã, which has economic potential for aquaculture farming. The mitochondrial genome was sequenced for the threatened Neotropical catfish L. alexandri. Assembly into scaffolds using MIRA and MITObim software produced the whole, circularized mitochondrial genome, which comprises 16,445 bp and presents the typical gene arrangement of Teleostei mitochondria. A phylogenomic analysis was performed after the concatenation of all proteins obtained from whole mitogenomes of 20 Siluriformes and two outgroups. The results confirmed the monophyly of nine families of catfishes and also clustered L. alexandri as a sister group to the family Pimelodidae, thus confirming the monophyly of the superfamily Pimelodoidea. This is the first mitochondrial phylogenomics study for Pimelodoidea and the first mitogenome described for the Pseudopimelodidae family, representing an important resource for phylogeography, evolutionary biology, and conservation genetics studies in Neotropical fishes.
- Evolutionary analysis of apolipoprotein E by Maximum Likelihood and
complex network methods
Abstract: Apolipoprotein E (apo E) is a human glycoprotein with 299 amino acids, and it is a major component of very low density lipoproteins (VLDL) and a group of high-density lipoproteins (HDL). Phylogenetic studies are important to clarify how various apo E proteins are related in groups of organisms and whether they evolved from a common ancestor. Here, we aimed at performing a phylogenetic study on apo E carrying organisms. We employed a classical and robust method, such as Maximum Likelihood (ML), and compared the results using a more recent approach based on complex networks. Thirty-two apo E amino acid sequences were downloaded from NCBI. A clear separation could be observed among three major groups: mammals, fish and amphibians. The results obtained from ML method, as well as from the constructed networks showed two different groups: one with mammals only (C1) and another with fish (C2), and a single node with the single sequence available for an amphibian. The accordance in results from the different methods shows that the complex networks approach is effective in phylogenetic studies. Furthermore, our results revealed the conservation of apo E among animal groups.
- Contribution of WUSCHEL-related homeobox (WOX) genes to identify the
phylogenetic relationships among Petunia species
Abstract: Developmental genes are believed to contribute to major changes during plant evolution, from infrageneric to higher levels. Due to their putative high sequence conservation, developmental genes are rarely used as molecular markers, and few studies including these sequences at low taxonomic levels exist. WUSCHEL-related homeobox genes (WOX) are transcription factors exclusively present in plants and are involved in developmental processes. In this study, we characterized the infrageneric genetic variation of Petunia WOX genes. We obtained phylogenetic relationships consistent with other phylogenies based on nuclear markers, but with higher statistical support, resolution in terminals, and compatibility with flower morphological changes.
- Oxytocin and arginine vasopressin receptor evolution: implications for
adaptive novelties in placental mammals
Abstract: Oxytocin receptor (OXTR) and arginine vasopressin receptors (AVPR1a, AVPR1b, and AVPR2) are paralogous genes that emerged through duplication events; along the evolutionary timeline, owing to speciation, numerous orthologues emerged as well. In order to elucidate the evolutionary forces that shaped these four genes in placental mammals and to reveal specific aspects of their protein structures, 35 species were selected. Specifically, we investigated their molecular evolutionary history and intrinsic protein disorder content, and identified the presence of short linear interaction motifs. OXTR seems to be under evolutionary constraint in placental mammals, whereas AVPR1a, AVPR1b, and AVPR2 exhibit higher evolutionary rates, suggesting that they have been under relaxed or experienced positive selection. In addition, we describe here, for the first time, that the OXTR, AVPR1a, AVPR1b, and AVPR2 mammalian orthologues preserve their disorder content, while this condition varies among the paralogues. Finally, our results reveal the presence of short linear interaction motifs, indicating possible functional adaptations related to physiological and/or behavioral taxa-specific traits.
- Gene expression analysis reveals important pathways for drought response
in leaves and roots of a wheat cultivar adapted to rainfed cropping in the
Abstract: Drought limits wheat production in the Brazilian Cerrado biome. In order to search for candidate genes associated to the response to water deficit, we analyzed the gene expression profiles, under severe drought stress, in roots and leaves of the cultivar MGS1 Aliança, a well-adapted cultivar to the Cerrado. A set of 4,422 candidate genes was found in roots and leaves. The number of down-regulated transcripts in roots was higher than the up-regulated transcripts, while the opposite occurred in leaves. The number of common transcripts between the two tissues was 1,249, while 2,124 were specific to roots and 1,049 specific to leaves. Quantitative RT-PCR analysis revealed a 0.78 correlation with the expression data. The candidate genes were distributed across all chromosomes and component genomes, but a greater number was mapped on the B genome, particularly on chromosomes 3B, 5B and 2B. When considering both tissues, 116 different pathways were induced. One common pathway, among the top three activated pathways in both tissues, was starch and sucrose metabolism. These results pave the way for future marker development and selection of important genes and are useful for understanding the metabolic pathways involved in wheat drought response.
- Molecular cloning and characterization of a novel freezing-inducible
DREB1/CBF transcription factor gene in boreal plant Iceland poppy (Papaver
Abstract: DREB1 of the AP2/ERF superfamily plays a key role in the regulation of plant response to low temperatures. In this study, a novel DREB1/CBF transcription factor, PnDREB1, was isolated from Iceland poppy (Papaver nudicaule), a plant adaptive to low temperature environments. It is homologous to the known DREB1s of Arabidopsis and other plant species. It also shares similar 3D structure, and conserved and functionally important motifs with DREB1s of Arabidopsis. The phylogenetic analysis indicated that the AP2 domain of PnDREB1 is similar to those of Glycine max, Medicago truncatula, and M. sativa. PnDREB1 is constitutively expressed in diverse tissues and is increased in roots. qPCR analyses indicated that PnDREB1 is significantly induced by freezing treatment as well as by abscissic acid. The expression levels induced by freezing treatment were higher in the variety with higher degree of freezing tolerance. These results suggested that PnDREB1 is a novel and functional DREB1 transcription factor involved in freezing response and possibly in other abiotic stresses. Furthermore, the freezing-induction could be suppressed by exogenous gibberellins acid, indicating that PnDREB1 might play some role in the GA signaling transduction pathway. This study provides a basis for better understanding the roles of DREB1 in adaption of Iceland poppy to low temperatures.
- The rearranged mitochondrial genome of Leptopilina boulardi (Hymenoptera:
Figitidae), a parasitoid wasp of Drosophila
Abstract: The partial mitochondrial genome sequence of Leptopilina boulardi (Hymenoptera: Figitidae) was characterized. Illumina sequencing was used yielding 35,999,679 reads, from which 102,482 were utilized in the assembly. The length of the sequenced region of this partial mitochondrial genome is 15,417 bp, consisting of 13 protein-coding, two rRNA, and 21tRNA genes (the trnaM failed to be sequenced) and a partial A+T-rich region. All protein-coding genes start with ATN codons. Eleven protein-coding genes presented TAA stop codons, whereas ND6 and COII that presented TA, and T nucleotides, respectively. The gene pattern revealed extensive rearrangements compared to the typical pattern generally observed in insects. These rearrangements involve two protein-coding and two ribosomal genes, along with the 16 tRNA genes. This gene order is different from the pattern described for Ibalia leucospoides (Ibaliidae, Cynipoidea), suggesting that this particular gene order can be variable among Cynipoidea superfamily members. A maximum likelihood phylogenetic analysis of the main groups of Apocrita was performed using amino acid sequence of 13 protein-coding genes, showing monophyly for the Cynipoidea superfamily within the Hymenoptera phylogeny.
- Wolbachia in guilds of Anastrepha fruit flies (Tephritidae) and parasitoid
Abstract: The endosymbiont Wolbachia is efficiently transmitted from females to their progenies, but horizontal transmission between different taxa is also known to occur. Aiming to determine if horizontal transmission might have occurred between Anastrepha fruit flies and associated braconid wasps, infection by Wolbachia was screened by amplification of a fragment of the wsp gene. Eight species of the genus Anastrepha were analyzed, from which six species of associated parasitoid wasps were recovered. The endosymbiont was found in seven Anastrepha species and in five species of braconids. The WSP Typing methodology detected eight wsp alleles belonging to Wolbachia supergroup A. Three were already known and five were new ones, among which four were found to be putative recombinant haplotypes. Two samples of Anastrepha obliqua and one sample of Doryctobracon brasiliensis showed multiple infection. Single infection by Wolbachia was found in the majority of samples. The distribution of Wolbachia harboring distinct alleles differed significantly between fruit flies and wasps. However, in nine samples of fruit flies and associated wasps, Wolbachia harbored the same wsp allele. These congruences suggest that horizontal transfer of Wolbachia might have occurred in the communities of fruit flies and their braconid parasitoids.
- The histone genes cluster in Rhynchosciara americana and its transcription
profile in salivary glands during larval development
Abstract: In this work we report the characterization of the Rhynchosciara americana histone genes cluster nucleotide sequence. It spans 5,131 bp and contains the four core histones and the linker histone H1. Putative control elements were detected. We also determined the copy number of the tandem repeat unit through quantitative PCR, as well as the unequivocal chromosome location of this unique locus in chromosome A band 13. The data were compared with histone clusters from the genus Drosophila, which are the closest known homologues.
- Expression of myogenes in longissimus dorsi muscle during prenatal
development in commercial and local Piau pigs
Abstract: This study used qRT-PCR to examine variation in the expression of 13 myogenes during muscle development in four prenatal periods (21, 40, 70 and 90 days post-insemination) in commercial (the three-way Duroc, Landrace and Large-White cross) and local Piau pig breeds that differ in muscle mass. There was no variation in the expression of the CHD8, EID2B, HIF1AN, IKBKB, RSPO3, SOX7 and SUFU genes at the various prenatal ages or between breeds. The MAP2K1 and RBM24 genes showed similar expression between commercial and Piau pigs but greater expression (p < 0.05) in at least one prenatal period. Pair-wise comparisons of prenatal periods in each breed showed that only the CSRP3, LEF1, MRAS and MYOG genes had higher expression (p < 0.05) in at least one prenatal period in commercial and Piau pigs. Overall, these results identified the LEF1 gene as a primary candidate to account for differences in muscle mass between the pig breeds since activation of this gene may lead to greater myoblast fusion in the commercial breed compared to Piau pigs. Such fusion could explain the different muscularity between breeds in the postnatal periods.
- Uniparental ancestry markers in Chilean populations
Abstract: The presence of Native Americans, Europeans, and Africans has led to the development of a multi-ethnic, admixed population in Chile. This study aimed to contribute to the characterization of the uniparental genetic structure of three Chilean regions. Newborns from seven hospitals in Independencia, Providencia, Santiago, Curicó, Cauquenes, Valdívia, and Puerto Montt communes, belonging to the Chilean regions of Santiago, Maule, and Los Lagos, were studied. The presence of Native American mitochondrial DNA (mtDNA) haplogroups and two markers present in the non-recombinant region of the Y chromosome, DYS199 and DYS287, indicative of Native American and African ancestry, respectively, was determined. A high Native American matrilineal contribution and a low Native American and African patrilineal contributions were found in all three studied regions. As previously found in Chilean admixed populations, the Native American matrilineal contribution was lower in Santiago than in the other studied regions. However, there was an unexpectedly higher contribution of Native American ancestry in one of the studied communes in Santiago, probably due to the high rate of immigration from other regions of the country. The population genetic sub-structure we detected in Santiago using few uniparental markers requires further confirmation, owing to possible stratification for autosomal and X-chromosome markers.
- Genetic frequencies related to severe or profound sensorineural hearing
loss in Inner Mongolia Autonomous Region
Abstract: The aim was to study the frequencies of common deafness-related mutations and their contribution to hearing loss in different regions of Inner Mongolia. A total of 738 deaf children were recruited from five different ethnic groups of Inner Mongolia, including Han Chinese (n=486), Mongolian (n=216), Manchurian (n=24), Hui (n=6) and Daur (n=6). Nine common mutations in four genes (GJB2, SLC26A4, GJB3 and mitochondrial MT-RNR1 gene) were detected by allele-specific PCR and universal array. At least one mutated allele was detected in 282 patients. Pathogenic mutations were detected in 168 patients: 114 were homozygotes and 54 were compound heterozygotes. The 114 patients were carriers of only one mutated allele. The frequency of GJB2 variants in Han Chinese (21.0%) was higher than that in Mongolians (16.7%), but not significantly different. On the other hand, the frequency of SLC26A4 variants in Han Chinese (14.8%) was lower than that in Mongolians (19.4%), but also not significantly different. The frequency of patients with pathogenic mutations was different in Ulanqab (21.4%), Xilingol (40.0%), Chifeng (40.0%), Hulunbeier (30.0%), Hohhot (26.3%), and in Baotou (0%). In conclusion, the frequency of mutated alleles in deafness-related genes did not differ between Han Chinese and Mongolians. However, differences in the distribution of common deafness-related mutations were found among the investigated areas of Inner Mongolia.
- Association between interleukin 6 -174 G/C promoter gene polymorphism and
runners' responses to the dietary ingestion of antioxidant supplementation
based on pequi (Caryocar brasiliense Camb.) oil: a before-after study
Abstract: Exercise is a double-edged sword: when practiced in moderation, it increases the expression of antioxidant enzymes, but when practiced strenuously it causes oxidative stress and cell damage. In this context, polymorphisms in the interleukin (IL)-6 gene should be investigated better because they can influence performance, at least in exercise that generates oxidative stress and leads to muscular injuries with consequent inflammation. In this work, we investigated the influence of IL-6 –174 G/C polymorphism on tissue damage and inflammation markers, lipid peroxidation, hemogram and lipid profile of runners before and after ingestion of 400 mg of pequi oil in capsules supplied daily for 14 consecutive days. The IL-6 genotypes were associated with significant differences in lipid peroxidation, with the CC mutant having lower values. There were also significant differences among these genotypes in the response to supplementation with pequi oil, exercise-induced damage and C-reactive protein (CRP) levels. The best protection against damage was observed with the heterozygous genotype. Although the CC genotype showed an increase in CRP levels after supplementation, the lack of a positive correlation between triglycerides and high-sensitivity CRP in this mutant genotype after supplementation indicated a protective effect of pequi. These findings deserve further investigation, particularly with regard to the quantification of circulating IL-6 concentrations.
- Polymorphisms FTO rs9939609, PPARG rs1801282 and ADIPOQ rs4632532 and
rs182052 but not lifestyle are associated with obesity related-traits in
Abstract: Concerning the genetic factors of obesity, no consistent association between populations has been reported, which may be due to the frequency of polymorphisms, the lifestyle of studied populations and its interaction with other factors. We studied a possible association of polymorphisms FTO rs9939609, PPARG rs1801282, and ADIPOQ rs4632532 and rs182052 with obesity phenotypes in 215 Mexican children. Glucose, triglycerides, cholesterol, HDL and LDL were measured. In addition, weight, height, waist circumference and triceps skin thickness were recorded. High-energy diets and sedentary behavior were evaluated with a validated questionnaire. In contrast with other reports, only FTO rs9939609 was associated with obesity related-traits, including BMI (p = 0.03), waist circumference (p = 0.02), triceps skinfold (p = 0.03) and waist/height ratio (p = 0.01), and also with cholesterol levels (p = 0.02) and LDL (p = 0.009). Lower levels of triglycerides (p=0.04) were related with presence of PPARG rs1801282, while ADIPOQ rs4632532 showed an effect on HDL (p = 0.03) levels. On the other hand, diet, physical activity and screen time were not related with obesity. In summary, only FTO rs9939609 was associated with obesity related-traits, while PPARG2 rs1801282 and ADIPOQ rs4632532 were involved in lipid metabolism.
- Molecular data highlight hybridization in squirrel monkeys
Abstract: Hybridization has been reported increasingly frequently in recent years, fueling the debate on its role in the evolutionary history of species. Some studies have shown that hybridization is very common in captive New World primates, and hybrid offspring have phenotypes and physiological responses distinct from those of the "pure" parents, due to gene introgression. Here we used the TA15 Alu insertion to investigate hybridization in the genus Saimiri. Our results indicate the hybridization of Saimiri boliviensis peruviensis with S. sciureus macrodon, and S. b. boliviensis with S. ustus. Unexpectedly, some hybrids of both S. boliviensis peruviensis and S. b. boliviensis were homozygous for the absence of the insertion, which indicates that the hybrids were fertile.
- Diversity and evolution of plant diacylglycerol acyltransferase (DGATs)
unveiled by phylogenetic, gene structure and expression analyses
Abstract: Since the first diacylglycerol acyltransferase (DGAT) gene was characterized in plants, a number of studies have focused on understanding the role of DGAT activity in plant triacylglycerol (TAG) biosynthesis. DGAT enzyme is essential in controlling TAGs synthesis and is encoded by different genes. DGAT1 and DGAT2 are the two major types of DGATs and have been well characterized in many plants. On the other hand, the DGAT3 and WS/DGAT have received less attention. In this study, we present the first general view of the presence of putative DGAT3 and WS/DGAT in several plant species and report on the diversity and evolution of these genes and its relationships with the two main DGAT genes (DGAT1 and DGAT2). According to our analyses DGAT1, DGAT2, DGAT3 and WS/DGAT are very divergent genes and may have distinct origin in plants. They also present divergent expression patterns in different organs and tissues. The maintenance of several types of genes encoding DGAT enzymes in plants demonstrates the importance of DGAT activity for TAG biosynthesis. Evolutionary history studies of DGATs coupled with their expression patterns help us to decipher their functional role in plants, helping to drive future biotechnological studies.
- The effects of old and recent migration waves in the distribution of HBB*S
globin gene haplotypes
Abstract: Sickle cell hemoglobin is the result of a mutation at the sixth amino acid position of the beta (β) globin chain. The HBB*S gene is in linkage disequilibrium with five main haplotypes in the β-globin-like gene cluster named according to their ethnic and geographic origins: Bantu (CAR), Benin (BEN), Senegal (SEN), Cameroon (CAM) and Arabian-Indian (ARAB). These haplotypes demonstrated that the sickle cell mutation arose independently at least five times in human history. The distribution of βS haplotypes among Brazilian populations showed a predominance of the CAR haplotype. American populations were clustered in two groups defined by CAR or BEN haplotype frequencies. This scenario is compatible with historical records about the slave trade in the Americas. When all world populations where the sickle cell gene occurs were analyzed, three clusters were disclosed based on CAR, BEN or ARAB haplotype predominance. These patterns may change in the next decades due to recent migrations waves. Since these haplotypes show different clinical characteristics, these recent migrations events raise the necessity to develop optimized public health programs for sickle cell disease screening and management.
- Agmatoploidy and symploidy: a critical review
Abstract: Agmatoploidy is a type of chromosome rearrangement that involves the fragmentation of an entire chromosome complement, generating a diploid with double its original chromosome number. Agmatoploidy and other related karyotype changes, such as symploidy (the opposite change, promoted by chromosome fusion), partial agmatoploidy, polyagmatoploidy, etc., are restricted to species with holokinetic chromosomes and are assumed to play an important role in their karyotype evolution. However, a critical review of the literature shows that examples of chromosome number doubling by agmatoploidy are rare and not clearly demonstrated, while partial agmatoploidy and partial symploidy seem to be the same as ascending and descending disploidy, respectively. It is therefore proposed here that these terms should be avoided or even abolished.
- Familial Dysautonomia: Mechanisms and Models
Abstract: Hereditary Sensory and Autonomic Neuropathies (HSANs) compose a heterogeneous group of genetic disorders characterized by sensory and autonomic dysfunctions. Familial Dysautonomia (FD), also known as HSAN III, is an autosomal recessive disorder that affects 1/3,600 live births in the Ashkenazi Jewish population. The major features of the disease are already present at birth and are attributed to abnormal development and progressive degeneration of the sensory and autonomic nervous systems. Despite clinical interventions, the disease is inevitably fatal. FD is caused by a point mutation in intron 20 of the IKBKAP gene that results in severe reduction in expression of IKAP, its encoded protein. In vitro and in vivo studies have shown that IKAP is involved in multiple intracellular processes, and suggest that failed target innervation and/or impaired neurotrophic retrograde transport are the primary causes of neuronal cell death in FD. However, FD is far more complex, and appears to affect several other organs and systems in addition to the peripheral nervous system. With the recent generation of mouse models that recapitulate the molecular and pathological features of the disease, it is now possible to further investigate the mechanisms underlying different aspects of the disorder, and to test novel therapeutic strategies.
- The second of a series of articles for the 60th anniversary of the
Brazilian Society of Genetics
- The diversity of citrus endophytic bacteria and their interactions with
Xylella fastidiosa and host plants
Abstract: The bacterium Xylella fastidiosa is the causal agent of citrus variegated chlorosis (CVC) and has been associated with important losses in commercial orchards of all sweet orange [Citrus sinensis (L.)] cultivars. The development of this disease depends on the environmental conditions, including the endophytic microbial community associated with the host plant. Previous studies have shown that X. fastidiosa interacts with the endophytic community in xylem vessels as well as in the insect vector, resulting in a lower bacterial population and reduced CVC symptoms. The citrus endophytic bacterium Methylobacterium mesophilicum can trigger X. fastidiosa response in vitro, which results in reduced growth and induction of genes associated with energy production, stress, transport, and motility, indicating that X. fastidiosa has an adaptive response to M. mesophilicum. Although this response may result in reduced CVC symptoms, the colonization rate of the endophytic bacteria should be considered in studies that intend to use this endophyte to suppress CVC disease. Symbiotic control is a new strategy that uses symbiotic endophytes as biological control agents to antagonize or displace pathogens. Candidate endophytes for symbiotic control of CVC must occupy the xylem of host plants and attach to the precibarium of sharpshooter insects to access the pathogen. In the present review, we focus on interactions between endophytic bacteria from sweet orange plants and X. fastidiosa, especially those that may be candidates for control of CVC.