Venom gland transcriptomes and proteomes of six
taxa (
,
,
,
,
, and
) were investigated, providing the most comprehensive, quantitative data on
venom composition to date, and more than tripling the ...number of
venom protein sequences previously available. The six venomes differ dramatically. All are dominated by 2-6 toxin classes that account for 91-99% of the toxin transcripts. The
venome is compositionally the simplest. In it, three-finger toxins (3FTxs) and phospholipases A₂ (PLA₂s) comprise >99% of the toxin transcripts, which include only four additional toxin families at levels ≥0.1%.
venom is the most complex, with at least 17 toxin families. However, in each venome, multiple structural subclasses of 3FTXs and PLA₂s are present. These almost certainly differ in pharmacology as well. All venoms also contain phospholipase B and vascular endothelial growth factors. Minor components (0.1-2.0%) are found in all venoms except that of
. Other toxin families are present in all six venoms at trace levels (<0.005%). Minor and trace venom components differ in each venom. Numerous novel toxin chemistries include 3FTxs with previously unknown 8- and 10-cysteine arrangements, resulting in new 3D structures and target specificities. 9-cysteine toxins raise the possibility of covalent, homodimeric 3FTxs or heterodimeric toxins with unknown pharmacologies. Probable muscarinic sequences may be reptile-specific homologs that promote hypotension via vascular mAChRs. The first complete sequences are presented for 3FTxs putatively responsible for liberating glutamate from rat brain synaptosomes.
C-type lectin-like proteins may have 6-9 cysteine residues and may be monomers, or homo- or heterodimers of unknown pharmacology. Novel KSPIs, 3× longer than any seen previously, appear to have arisen in three species by gene duplication and fusion. Four species have transcripts homologous to the nociceptive toxin, (MitTx) α-subunit, but all six species had homologs to the β-subunit. The first non-neurotoxic, non-catalytic elapid phospholipase A₂s are reported. All are probably myonecrotic. Phylogenetic analysis indicates that the six taxa diverged 15-35 million years ago and that they split from their last common ancestor with Old World elapines nearly 55 million years ago. Given their early diversification, many cryptic micrurine taxa are anticipated.
Stryphnodendron adstringens is a medicinal plant belonging to the Leguminosae family, and it is commonly found in the southeastern savannas, endemic to the Cerrado biome. The goal of this study was ...to assemble and annotate the chloroplast genome of S. adstringens and to compare it with previously known genomes of the mimosoid clade within Leguminosae. The chloroplast genome was reconstructed using de novo and referenced-based assembly of paired-end reads generated by shotgun sequencing of total genomic DNA. The size of the S. adstringens chloroplast genome was 162,169 bp. This genome included a large single-copy (LSC) region of 91,045 bp, a small single-copy (SSC) region of 19,014 bp and a pair of inverted repeats (IRa and IRb) of 26,055 bp each. The S. adstringens chloroplast genome contains a total of 111 functional genes, including 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. A total of 137 SSRs and 42 repeat structures were identified in S. adstringens chloroplast genome, with the highest proportion in the LSC region. A comparison of the S. adstringens chloroplast genome with those from other mimosoid species indicated that gene content and synteny are highly conserved in the clade. The phylogenetic reconstruction using 73 conserved coding-protein genes from 19 Leguminosae species was supported to be paraphyletic. Furthermore, the noncoding and coding regions with high nucleotide diversity may supply valuable markers for molecular evolutionary and phylogenetic studies at different taxonomic levels in this group.
Mantel test in population genetics Diniz-Filho, José Alexandre F; Soares, Thannya N; Lima, Jacqueline S ...
Genetics and Molecular Biology,
01/2013, Letnik:
36, Številka:
4
Journal Article
Recenzirano
Odprti dostop
The comparison of genetic divergence or genetic distances, estimated by pairwise FST and related statistics, with geographical distances by Mantel test is one of the most popular approaches to ...evaluate spatial processes driving population structure. There have been, however, recent criticisms and discussions on the statistical performance of the Mantel test. Simultaneously, alternative frameworks for data analyses are being proposed. Here, we review the Mantel test and its variations, including Mantel correlograms and partial correlations and regressions. For illustrative purposes, we studied spatial genetic divergence among 25 populations of Dipteryx alata ("Baru"), a tree species endemic to the Cerrado, the Brazilian savannas, based on 8 microsatellite loci. We also applied alternative methods to analyze spatial patterns in this dataset, especially a multivariate generalization of Spatial Eigenfunction Analysis based on redundancy analysis. The different approaches resulted in similar estimates of the magnitude of spatial structure in the genetic data. Furthermore, the results were expected based on previous knowledge of the ecological and evolutionary processes underlying genetic variation in this species. Our review shows that a careful application and interpretation of Mantel tests, especially Mantel correlograms, can overcome some potential statistical problems and provide a simple and useful tool for multivariate analysis of spatial patterns of genetic divergence.
Background: The species Pterodon emarginatus and P. pubescens , popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and ...reforestation. They are sister species with evolutionary proximity.
Objective: Considering that the chloroplast genome exhibits a conserved structure and genes, the analysis of its sequences can contribute to the understanding of evolutionary, phylogenetic, and diversity issues.
Methods: The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases.
Results: The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens . The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx , both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed.
Conclusion: The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%.
Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. ...guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq Illumina, assembled with NovoPlasty, and annotated using CHLOROBOX GeSeq. Addictionaly, comparative analysis were performed with six species from NCBI databases and primers were designed in Primer3 for hypervariable regions based on the consensus sequence of 16 species of the Rubiaceae family and validated on an in-silico PCR in OpenPrimeR. The genome size of U. guianensis and U. tomentosa was 155,505 bp and 156,390 bp, respectively. Both Species have 131 genes and GC content of 37.50%. The regions rpl32-ccsA, ycf1, and ndhF-ccsA showed the three highest values of nucleotide diversity within the species of the Rubiaceae family and within the Uncaria genus, these regions were trnH-psbA, psbM-trnY, and rps16-psbK. Our results indicates that the primer of the region ndhA had an amplification success for all species tested and can be promising for usage in the Rubiaceae family. The phylogenetic analysis recovered a congruent topology to APG IV. The gene content and the chloroplast genome structure of the analyzed species are conserved and most of the genes are under negative selection. We provide the cpDNA of Neotropical Uncaria species, an important genomic resource for evolutionary studies of the group.
The process of molecular identification of species known as DNA barcoding consists on discriminating taxa based on cumulative differences of their DNA sequences and is widely used within animals, ...including birds. Finding the best genomic tools, such as primers, to reach most of the species within the studied groups and evaluating the coverage breadth and physicochemical properties of primers before testing in the laboratory, can save time and financial resources. Therefore, this work aimed to retrieve the available primers for the COI gene currently used on the molecular identification of birds and evaluate them for its coverage range, physicochemical properties, and performance on in silico PCR. Afterwards, we provide the best primer subsets to cover the highest number of avian sequences and the best individual primers for each bird order in terms of coverage breadth. Thirty-one bird orders had at least one COI sequence to serve as template, 152 primers available for assessing the COI gene were evaluated, and 118 could bind to at least one template sequence. No primer subset alone could cover all template sequences; however, when combining two subsets, the complete coverage of avian COI sequences analyzed was achieved. We were able to find optimal primer subsets for more specific taxonomic groups or for analysis involving the complete avian group, in order to guide researchers in the process of choosing the best primer set for each individual barcoding goal.
Systematic Conservation Planning (SCP) involves a series of steps that should be accomplished to determine the most cost-effective way to invest in conservation action. Although SCP has been usually ...applied at the species level (or hierarchically higher), it is possible to use alleles from molecular analyses at the population level as basic units for analyses. Here we demonstrate how SCP procedures can be used to establish optimum strategies for in situ and
ex situ
conservation of a single species, using
Dipteryx alata
(a Fabaceae tree species widely distributed and endemics to Brazilian Cerrado) as a case study. Data for the analyses consisted in 52 alleles from eight microsatellite loci coded for a total of 644 individual trees sampled in 25 local populations throughout species’ geographic range. We found optimal solutions in which seven local populations are the smallest set of local populations of
D. alata
that should be conserved to represent the known genetic diversity. Combining these several solutions allowed estimating the relative importance of the local populations for conserving all known alleles, taking into account the current land-use patterns in the region. A germplasm collection for this species already exists, so we also used SCP approach to identify the smallest number of populations that should be further collected in the field to complement the existing collection, showing that only four local populations should be sampled for optimizing the species
ex situ
representation. The initial application of the SCP methods to genetic data showed here can be a useful starting point for methodological and conceptual improvements and may be a first important step towards a comprehensive and balanced quantitative definition of conservation goals, shedding light to new possibilities for in situ and
ex situ
designs within species.
Abstract The objective of this work was to describe and compare the patterns of genetic variation in 19 populations of Anacardium humile from the Cerrado biome of the Brazilian Midwestern region. The ...ex situ germplasm collection of Universidade Federal de Jataí, in the state of Goiás, Brazil, was used for the study. To quantify the genetic variability of A. humile, 529 plants from 17 populations in Goiás from 2 in the state of Mato Grosso were studied, from which nine microsatellite loci were genotyped by capillary electrophoresis. The populations showed high levels of genetic diversity, with an average value of 0.830, and high inbreeding values, which suggests a deficit of heterozygotes. The genetic differentiation value between populations was 0.065. The greatest variability, which is moderately structured, was observed within populations. There is a significant inbreeding within the A. humile population in the Cerrado biome of the Brazilian Midwestern region. The A. humile populations are divided into two groups.
Resumo O objetivo deste trabalho foi descrever e comparar os padrões de variação genética em 19 populações de Anacardium humile do bioma Cerrado da região Centro-Oeste brasileira. A coleção ex situ de germoplasma da Universidade Federal de Jataí, no estado de Goiás, Brasil, foi utilizada para o estudo. Para quantificar a variabilidade genética de A. humile, 529 plantas oriundas de 17 populações de Goiás e de 2 do estado de Mato Grosso foram estudadas, das quais nove loci microssatélites foram genotipados por eletroforese capilar. As populações apresentaram altos níveis de diversidade genética, com valor médio de 0,830, e altos valores de endogamia, o que sugere um déficit de heterozigotos. O valor de diferenciação genética entre as populações foi de 0,065. Já a maior variabilidade, estruturada de forma moderada, foi observada dentro das populações. Há endogamia significativa na população de A. humile no bioma Cerrado da região Centro-Oeste brasileira. As populações de A. humile estão divididas em dois grupos.
Background: Also known as Simple Sequence Repetitions (SSRs), microsatellites are profoundly informative molecular markers and powerful tools in genetics and ecology studies on plants. Objective: ...This research presents a workflow for developing microsatellite markers using genome skimming. Methods: The pipeline was proposed in several stages that must be performed sequentially: obtaining DNA sequences, identifying microsatellite regions, designing primers, and selecting candidate microsatellite regions to develop the markers. Our pipeline efficiency was analyzed using Illumina sequencing data from the non-model tree species Pterodon emarginatus Vog. Results: The pipeline revealed 4,382 microsatellite regions and drew 7,411 pairs of primers for P. emarginatus. However, a much larger number of microsatellite regions with the potential to develop markers were discovered from our pipeline. We selected 50 microsatellite regions with high potential for developing markers and organized 29 microsatellite regions in sets for multiplex PCR. Conclusion: The proposed pipeline is a powerful tool for fast and efficient development of microsatellite markers on a large scale in several species, especially nonmodel plant species.
The conservation of plant genetic resources is essential for breeding programs. Regarding the native species of the Brazilian Cerrado biome, many studies have demonstrated their high potential for ...use in both medicines and foods.
Hymenaea stigonocarpa
, a tree with wide occurrence in the Cerrado, has economic importance, and due its extractive use, the establishment of a breeding program is relevant for sustainable use and conservation. Thus, the first germplasm collection of the species was installed at the Federal University of Goiás (UFG). To know the magnitude of genetic variability and how it was distributed in the collection, 353 individuals, distributed in 119 families from 24 subpopulations collected in the Cerrado biome, were genotyped using capillary electrophoresis. Nine pairs of microsatellite markers were genotyped. The UFG germplasm collection showed a high level of genetic diversity (mean
H
¯
e
= 0.554) at the evaluated loci. By Analysis of Molecular Variance (AMOVA), a significant genetic structure was detected (
θ
P
= 0.152, p < 0.01), which was expected since the subpopulations that originated the germplasm collection were collected in geographically distant locations. In addition, the germplasm collection had a population effective size of 54.9 and presented an allelic representation of 79.89% compared to 32 natural subpopulations. These results demonstrate that the germplasm collection preserves a high genetic diversity of
H. stigonocarpa
with a population effective size considered sufficient for the conduction of a breeding program.
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