Demographic history and genetic differentiation in apes

SummaryComparisons of genetic variation between humans and great apes are hampered by the fact that we still know little about the demographics and evolutionary history of the latter species [1–4]. In addition, characterizing ape genetic variation is important because they are threatened with extinction, and knowledge about genetic differentiation among groups may guide conservation efforts [5]. We sequenced multiple intergenic autosomal regions totaling 22,400 base pairs (bp) in ten individuals each from western, central, and eastern chimpanzee groups and in nine bonobos, and 16,000 bp in ten Bornean and six Sumatran orangutans. These regions are analyzed together with homologous information from three human populations and gorillas. We find that whereas orangutans have the highest diversity, western chimpanzees have the lowest, and that the demographic histories of most groups differ drastically. Special attention should therefore be paid to sampling strategies and the statistics chosen when comparing levels of variation within and among groups. Finally, we find that the extent of genetic differentiation among “subspecies” of chimpanzees and orangutans is comparable to that seen among human populations, calling the validity of the “subspecies” concept in apes into question

Obtenção de material propagativo livre de vírus e diagnóstico de vírus em macieiras e pereiras.

Principais vírus da macieira e da pereira. Danos causados por vírus. Limpeza clonal: produção de macieiras e pereiras livres de vírus. Análises e testes de avaliação de sanidade.bitstream/item/60758/1/CNPUV-DOC.-69-09.pd

Detection of Viruses in Apples and Pears by Real Time RT-PCR Using 5'-Hydrolysis Probes

Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV), Apple chlorotic leaf spot virus (ACLSV) and Apple mosaic virus (ApMV) are common in apples and pears and the main targets of virus elimination from propagation material. The objective of this work was to design primers and probes for a real time RT-PCR protocol for detection of the four above viruses. FAM/TAMRA-labeled probes and primers were designed by searching for highly conserved nucleotide regions in the coat protein gene of the four viruses. Infection levels in analyzed apple samples were 92.6, 96.4, 100 and 88% for ASGV, ASPV, ACLSV and ApMV, respectively. In pears, all pre-existing ASPV infections were detected. Viral infections were confirmed in a selection of commercial cultivars of apples and pear scions, and quince rootstocks, demonstrating the sensitivity and reliability of the designed primers and probes. Real time RT-PCR using 5'-labeled probes is suitable for checking sanitary quality as a routine test in certification programs

A situação atual da sorose dos citros no mundo.

O grupo de doenças da sorose dos citros causa descascamento de troncos, galhos e ramos de laranjeiras doces, pomeleiros e tangerineiras, além de sintomas foliares e em frutos. Nesta revisão se discute a relação da sorose dos citros com doenças similares, características e ocorrência de isolados em varias regiões, transmissibilidade, disseminação, indexação, limpeza de material propagativo e controle. Distingue-se a sorose A (longa incubação) e a sorose B (virulenta, incubação curta). Alguns isolados induzem depressões em forma de sulcos e anéis em frutos e manchas anelares em folhas. Sob temperaturas amenas e comum observar-se um bandeamento clorótico entre as nervuras secundárias de folhas jovens, que se pode considerar o sintoma precoce da sorose A. No Recôncavo Baiano observa-se a ocorrência de um descascamento de troncos de laranjeiras doces e pomeleiros (sorose tipo Bahia, tBA), de etiologia desconhecida, similar a sorose A/B. A profusão de exsudação de goma resinosa hidrossolúvel das lesões a aproxima de sorose/CRSV (vírus da mancha anelar dos citros) da Argentina.bitstream/item/81393/1/A-situacao-atual-Sorose-O-Nikel-Documentos-72-1998.pdfMemória

First report on detection of three Bunya-Like Viruses in apples in Brazil.

Apple chlorotic leaf spot virus (ACLSV), apple stem grooving virus (ASGV), and apple stem pitting virus (ASPV) cause significant losses to Brazilian (BR) apple production. Looking beyond these latent viruses, high-throughput sequencing (HTS) of three samples (Vacaria, Brazil) was performed on an Illumina HiSeq X Ten platform (USA), cv. Braeburn (BB), and a BGISEQ-500 platform (China), cvs. Royal Gala (RG) and Mishima (MI)

Detecção e caracterização molecular dos genes da proteína capsidial de ilarvírus e ampelovírus que infectam fruteiras temperadas.

Dentre os principais patógenos que incidem em fruteiras temperadas, destacam-se o Prune dwarf virus (PDV), o Apple mosaic virus (ApMV) e o Grapevine leafroll-associated virus 1 (GLRaV-1). Neste trabalho foram realizadas a detecção e a caracterização molecular dos genes da proteína capsidial de isolados destas três espécies virais. RNAs totais foram extraídos de amostras de folhas de pessegueiros, macieiras e videiras e, nas reações de RT-PCR, foram utilizados oligonucleotídeos específicos para cada espécie viral. Os cDNAs amplificados foram clonados e sequenciados. Foram verificadas altas identidades entre as sequências de nucleotídeos dos genes da proteína capsidial dos isolados brasileiros de PDV, ApMV e GLRaV-1 e isolados de outros países, independente da origem geográfica e da hospedeira. O peso molecular da proteína capsidial destes vírus foi estimado por meio de Western blot em cerca de 24kDa (PDV), 26kDa (ApMV) e 39kDa (GLRaV-1).Nota técnica

Detection and molecular characterization of Grapevine yellow speckle viroid 1 isolates infecting grapevines in Brazil.

Presently, Hop stunt viroid(HSVd) and Citrus exocortis viroid (CEVd) are the only viroids reported to infect grapevines (Vitis spp.) in Brazil, among the seven viroid species already reported infecting this host in other countries. All grapevine viroid diseases are graft-transmissible and can induce losses especially when associated with viruses. The aim of this work was to confirm infection by Grapevine yellow speckle viroid 1(GYSVd-1) in grapevine samples exhibiting yellow speckle symptoms in the leaves and in asymptomatic samples sequenced by next generation sequencing (NGS). The occurrence of this viroid in Brazil was further investigated in a second study. Total RNAs and dsRNAs were extracted from five symptomatic plants and 16 asymptomatic samples, respectively. Specific primers were used for RT-PCR and amplified DNA fragments were cloned and sequenced by the Sanger method. Eleven complete nucleotide sequences of GYSVd-1 isolates (366 ?367 nt) were obtained from NGS and from RT-PCR amplicons. Comparisons showed high identities (95.9 ?100 %) among ten isolates and an identity of 87.2 ?90.4 % with a divergent isolate (RM-BR). Phylogenetic analyses placed GYSVd-1 isolates in four clusters (types 1, 2, 3 and 4). All GYSVd-1 infections were confirmed by conventional RT-PCR and RT-qPCR using specific oligonucleo-tides and a labeled probe. This is the first report and molecular characterization of GYSVd-1 infecting grapevines in Brazil, and our survey indicates that this viroid could be widespread in the major grape producing regions of Brazil. Keywords GYSVd-1 . Incidence . Next generation sequencing. Secondary structure. Vine