Molecular characterization

Molecular cloning and characterization of the pseudorabies virus UL31 gene

M. L. Li, Zhao, Z. Y., Cui, W., Mo, C. C., Wang, J. L., and Cai, M. S., “Molecular cloning and characterization of the pseudorabies virus UL31 gene”, vol. 13, pp. 1832-1847, 2014.

We amplified a 816-bp sequence of the UL31 gene from the pseudorabies virus (PRV) Becker strain genome. Evidence that this was the UL31 gene was confirmed by cloning and sequencing. The PRV UL31 gene encodes a putative protein of 271-amino acid residues, which was designated the UL31 protein. Bioinformatic analysis indicated that PRV UL31 contains a conserved PHA03328 domain, closely related with the herpes virus nuclear egress lamina protein UL31 family and highly conserved among counterparts encoded by herpes UL31 genes.

Molecular and morphological characterization of pomegranate (Punica granatum L.) genotypes sampled from Coruh Valley in Turkey

E. Orhan, Ercisli, S., Esitken, A., and Sengul, M., “Molecular and morphological characterization of pomegranate (Punica granatum L.) genotypes sampled from Coruh Valley in Turkey”, vol. 13, pp. 6375-6382, 2014.

The pomegranate is one of the oldest fruits that are traditionally consumed by the local inhabitants of the Coruh Valley, Turkey. In this study, the molecular and morphological characteristics of 19 promising pomegranate genotypes selected from the Coruh Valley were evaluated. For the morphological evaluation, 22 quantitative fruit characteristics were used. For the molecular evaluation, 47 random amplified polymorphic DNA (RAPD) primers were used for polymerase chain reaction analysis.

Morphological and genetic relationships between wild and domesticated forms of peppers (Capsicum frutescens L. and C. chinense Jacquin)

S. I. C. Carvalho, Ragassi, C. F., Bianchetti, L. B., Reifschneider, F. J. B., Buso, G. S. C., and Faleiro, F. G., “Morphological and genetic relationships between wild and domesticated forms of peppers (Capsicum frutescens L. and C. chinense Jacquin)”, vol. 13, pp. 7447-7464, 2014.

Capsicum chinense and C. frutescens peppers are part of the Brazilian biodiversity, and the Amazon basin is the area of greatest diversity for them, especially for that former species. Nevertheless, little is known about their evolutionary history. Aiming to identify genotypes with wild and domesticated characteristics, 30 accessions of the germplasm bank of Embrapa were characterized using morphological descriptors and ISSR molecular markers.

Molecular characterization of the Andean blackberry, Rubus glaucus, using SSR markers

M. Marulanda, López, A. M., and Uribe, M., “Molecular characterization of the Andean blackberry, Rubus glaucus, using SSR markers”, vol. 11, pp. 322-331, 2012.

The species Rubus glaucus, also known as the Andean or “Castilla” blackberry, is one of nine edible species of this genus that grow naturally in Central and South America. In Colombia, this species is the most important of all Rubus species for agricultural and commercial purposes. We used 20 SSRs developed for other Rubus species to characterize 44 Colombian R. glaucus genotypes, collected from eight different departments, and to look for molecular differences between thornless and thorny cultivated blackberries.

Molecular characterization of an opossum Didelphis albiventris (Marsupialia: Didelphidae) population in an urban fragment of the Brazilian Atlantic Rainforest and support to species barcode identification

L. C. C. Sousa, Gontijo, C. M. F., Lacorte, G. A., Meireles, S. N., Silva, A. P., and Fonseca, C. G., “Molecular characterization of an opossum Didelphis albiventris (Marsupialia: Didelphidae) population in an urban fragment of the Brazilian Atlantic Rainforest and support to species barcode identification”, vol. 11, pp. 2487-2496, 2012.

We made a molecular study of 40 opossums, Didelphis albiventris, from an urban fragment of the Atlantic Rainforest in southeastern Brazil, analyzing a 653-bp sequence of cytochrome c oxidase, subunit I. We found three close connected haplotypes, with low nucleotide diversity and a haplotype diversity of 59.1% and confirmed sympatry between D. albiventris and D. aurita in this region. The clear phylogenetic separation shows the appropriateness of DNA barcode identification methodology for effectively discriminating between these opossum species.

Molecular cloning and characterization of the pseudorabies virus US1 gene

M. L. Li, Chen, J. H., Zhao, Z. Y., Zhang, K. J., Li, Z., Li, J., Mai, J. Y., Zhu, X. M., and Cai, M. S., “Molecular cloning and characterization of the pseudorabies virus US1 gene”, vol. 12, pp. 85-98, 2013.

Using polymerase chain reaction, a 1050-bp sequence of the US1 gene was amplified from the pseudorabies virus (PRV) Becker strain genome; identification of the US1 gene was confirmed by further cloning and sequencing. Bioinformatics analysis indicated that the PRV US1 gene encodes a putative polypeptide with 349 amino acids.

Molecular characterization of the pseudorabies virus UL2 gene

M. S. Cai, Wang, B. Y., Cui, W., Zhao, Z. Y., Chen, J. H., Wen, X. M., Li, Z., and Li, M. L., “Molecular characterization of the pseudorabies virus UL2 gene”, vol. 12, pp. 4147-4161, 2013.

A 948-bp sequence of the UL2 gene was amplified from the pseudorabies virus (PRV) Becker strain genome using polymerase chain reaction, and the gene identity was confirmed through further cloning and sequencing. Bioinformatic analysis indicated that the PRV UL2 gene encodes a putative polypeptide with 315-amino acid residues. Its encoding protein, designated UL2, has a conserved uracil-DNA glycosylase (UDG)_F1 domain, which is closely related to the herpesvirus UDG family and is highly conserved among its counterparts encoded by UDG genes.

Construction of a molecular database for soybean cultivar identification in Brazil

M. B. Oliveira, Vieira, E. S. N., and Schuster, I., “Construction of a molecular database for soybean cultivar identification in Brazil”, vol. 9, pp. 705-720, 2010.

The narrow genetic base of soybean makes cultivar characterization based on morphological descriptors difficult; this characterization is mainly done for registration and protection. Correct characterization of cultivars could be achieved through molecular markers, since the frequencies of each allele in the population are known. Consequently, we developed a molecular characterization method and initiated the construction of a molecular database for soybean cultivar identification. Thirty-two soybean cultivars were analyzed with 48 fluorescent-labeled microsatellite markers.

RAPD analysis of selected local Turkish grape cultivars (Vitis vinifera)

H. Karataş and Ağaoğlu, Y. S., “RAPD analysis of selected local Turkish grape cultivars (Vitis vinifera)”, vol. 9, pp. 1980-1986, 2010.

Turkey is very rich in local grape varieties. The solution to the problem of identifying local cultivars, which is considered an important deficiency for the region, will only be possible when they can be defined with molecular markers. Forty-nine local grapevine cultivars from Şanlıurfa (Turkey) were characterized with RAPD markers. Twenty-five decamer primers selected from 60 primers were used in this analysis. A total of 171 bands were obtained with the 25 primers, of which 112 were polymorphic; the level of DNA polymorphism was 65.49% in these local cultivars.

MtDNA variability in whitefly (Bemisia tabaci) populations in Brazil

G. E. Valle, Lourenção, A. L., Zucchi, M. I., Pinheiro, J. B., and Abreu, A. G., “MtDNA variability in whitefly (Bemisia tabaci) populations in Brazil”, vol. 10, pp. 2155-2164, 2011.

Bemisia tabaci (Hemiptera: Aleyrodidae) consists of a complex of morphologically indistinct biotypes that vary mainly in their capacity to transmit plant viruses and to induce physiological disorders in plants of economic importance. The adaptability of B. tabaci to many regions of the world has fostered the appearance of various biotypes and has resulted in a broad spectrum of host plants. Our goal was to identify which biotypes were present in four B. tabaci populations in Brazil. We quantified genetic variability between and within populations.

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