Java Merging Copy Number Variants (JM-CNV): a new algorithm for identifying Copy Number Variant Regions (CNVR).

CNVs (Copy Number Variations) are defined as copy number variations of DNA fragments typically larger than one kilobase (Kb), but less than five megabases (Mb). They represent a genomic disequilibrium that alters the ploidy in a specific locus within an individual, which may also be observed with varying frequencies within a population. An initial study estimated that 12% of the human genome shows this type of structural variation. Reliable tools have been developed to detect CNVs from molecular data produced with three main platforms: Comparative Genomic Hybridization (CGH) arrays, Single Nucleotide Polymorphism (SNP) genotyping arrays, and DNA Next-Generation Sequencing (NGS). However, processes for merging overlapping CNVs into a meaningful set of discrete Copy Number Variable Regions (CNVRs) need improvement, particularly when several CNV patterns co-exist within the same genomic locus. Available algorithms frequently merge noncontiguous CNVRs or fragment large CNVRs into multiple regions. A new web-based software (Java Merging Copy Number Variants: JM-CNV) was developed to address the aforementioned issues.PAG 2015. Pôster P1170

Pilea brasiliensis Gaglioti, Romaniuc & A. K. Monro 2011, sp. nov.

Pilea brasiliensis Gaglioti, Romaniuc & A.K. Monro, sp. nov. (Fig. 1) A Pilea lippioides similis, sed foliis et petiolis eadem node aequalis aut subaequales longitudine, inflorescentiis staminalibus in panicula, seminibus minoribus, differt. Type:— BRAZIL. Distrito Federal: Rio Maranhão, Via DF-2 Fazenda Maranhão, 27 February 1979, Heringer et al. 1039 (holotype IBGE!, isotype UEC!). Perennial herb to 30 cm, terrestrial, epipetric, monoecious. Stem erect, sparsely branched to unbranched, drying brown-green to grey-green, glabrous; cystoliths elliptic; rooting at the base; internodes 8–45 mm, woody stems striate, hollow at 5 mm in diameter. Stipules persistent, 0.8–1.5 × 0.5–1.0 mm, deltate, drying brown-green, membranous, base triangular, apex obtuse. Leaves petiolate, petiole 4–30 mm, of equal or subequal length at the same node, glabrous; laminas of leaves equal or subequal at the same node, 15–55 × 1.5–40.0 mm, ovate to narrowly ovate, elliptic, smaller leaves, 4–10 × 4–8, frequently deltoid to suborbicular, membranous to chartaceous; upper surface drying dark green, green to yellowish green and often translucent, glabrous, lower surface drying dark green, green to yellowish green and often translucent, glabrous, cystoliths fusiform, occasionally appearing V- or Y-shaped, scattered; primary venation pinnate, secondary veins 4–11 pairs, 55°–75° to the midrib, weakly curved to curved; base obtuse to rounded; margin serrate or entire; apex acute. Inflorescences 4–12 per stem, unisexual, peduncular bracts 0.8–1.2 mm, narrowly ovate. Staminate inflorescences 1 or 2 per axil, 6–24 mm, bearing 6–28 flowers in an asymmetrical panicle; peduncle ¼–⅓ of the inflorescence length, glabrous; flowers 1.2–2.5 mm immediately prior to anthesis, drying cream, apically green; pedicels 0.8–1.2 mm, glabrous; tepals 4, 1.5–2.8 mm, glabrous, the subapical appendage 0.5 mm, corniculate. Pistillate inflorescences 1 or 2 per axil, 5–25 mm, bearing 22–85 flowers in an asymmetrical panicle, ¼–½ of the inflorescence length, glabrous; pedicels 0.25–0.5 mm, glabrous; tepals 3, unequal, dorsal tepal 0.5–1.0 mm, oblong, lateral tepals 0.25–0.5 mm, narrowly ovate. Infructescences 10–35 mm, tepals persistent; achenes 0.75–1.00 × 0.50–0.75 mm, compressed, narrowly ovoid to elliptic, greenish brown, glabrous. Distribution:— Central Brazil. Distrito Federal, Mato Grosso, Minas Gerais and Goiás. Using Google Earth (accessed 13 June 2011) we calculated an Extent of Occurrence of ca 52,000 km 2, at 400 to 1200 m in semi-deciduous forest on limestone outcrops. Etymology: — Named for the country in which the species is known to occur. Additional specimens examined: — BRAZIL. Distrito Federal: Brasília, Rio Maranhão, Via DF-2 Fazenda Maranhão, 15°37’20”S, 47°40’38”W, fl. ♂ ♀, 27 February 1979, Heringer et al. 1039 (IBGE, UEC); Catetinho, 15°56’08”S, 48°00’35”W, fl. ♂ ♀, 8 March 1965, Smith A-2 (UB); Fercal, 15°38’01”S, 47°49’01”W, fr., 5 March 1965, Smith 15022 (P). Mato Grosso: Nobres, about 42 km NE (straight) of Nobres, area of Lago Azul, 14°35’00”S, 56°12’00”W, fl. ♂ ♀, 24 May 1997, Souza et al. 17155 (ESA). Minas Gerais: Januária, river valley Peruaçu, Boqueirão da Onça, 15°07’35”S, 44°15’17”W, fr., 24 May 1997, Salino 3086 (RB). Goiás: 50 km N of Corumbá on road to Niquelândia, in valley of Rio Maranhão, 800 m, 15°25’14”S, 48°19’50”W, fl. ♂ ♀, 24 January 1968, Irwin et al. 19106 (MBM). Discussion: — Pilea brasiliensis belongs to the Dentatae -group of Weddell (1869) and the Fallaces - group of Killip (1936). It represents the first record of the Fallaces -group in Brazil. It is characterised by being glabrous, with toothed pinnately veined leaves, petioles of up to 3 cm long and paniculate inflorescences. Pilea brasiliensis closely resembles P. lippioides Killip (1925: 296), which occurs in the eastern and central Cordillera of Colombia, at elevations between 2400 and 3000 m. The two species may be readily distinguished by leaf and petiole morphology, staminate inflorescence arrangement and achene size as summarized here: Pilea brasiliensis Leaf and petiole lengthequal or subequal at the same node Staminate inflorescenceflowers borne in a panicle Achenes0.75–1.00 mm Pilea lippioidesunequal by ratio 1.0:1.5–3.0 at the same nodeflowers borne in a compact head1.20–1.50 mmPublished as part of Gaglioti, A. L., Romaniuc, S. & Monro, A. K., 2011, Pilea brasiliensis: a new species of Pilea (Urticaceae) from Central Brazil, pp. 17-20 in Phytotaxa 26 on page 18, DOI: 10.11646/phytotaxa.26.1.3, http://zenodo.org/record/489411