SPLACE: A tool to automatically SPLit, Align, and ConcatenatE genes for phylogenomic inference of several organisms

The reconstruction of phylogenomic trees containing multiple genes is best achieved by using a supermatrix. The advent of NGS technology made it easier and cheaper to obtain multiple gene data in one sequencing run. When numerous genes and organisms are used in the phylogenomic analysis, it is difficult to organize all information and manually align the gene sequences to further concatenate them. This study describes SPLACE, a tool to automatically SPLit, Align, and ConcatenatE the genes of all species of interest to generate a supermatrix file, and consequently, a phylogenetic tree, while handling possible missing data. In our findings, SPLACE was the only tool that could automatically align gene sequences and also handle missing data; and, it required only a few minutes to produce a supermatrix FASTA file containing 83 aligned and concatenated genes from the chloroplast genomes of 270 plant species. It is an open-source tool and is publicly available at https://github.com/reinator/splace

Recognition of the genus Thaumatophyllum Schott − formerly Philodendron subg. Meconostigma (Araceae) − based on molecular and morphological evidence

Philodendron subgenus Meconostigma has been a well-circumscribed group since 1829. Members of this group are easily distinguished by diagnostic morphological characters as well as by a distinct ecology and geographical distribution. Based on molecular, morphological and cytological evidence, we propose the recognition of P. subg. Meconostigma as a distinct genus, Thaumatophyllum Schott. We also present the necessary new combinations, an emended key and some nomenclatural and taxonomic corrections regarding 21 names of Thaumatophyllum

Blind Testing: DNA Barcoding Sheds Light Upon the Identity of Plant Fragments as a Subsidy for Cave Conservation

Plants living above and around caves represent an important, albeit poorly studied, resource within cave ecosystems. The presence of plant material (root-like structures or rhizothemes, saplings, seeds, and seedlings) correlates positively with the biodiversity of the cave dwelling animals as shown for iron-ore caves in Carajás, Pará, Brazil. Plant material collected in caves has proven to be difficult to identify by traditional botanical methods, thus this research aims to provide a qualitative insight into the taxonomy and morphology of rhizothemes and other plant fragments found in the caves. The identification process used a combination of different molecular markers (ITS2, rbcL, and trnH-psbA) followed by a comparison of the sequences obtained against publicly available databases. The rhizothemes were submitted to micromorphological analysis to ascertain their putative root or stem origin and to compare their anatomy with known patterns found in the plant families or genera recovered through molecular matches. All studied samples were Angiosperms, mostly belonging to subclass Rosideae, within four orders: Malpighiales (Euphorbiaceae, Hypericaceae), Sapindales (Anacardiaceae and Sapindaceae), Myrtales (Myrtaceae), Fabales (Fabaceae), and only two belonging to subclass Asteridae, order Gentianales (Apocynaceae). Some of the samples were matched to generic level, with ITS2 being the best marker to identify the fragments because it shows high degree of sequence variation even at specific level and result reliability. All rhizothemes turned out to be roots, and correspondence was found between the existing literature and the individual anatomical patterns for the families and genera retrieved. DNA barcode has proved to be a useful tool to identify plant fragments found in this challenging environment. However, the existence of well curated, authoritatively named collections with ample biological information has proven to be essential to achieve a reliable identification

Geography is essential for reproductive isolation between florally diversified morning glory species from Amazon canga savannahs

peer-reviewedThe variety, relative importance and eco-evolutionary stability of reproductive barriers are critical to understanding the processes of speciation and species persistence. Here we evaluated the strength of the biotic prezygotic and postzygotic isolation barriers between closely related morning glory species from Amazon canga savannahs. The flower geometry and flower visitor assemblage analyses supported pollination by the bees in lavender-flowered Ipomoea marabaensis and recruitment of hummingbirds as pollinators in red-flowered Ipomoea cavalcantei. Nevertheless, native bee species and alien honeybees foraged on flowers of both species. Real-time interspecific hybridization underscored functionality of the overlap in flower visitor assemblages, questioning the strength of prezygotic isolation underpinned by diversification in flower colour and geometry. Interspecific hybrids were fertile and produced offspring in nature. No significant asymmetry in interspecific hybridization and hybrid incompatibilities among offspring were found, indicating weak postmating and postzygotic isolation. The results suggested that despite floral diversification, the insular-type geographic isolation remains a major barrier to gene flow. Findings set a framework for the future analysis of contemporary evolution of plant-pollinator networks at the population, community, and ecosystem levels in tropical ecosystems that are known to be distinct from the more familiar temperate climate models.Instituto Tecnológico Vale (ITV) project “Biodiversidade na mineração

Análise da diversidade genética entre genótipos de Mamona (Ricinus communis Euphorbiaceae) através de Fingerprinting de DNA com marcadores AFLP e ISSR

A mamoneira (Ricinus communis L.) é uma das oleaginosas cultivadas mais importantes em todo o planeta, e no Brasil, uma das principais aplicações para o óleo de rícino é a produção de biodiesel. Apesar da grande importância da cultura para o Nordeste brasileiro, pouco é conhecido a respeito da diversidade genética de genótipos adaptados às condições ambientais encontradas na região. Com o intuito de prover informações acerca dos níveis de diversidade genética de acessos de mamona provenientes da Embrapa Algodão, perfis de fingerprinting de DNA foram descritos utilizando marcadores AFLP e ISSR. A partir da amplificação de 749 marcas no total (496 de AFLP e 253 de ISSR), foi observado o total de 53,4% de bandas polimórficas (44,4% para o AFLP e 71,1% para o ISSR). O AFLP apresentou a média mais alta de fragmentos amplificados por combinação de primers (33,1) em comparação com os primers únicos de ISSR (16,9). As médias obtidas para os índices PIC e MI foram mais altas para os primers de ISSR. No entanto, a média mais alta de RP foi observada para as combinações de primers de AFLP. Uma forte correlação positiva foi observada entre os parâmetros calculados, indicando a validade dos índices para a escolha de marcadores AFLP e ISSR informativos. Os valores de dissimilaridade genética entre os acessos variaram de 0,104 a 0,312 (AFLP), de 0,156 a 0,454 (ISSR) e de 0,143 a 0,339 (AFLP+ISSR). Em relação à análise fenética, os 27 genótipos analisados dividiram-se em cinco grupos principais, os quais, no entanto, não apresentaram indícios de estruturação (Fst = 0,108), com maior variação dentro dos grupos (89,2%) sendo muito superior em relação à variação entre grupos (10,8%). Apesar dos indícios de baixa diversidade genética e ausência de estruturação entre os acessos, a associação de marcas específicas a determinados genótipos de mamona revelam o potencial da aplicação das metodologias de fingerprinting de DNA para acessar a variabilidade existente na espécie. Adicionalmente, a descrição de primers capazes de gerar várias marcas polimórficas capazes de diferenciar genótipos fornece subsídios para o melhor direcionamento de cruzamentos entre acessos com características de interess

Updating the list of chromosome numbers for Philodendron (Araceae)

ABSTRACT Aiming for a better understanding of karyotype evolution within Philodendron, we report chromosome counts for 23 species of the genus, of which 19 are being reported for the first time, thus increasing to 84 ( ca. 17 % of the genus) the total number of species with available chromosome counts. The diploid numbers 2 n = 32 and 2 n = 34 were the most common, with 10 and 11 species, respectively, whereas only two species presented different chromosome numbers ( P. giganteum with 2 n = 30 and P. adamantinum with 2 n = 36). The results are discussed in the context of previous analyses of karyotypes of Philodendron spp., taking into account bidirectional dysploidy as the main mechanism of chromosome number evolution within the genus

Karyotype heterogeneity in Philodendron s.l. (Araceae) revealed by chromosome mapping of rDNA loci.

Philodendron s.l. (Araceae) has been recently focus of taxonomic and phylogenetic studies, but karyotypic data are limited to chromosome numbers and a few published genome sizes. In this work, karyotypes of 34 species of Philodendron s.l. (29 species of Philodendron and five of Thaumatophyllum), ranging from 2n = 28 to 36 chromosomes, were analyzed by fluorescence in situ hybridization (FISH) with rDNA and telomeric probes, aiming to understand the evolution of the karyotype diversity of the group. Philodendron presented a high number variation of 35S rDNA, ranging from two to 16 sites, which were mostly in the terminal region of the short arms, with nine species presenting heteromorphisms. In the case of Thaumatophyllum species, we observed a considerably lower variation, which ranged from two to four terminal sites. The distribution of the 5S rDNA clusters was more conserved, with two sites for most species, being preferably located interstitially in the long chromosome arms. For the telomeric probe, while exclusively terminal sites were observed for P. giganteum (2n = 30) chromosomes, P. callosum (2n = 28) presented an interstitial distribution associated with satellite DNA. rDNA sites of the analyzed species of Philodendron s.l. species were randomly distributed considering the phylogenetic context, probably due to rapid evolution and great diversity of these genomes. The observed heteromorphisms suggest the accumulation of repetitive DNA in the genomes of some species and the occurrence of chromosomal rearrangements along the karyotype evolution of the group