Comparative chloroplast genomics and insights into the molecular evolution of Tanaecium (Bignonieae, Bignoniaceae

We assembled new plastomes of 19 species of Mikania and of Ageratina fastigiata, Litothamnus nitidus, and Stevia collina, all belonging to tribe Eupatorieae (Asteraceae). We analyzed the structure and content of the assembled plastomes and used the newly generated sequences to infer phylogenetic relationships and study the effects of different data partitions and inference methods on the topologies. Most phylogenetic studies with plastomes ignore that processes like recombination and biparental inheritance can occur in this organelle, using the whole genome as a single locus. Our study sought to compare this approach with multispecies coalescent methods that assume that different parts of the genome evolve at different rates. We found that the overall gene content, structure, and orientation are very conserved in all plastomes of the studied species. As observed in other Asteraceae, the 22 plastomes assembled here contain two nested inversions in the LSC region. The plastomes show similar length and the same gene content. The two most variable regions within Mikania are rpl32-ndhF and rpl16-rps3, while the three genes with the highest percentage of variable sites are ycf1, rpoA, and psbT. We generated six phylogenetic trees using concatenated maximum likelihood and multispecies coalescent methods and three data partitions: coding and non-coding sequences and both combined. All trees strongly support that the sampled Mikania species form a monophyletic group, which is further subdivided into three clades. The internal relationships within each clade are sensitive to the data partitioning and inference methods employed. The trees resulting from concatenated analysis are more similar among each other than to the correspondent tree generated with the same data partition but a different method. The multispecies coalescent analysis indicate a high level of incongruence between species and gene trees. The lack of resolution and congruence among trees can be explained by the sparse sampling (~ 0.45% of the currently accepted species) and by the low number of informative characters present in the sequences. Our study sheds light into the impact of data partitioning and methods over phylogenetic resolution and brings relevant information for the study of Mikania diversity and evolution, as well as for the Asteraceae family as a whole

Novos registros da tribo Bignonieae (Bignoniaceae) na Paraíba, Nordeste do Brasil

This study reports eight new records of the tribe Bignonieae (Bignoniaceae) for Paraiba state, northeastern Brazil: Anemopaegma album (Mart. ex DC.), Anemopaegma gracile Bureau & K.Schum., Bignonia corymbosa (Vent.) L.G. Lohmann, Bignonia ramentacea (Mart. ex DC.) L.G. Lohmann, Bignonia sciuripabulum (K. Schum.) L.G. Lohmann, Cuspidaria argentea (Wawra) Sandwith, Cuspidaria lateriflora (Mart.) DC., and Fridericia conjugata (Vell.) L.G. Lohmann. These species were found in the Caatinga and/or the Atlantic Forest, growing on sandy and clay soils of dry and humid forests, from lowlands to high altitudes. For each new occurrence for the state of Paraiba, we present detailed description, taxonomic notes, and information on phenology, geographic distribution, illustrations and photographs.Este estudo reporta oito novos registros da tribo Bignonieae (Bignoniaceae) para o estado da Paraíba, nordeste de Brasil: Anemopaegma album Mart. ex DC., Anemopaegma gracile Bureau & K. Schum., Bignonia corymbosa (Vent.) L.G. Lohmann, Bignonia ramentacea (Mart. ex DC.) L.G. Lohmann, Bignonia sciuripabulum (K. Schum.) L.G. Lohmann, Cuspidaria argentea (Wawra) Sandwith, Cuspidaria lateriflora (Mart.) DC. e Fridericia conjugata (Vell.) L.G. Lohmann. Estas espécies são encontradas na Caatinga e/ou Mata Atlântica, crescendo em solos arenosos e argilosos de florestas secas e úmidas, desde áreas baixas até altas altitudes. Para cada novo registro do estado da Paraíba, apresentamos descrições detalhadas, notas taxonômicas e informações sobre fenologia, distribuição geográfica, ilustrações e fotografias

Spatio-temporal evolution of the catuaba clade in the Neotropics: morphological shifts correlate with habitat transitions

Aim: The biotic assembly of one of the most species-rich savannas, the Brazilian Cerrado, has involved recruitment of lineages from several surrounding regions. However, we lack a clear understanding about the timing and pathways of biotic exchanges among these regions and about the role those interchanges had in the assembly of Neotropical biodiversity. We investigated the timing and routes of species movements between wet or seasonally dry habitats across Neotropical regions and assessed the potential for ecological adaptation by evaluating the habitat transitions correlated with morphological shifts. Location: Neotropics. Taxon: The plant genus Anemopaegma (Bignonieae, Bignoniaceae). Methods: We inferred a Bayesian molecular phylogeny of Anemopaegma using one nuclear and two chloroplast markers. We sampled more than 90% of the known species diversity of Anemopaegma, covering its full geographical range. We estimated divergence times using a Bayesian relaxed-clock approach and inferred ancestral ranges as well as shifts in habitat and morphological characters. Results: Phylogenetic analyses recovered seven main clades within Anemopaegma. The genus likely originated in Amazonia in the late Oligocene. Early-diverging lineages diversified in situ in Amazonia, particularly during the Miocene, with independent dispersal events to the Andes, Atlantic Forest and Cerrado. Shifts from seasonally dry forest to savanna habitats were correlated with shifts from liana to shrub and the loss of tendrils. Main Conclusions: The timing of diversification of major lineages within Anemopaegma is consistent with major geological and climatic events that occurred during the late Palaeogene and Neogene, such as the Andean uplift and the Middle Miocene Climatic Optimum. Movements across different regions within the Neotropics were relatively common but shifts between habitats were not. The correlation in the evolution of the shrubby habit, the loss of tendrils and the shifts from forest to savanna are consistent with a scenario of ecological adaptation

Checklist of Spermatophyta of the São Paulo State, Brazil

The Phanerogamic Flora of São Paulo State project has been dedicated to create an inventory of the flora for 20 years. More than 200 collaborators are involved, mostly from the State of São Paulo, with the contributions of researchers from other states and from abroad. Since 2001, seven books with monographs of 151 families were published, dealing with 3,237 species within 722 genera. This project was the starting-point of the gathering of information about the diversity of spermatophytes of the State of São Paulo. The current checklist, at this point, presents an updated and virtually complete list of species, all certified by specialists. It also contains references to scientific collections for most of the taxa (vouchers) or to bibliography referring to the natural or subspontaneous occurrence of the species in the State. The list now contains 7,305 species distributed in 1,776 genera and in 197 spermatophyte families (according to Cronquist 1981) or 195 (according to APG III). 23% of the 31,728 species of spermatophytes listed in the Flora of Brazil occur in São Paulo State. The most representative families are Orchidaceae (797 species), Asteraceae (676 species), Fabaceae (513 species), Poaceae (500 species), Myrtaceae (304), Rubiaceae (265 species) and Melastomataceae (253 species), which, altogether, accumulate 3,308 species and constitute 45% of total species of spermatophytes in the state. The wealth of the Brazilian plant diversity, partially expressed in São Paulo, shows how important is the continuity of floristic studies in a country that is very likely to hold the largest plant diversity in the planet.O projeto Flora Fanerogâmica do Estado de São Paulo tem se dedicado a inventariar a flora paulistana há quase 20 anos. Conta com a atuação de mais de 200 colaboradores, a maioria do próprio estado, além de pesquisadores de outros estados e do exterior. Desde 2001, foram publicados sete volumes com as monografias de 151 famílias, contendo 3.237 espécies em 722 gêneros. Este projeto foi o ponto de partida para o conhecimento da diversidade das espécies de espermatófitas do estado de São Paulo. A apresentação do checklist neste momento é oportuna por constituir a produção de uma listagem das espécies com identificações certificadas pelos especialistas, além de conter a referência de uma coleção de herbário para a maior parte dos táxons (material-testemunho) ou referência à bibliografia em que a espécie é citada como ocorrente, de forma nativa ou subespontânea, no estado. Dessa forma, é aqui apresentada a listagem das espermatófitas do estado de São Paulo, com 7.305 espécies, distribuídas em 1.776 gêneros e em 197 famílias (segundo Cronquist 1981) ou então 195 (segundo o APG III). Em relação à flora do Brasil, com 31.728 espécies de espermatófitas, o estado São Paulo compartilha de 23% dessas espécies. As famílias mais representativas são Orchidaceae (797 espécies), Asteraceae (676 espécies), Fabaceae (513 espécies), Poaceae (500 espécies), Myrtaceae (304), Rubiaceae (265 espécies) e Melastomataceae (253 espécies) que, juntas, somam 3.308 espécies e constituem mais de 45% do total de espécies de espermatófitas do estado. Considerando a grande diversidade vegetal brasileira, parcialmente expressa em um estado, depreende-se a grande importância da continuidade dos estudos florísticos no Brasil, país provavelmente detentor da maior diversidade vegetal do planeta.19138

Comparison of chloroplast genomes among four species of Lamiales.

<p>Comparison of chloroplast genomes among four species of Lamiales.</p

Percent identity plot comparing the chloroplast genomes of four species of Lamiales, using <i>Nicotiana tabacum</i> as reference.

<p>Vertical scale indicates the percentage of identity, ranging from 50% to 100%. Horizontal axis indicates the coordinates within the chloroplast genome. Arrows indicate the annotated genes and their transcriptional direction. Genome regions are color coded as exon, untranslated region (UTR), conserved noncoding sequences (CNS), and mRNA. BH: <i>Boea hygrometrica</i>; OE: <i>Olea europaea</i>; SI: <i>Sesamum indicum</i>, and TT: <i>Tanaecium tetragonolobum</i>.</p

Total number of perfect simple sequence repeats (SSRs) identified within the chloroplast genome of <i>Tanaecium tetragonolobum</i> (Jacq.) L.G. Lohmann.

<p>N indicates a degenerate base (not a gap) following the IUPAC system.</p><p>Total number of perfect simple sequence repeats (SSRs) identified within the chloroplast genome of <i>Tanaecium tetragonolobum</i> (Jacq.) L.G. Lohmann.</p

One hundred and twenty-one genes contained within the chloroplast genome of <i>Tanaecium tetragonolobum</i> (Jacq.) L.G. Lohmann.

<p>Asterisks indicate genes containing one or more introns.</p><p>One hundred and twenty-one genes contained within the chloroplast genome of <i>Tanaecium tetragonolobum</i> (Jacq.) L.G. Lohmann.</p

Complete Chloroplast Genome of <i>Tanaecium tetragonolobum</i>: The First Bignoniaceae Plastome

<div><p>Bignoniaceae is a Pantropical plant family that is especially abundant in the Neotropics. Members of the Bignoniaceae are diverse in many ecosystems and represent key components of the Tropical flora. Despite the ecological importance of the Bignoniaceae and all the efforts to reconstruct the phylogeny of this group, whole chloroplast genome information has not yet been reported for any members of the family. Here, we report the complete chloroplast genome sequence of <i>Tanaecium tetragonolobum</i> (Jacq.) L.G. Lohmann, which was reconstructed using <i>de novo</i> and referenced-based assembly of single-end reads generated by shotgun sequencing of total genomic DNA in an Illumina platform. The gene order and organization of the chloroplast genome of <i>T</i>. <i>tetragonolobum</i> exhibits the general structure of flowering plants, and is similar to other Lamiales chloroplast genomes. The chloroplast genome of <i>T</i>. <i>tetragonolobum</i> is a circular molecule of 153,776 base pairs (bp) with a quadripartite structure containing two single copy regions, a large single copy region (LSC, 84,612 bp) and a small single copy region (SSC, 17,586 bp) separated by inverted repeat regions (IRs, 25,789 bp). In addition, the chloroplast genome of <i>T</i>. <i>tetragonolobum</i> has 38.3% GC content and includes 121 genes, of which 86 are protein-coding, 31 are transfer RNA, and four are ribosomal RNA. The chloroplast genome of <i>T</i>. <i>tetragonolobum</i> presents a total of 47 tandem repeats and 347 simple sequence repeats (SSRs) with mononucleotides being the most common and di-, tri-, tetra-, and hexanucleotides occurring with less frequency. The results obtained here were compared to other chloroplast genomes of Lamiales available to date, providing new insight into the evolution of chloroplast genomes within Lamiales. Overall, the evolutionary rates of genes in Lamiales are lineage-, locus-, and region-specific, indicating that the evolutionary pattern of nucleotide substitution in chloroplast genomes of flowering plants is complex. The discovery of tandem repeats within <i>T</i>. <i>tetragonolobum</i> and the presence of divergent regions between chloroplast genomes of Lamiales provides the basis for the development of markers at various taxonomic levels. The newly developed markers have the potential to greatly improve the resolution of molecular phylogenies.</p></div