Dataset Information

Two new species of Tynanthus Miers (Bignonieae, Bignoniaceae) from Brazil.

ABSTRACT: Tynanthus is a genus of lianas that is broadly distributed through the Neotropics. Two new species of Tynanthus from Brazil are here described and illustrated: Tynanthusdensiflorus, from Amazonas, and Tynanthusespiritosantensis, from Espírito Santo. Tynanthusdensiflorus is recognized by the conspicuous interpetiolar glandular fields, a feature rarely found in Tynanthus, and the dense thyrses. Tynanthusespiritosantensis, on the other hand, is recognized by the bromeliad-like prophylls of the axillary buds and the lax thyrses. Information on the distribution, conservation status and morphologically similar species are provided.

SUBMITTER: de Medeiros MC

PROVIDER: S-EPMC4225076 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Two new species of Tynanthus Miers (Bignonieae, Bignoniaceae) from Brazil.

de Medeiros Maria Cláudia M P MC Lohmann Lúcia G LG

PhytoKeys 20141024 42

Tynanthus is a genus of lianas that is broadly distributed through the Neotropics. Two new species of Tynanthus from Brazil are here described and illustrated: Tynanthusdensiflorus, from Amazonas, and Tynanthusespiritosantensis, from Espírito Santo. Tynanthusdensiflorus is recognized by the conspicuous interpetiolar glandular fields, a feature rarely found in Tynanthus, and the dense thyrses. Tynanthusespiritosantensis, on the other hand, is recognized by the bromeliad-like prophylls of the axil ...[more]

PMID: 25383013

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Project description:The chloroplast is one of the most important organelles of plants. This organelle has a circular DNA with approximately 130 genes. The use of plastid genomic data in phylogenetic and evolutionary studies became possible with high-throughput sequencing methods, which allowed us to rapidly obtain complete genomes at a reasonable cost. Here, we use high-throughput sequencing to study the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae). More specifically, we use Hi-Seq Illumina technology to sequence 10 complete plastid genomes. Plastomes were assembled using selected plastid reads and de novo approach with SPAdes. The 10 assembled genomes were analyzed in a phylogenetic context using five different partition schemes: (1) 91 protein-coding genes ("coding"); (2) 76 introns and spacers with alignment manually edited ("non-coding edited"); (3) 76 non-coding regions with poorly aligned regions removed using T-Coffee ("non-coding filtered"); (4) 91 coding regions plus 76 non-coding regions edited ("coding + non-coding edited"); and, (5) 91 protein-coding regions plus the 76 filtered non-coding regions ("coding + non-coding filtered"). Fragmented regions were aligned using Mafft. Phylogenetic analyses were conducted using Maximum Likelihood (ML) and Bayesian Criteria (BC). The analyses of the individual plastomes consistently recovered an expansion of the Inverted Repeated (IRs) regions and a compression of the Small Single Copy (SSC) region. Major genomic translocations were observed at the Large Single Copy (LSC) and IRs. ML phylogenetic analyses of the individual datasets led to the same topology, with the exception of the analysis of the "non-coding filtered" dataset. Overall, relationships were strongly supported, with the highest support values obtained through the analysis of the "coding + non-coding edited" dataset. Four regions at the LSC, SSC, and IR were selected for primer development. The "Adenocalymma-Neojobertia" clade shows an unusual pattern of plastid structure variation, including four major genomic translocations. These rearrangements challenge the current view of conserved plastid genome architecture in terms of gene order. It also complicates both genomic assemblies using reference genomes and sequence alignments using whole plastomes. Therefore, strategies that employ de novo assemblies and manual evaluation of sequence alignments are required to prevent assembly and alignment errors.

Dataset Information

Two new species of Tynanthus Miers (Bignonieae, Bignoniaceae) from Brazil.

Publications

Two new species of Tynanthus Miers (Bignonieae, Bignoniaceae) from Brazil.

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