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Primers for low-copy nuclear genes in the Melastomataceae.

ABSTRACT: PREMISE OF THE STUDY:Low-copy nuclear gene primers were developed for phylogenetic studies across the Melastomataceae. METHODS AND RESULTS:Total genomic libraries from eight species in the Melastomataceae along with one transcriptome were used for marker identification and primer design. Eight exon-primed intron-crossing markers were amplified with success in taxa of nine tribes in the Melastomataceae. The new markers were directly sequenced for eight samples of closely related species of Miconia (Chaenanthera clade) in the tribe Miconieae. The DNA sequences for the eight loci ranged from 660 to 818 aligned base pairs. Compared with four commonly used markers in other studies, the loci developed here had a higher number of variable sites than plastid spacers (7-16 vs. 26-45) and comparable variation to the ribosomal spacers (28-39). CONCLUSIONS:The novel primer pairs should be useful for a broad range of studies of systematics and evolution in the diverse Melastomataceae.

SUBMITTER: Reginato M

PROVIDER: S-EPMC4716781 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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Primers for low-copy nuclear genes in the Melastomataceae.

Reginato Marcelo M Michelangeli Fabián A FA

Applications in plant sciences 20160107 1

<h4>Premise of the study</h4>Low-copy nuclear gene primers were developed for phylogenetic studies across the Melastomataceae.<h4>Methods and results</h4>Total genomic libraries from eight species in the Melastomataceae along with one transcriptome were used for marker identification and primer design. Eight exon-primed intron-crossing markers were amplified with success in taxa of nine tribes in the Melastomataceae. The new markers were directly sequenced for eight samples of closely related sp ...[more]

PMID: 26819862

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Project description:BackgroundEvolutionary relationships among the 11 extant orders of insects that undergo complete metamorphosis, called Holometabola, remain either unresolved or contentious, but are extremely important as a context for accurate comparative biology of insect model organisms. The most phylogenetically enigmatic holometabolan insects are Strepsiptera or twisted wing parasites, whose evolutionary relationship to any other insect order is unconfirmed. They have been controversially proposed as the closest relatives of the flies, based on rDNA, and a possible homeotic transformation in the common ancestor of both groups that would make the reduced forewings of Strepsiptera homologous to the reduced hindwings of Diptera. Here we present evidence from nucleotide sequences of six single-copy nuclear protein coding genes used to reconstruct phylogenetic relationships and estimate evolutionary divergence times for all holometabolan orders.ResultsOur results strongly support Hymenoptera as the earliest branching holometabolan lineage, the monophyly of the extant orders, including the fleas, and traditionally recognized groupings of Neuropteroidea and Mecopterida. Most significantly, we find strong support for a close relationship between Coleoptera (beetles) and Strepsiptera, a previously proposed, but analytically controversial relationship. Exploratory analyses reveal that this relationship cannot be explained by long-branch attraction or other systematic biases. Bayesian divergence times analysis, with reference to specific fossil constraints, places the origin of Holometabola in the Carboniferous (355 Ma), a date significantly older than previous paleontological and morphological phylogenetic reconstructions. The origin and diversification of most extant insect orders began in the Triassic, but flourished in the Jurassic, with multiple adaptive radiations producing the astounding diversity of insect species for which these groups are so well known.ConclusionThese findings provide the most complete evolutionary framework for future comparative studies on holometabolous model organisms and contribute strong evidence for the resolution of the 'Strepsiptera problem', a long-standing and hotly debated issue in insect phylogenetics.

Dataset Information

Primers for low-copy nuclear genes in the Melastomataceae.

Publications

Primers for low-copy nuclear genes in the Melastomataceae.

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