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Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles

View Article: PubMed Central - PubMed

ABSTRACT

Deep level insect relationships are generally difficult to resolve, especially within taxa of the most diverse and species rich holometabolous orders. In beetles, the major diversity occurs in the Phytophaga, including charismatic groups such as leaf beetles, longhorn beetles and weevils. Bark and ambrosia beetles are wood boring weevils that contribute 12 percent of the diversity encountered in Curculionidae, one of the largest families of beetles with more than 50000 described species. Phylogenetic resolution in groups of Cretaceous age has proven particularly difficult and requires large quantity of data. In this study, we investigated 100 nuclear genes in order to select a number of markers with low evolutionary rates and high phylogenetic signal. A PCR screening using degenerate primers was applied to 26 different weevil species. We obtained sequences from 57 of the 100 targeted genes. Sequences from each nuclear marker were aligned and examined for detecting multiple copies, pseudogenes and introns. Phylogenetic informativeness (PI) and the capacity for reconstruction of previously established phylogenetic relationships were used as proxies for selecting a subset of the 57 amplified genes. Finally, we selected 16 markers suitable for large-scale phylogenetics of Scolytinae and related weevil taxa.

No MeSH data available.


Structure of the PCR amplified gene fragments.The graphics illustrate intron-exon patterns in 16 markers with coding regions shown as black bars and introns as thin black lines. Length variable coding regions (indels) were colored in light grey (Iap2 and Arr2).
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pone.0163529.g002: Structure of the PCR amplified gene fragments.The graphics illustrate intron-exon patterns in 16 markers with coding regions shown as black bars and introns as thin black lines. Length variable coding regions (indels) were colored in light grey (Iap2 and Arr2).

Mentions: We selected 16 genes that revealed a relatively high and stable PCR and sequencing success (from 50 to 100%) as the best candidates for Scolytinae phylogenetics (Table 3). All the verified sequences obtained in this study were deposited in GenBank database under the accession numbers KX160539—KX160803 (S1 Table). The species Xyleborus affinis was the most successful in PCR and sequencing (15 out of 16 possible sequences obtained); the other samples varied considerably in this respect with only 4 sequences obtained for Larinus sp. (S1 Table). The total fragment length, the presence of length-variable regions, and the number and position of introns, were mapped on the annotated genomes of T. castaneum and D. ponderosae (eventually transcriptomic and genomic data of other insect species) to create a map of the gene structure (Fig 2; see also Table 4).


Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles
Structure of the PCR amplified gene fragments.The graphics illustrate intron-exon patterns in 16 markers with coding regions shown as black bars and introns as thin black lines. Length variable coding regions (indels) were colored in light grey (Iap2 and Arr2).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5036811&req=5

pone.0163529.g002: Structure of the PCR amplified gene fragments.The graphics illustrate intron-exon patterns in 16 markers with coding regions shown as black bars and introns as thin black lines. Length variable coding regions (indels) were colored in light grey (Iap2 and Arr2).
Mentions: We selected 16 genes that revealed a relatively high and stable PCR and sequencing success (from 50 to 100%) as the best candidates for Scolytinae phylogenetics (Table 3). All the verified sequences obtained in this study were deposited in GenBank database under the accession numbers KX160539—KX160803 (S1 Table). The species Xyleborus affinis was the most successful in PCR and sequencing (15 out of 16 possible sequences obtained); the other samples varied considerably in this respect with only 4 sequences obtained for Larinus sp. (S1 Table). The total fragment length, the presence of length-variable regions, and the number and position of introns, were mapped on the annotated genomes of T. castaneum and D. ponderosae (eventually transcriptomic and genomic data of other insect species) to create a map of the gene structure (Fig 2; see also Table 4).

View Article: PubMed Central - PubMed

ABSTRACT

Deep level insect relationships are generally difficult to resolve, especially within taxa of the most diverse and species rich holometabolous orders. In beetles, the major diversity occurs in the Phytophaga, including charismatic groups such as leaf beetles, longhorn beetles and weevils. Bark and ambrosia beetles are wood boring weevils that contribute 12 percent of the diversity encountered in Curculionidae, one of the largest families of beetles with more than 50000 described species. Phylogenetic resolution in groups of Cretaceous age has proven particularly difficult and requires large quantity of data. In this study, we investigated 100 nuclear genes in order to select a number of markers with low evolutionary rates and high phylogenetic signal. A PCR screening using degenerate primers was applied to 26 different weevil species. We obtained sequences from 57 of the 100 targeted genes. Sequences from each nuclear marker were aligned and examined for detecting multiple copies, pseudogenes and introns. Phylogenetic informativeness (PI) and the capacity for reconstruction of previously established phylogenetic relationships were used as proxies for selecting a subset of the 57 amplified genes. Finally, we selected 16 markers suitable for large-scale phylogenetics of Scolytinae and related weevil taxa.

No MeSH data available.