Limits...
A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae).

Folk RA, Mandel JR, Freudenstein JV - Appl Plant Sci (2015)

Bottom Line: Organellar phylogenies were also well-supported and conflicted with the nuclear signal.Our approach shows promise for resolving a recent radiation.Enrichment for introns is highly successful with little or no sequencing dropout at low taxonomic levels despite higher substitution and indel frequencies, and should be exploited in studies of species complexes.

View Article: PubMed Central - PubMed

Affiliation: Herbarium, The Ohio State University, Columbus, Ohio 43212 USA.

ABSTRACT

Premise of the study: Phylogenetic inference is moving to large multilocus data sets, yet there remains uncertainty in the choice of marker and sequencing method at low taxonomic levels. To address this gap, we present a method for enriching long loci spanning intron-exon boundaries in the genus Heuchera.

Methods: Two hundred seventy-eight loci were designed using a splice-site prediction method combining transcriptomic and genomic data. Biotinylated probes were designed for enrichment of these loci. Reference-based assembly was performed using genomic references; additionally, chloroplast and mitochondrial genomes were used as references for off-target reads. The data were aligned and subjected to coalescent and concatenated phylogenetic analyses to demonstrate support for major relationships.

Results: Complete or nearly complete (>99%) sequences were assembled from essentially all loci from all taxa. Aligned introns showed a fourfold increase in divergence as opposed to exons. Concatenated analysis gave decisive support to all nodes, and support was also high and relationships mostly similar in the coalescent analysis. Organellar phylogenies were also well-supported and conflicted with the nuclear signal.

Discussion: Our approach shows promise for resolving a recent radiation. Enrichment for introns is highly successful with little or no sequencing dropout at low taxonomic levels despite higher substitution and indel frequencies, and should be exploited in studies of species complexes.

No MeSH data available.


Coalescent tree estimated in MP-EST. Branch labels are bootstrap supports, based on 1000 bootstrap replicates per tree. The STAR result was topologically identical; where support values differed the two values are plotted as “MP-EST proportion/STAR proportion.” Branch coloring follows the sectional taxonomy as in Fig. 1; branch lengths are not to scale.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4542943&req=5

fig2: Coalescent tree estimated in MP-EST. Branch labels are bootstrap supports, based on 1000 bootstrap replicates per tree. The STAR result was topologically identical; where support values differed the two values are plotted as “MP-EST proportion/STAR proportion.” Branch coloring follows the sectional taxonomy as in Fig. 1; branch lengths are not to scale.

Mentions: The concatenated nuclear tree (Fig. 1) was completely resolved with strong support on all nodes (99% on one node in sect. Rhodoheuchera concerning the placement of H. rubescens Torr. var. versicolor (Greene) M. G. Stewart; otherwise 100%). Coalescent analyses in MP-EST and STAR (Fig. 2) likewise had primarily high support values. There was only one point of discord between these methods: coalescent methods found H. pulchella Wooton & Standl. and H. rubescens var. versicolor as sister to each other, whereas concatenation inferred these as successively sister to H. parishii, H. elegans, and H. abramsii. The phylogenetic analyses of organellar data (chloroplast, Fig. 3; mitochondrial, Fig. 4) likewise resulted in high support values, although these relationships differed greatly from those suggested by nuclear data.


A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae).

Folk RA, Mandel JR, Freudenstein JV - Appl Plant Sci (2015)

Coalescent tree estimated in MP-EST. Branch labels are bootstrap supports, based on 1000 bootstrap replicates per tree. The STAR result was topologically identical; where support values differed the two values are plotted as “MP-EST proportion/STAR proportion.” Branch coloring follows the sectional taxonomy as in Fig. 1; branch lengths are not to scale.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4542943&req=5

fig2: Coalescent tree estimated in MP-EST. Branch labels are bootstrap supports, based on 1000 bootstrap replicates per tree. The STAR result was topologically identical; where support values differed the two values are plotted as “MP-EST proportion/STAR proportion.” Branch coloring follows the sectional taxonomy as in Fig. 1; branch lengths are not to scale.
Mentions: The concatenated nuclear tree (Fig. 1) was completely resolved with strong support on all nodes (99% on one node in sect. Rhodoheuchera concerning the placement of H. rubescens Torr. var. versicolor (Greene) M. G. Stewart; otherwise 100%). Coalescent analyses in MP-EST and STAR (Fig. 2) likewise had primarily high support values. There was only one point of discord between these methods: coalescent methods found H. pulchella Wooton & Standl. and H. rubescens var. versicolor as sister to each other, whereas concatenation inferred these as successively sister to H. parishii, H. elegans, and H. abramsii. The phylogenetic analyses of organellar data (chloroplast, Fig. 3; mitochondrial, Fig. 4) likewise resulted in high support values, although these relationships differed greatly from those suggested by nuclear data.

Bottom Line: Organellar phylogenies were also well-supported and conflicted with the nuclear signal.Our approach shows promise for resolving a recent radiation.Enrichment for introns is highly successful with little or no sequencing dropout at low taxonomic levels despite higher substitution and indel frequencies, and should be exploited in studies of species complexes.

View Article: PubMed Central - PubMed

Affiliation: Herbarium, The Ohio State University, Columbus, Ohio 43212 USA.

ABSTRACT

Premise of the study: Phylogenetic inference is moving to large multilocus data sets, yet there remains uncertainty in the choice of marker and sequencing method at low taxonomic levels. To address this gap, we present a method for enriching long loci spanning intron-exon boundaries in the genus Heuchera.

Methods: Two hundred seventy-eight loci were designed using a splice-site prediction method combining transcriptomic and genomic data. Biotinylated probes were designed for enrichment of these loci. Reference-based assembly was performed using genomic references; additionally, chloroplast and mitochondrial genomes were used as references for off-target reads. The data were aligned and subjected to coalescent and concatenated phylogenetic analyses to demonstrate support for major relationships.

Results: Complete or nearly complete (>99%) sequences were assembled from essentially all loci from all taxa. Aligned introns showed a fourfold increase in divergence as opposed to exons. Concatenated analysis gave decisive support to all nodes, and support was also high and relationships mostly similar in the coalescent analysis. Organellar phylogenies were also well-supported and conflicted with the nuclear signal.

Discussion: Our approach shows promise for resolving a recent radiation. Enrichment for introns is highly successful with little or no sequencing dropout at low taxonomic levels despite higher substitution and indel frequencies, and should be exploited in studies of species complexes.

No MeSH data available.