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A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea.

Granados Mendoza C, Naumann J, Samain MS, Goetghebeur P, De Smet Y, Wanke S - BMC Evol. Biol. (2015)

Bottom Line: Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths.While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution.The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium. carolina.granados@st.ib.unam.mx.

ABSTRACT

Background: Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other "fast" evolving plastid markers.

Results: Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae).

Conclusions: While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales.

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Retained potential NSCG after the entire data mining and filtering process. Genes have been ordered by their percent of variability among Cornales representatives. Orange bars denote the percent of variable sites among the six Cornales taxa, whereas green and blue bars represent the percent of variable sites among the four Hydrangeaceae representatives and the two tribe Hydrangeeae taxa, respectively
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Fig2: Retained potential NSCG after the entire data mining and filtering process. Genes have been ordered by their percent of variability among Cornales representatives. Orange bars denote the percent of variable sites among the six Cornales taxa, whereas green and blue bars represent the percent of variable sites among the four Hydrangeaceae representatives and the two tribe Hydrangeeae taxa, respectively

Mentions: Our data mining process retrieved 4949 Cornales scaffolds that could be aligned to 546 A. thaliana single-copy gene orthologs. This pool of genes was used to select the most promising and the easiest to handle markers for H. sect. Cornidia. We were aiming for gene alignments where a major part of the gene was covered by at least four of the 1KP Cornales species. This is crucial for estimating phylogenetic utility of the candidate markers, as well as for successful primer design. Among the 546 initial alignments, 444 showed low coverage of Cornales representatives and additional 16 showed low coverage of the two Hydrangeeae taxa (Fig. 1). Therefore these alignments were not considered any further. Multiple scaffold sequences were detected for H. quercifolia in 13 of the remaining alignments and were therefore excluded from further steps. A total of 73 potential NSCG were retained after filtering (Fig. 1). From these alignments, 14 contained the six Cornales representatives, whereas 53 lacked either Curtisia dentata or Deutzia scabra and six did not have either Philadelphus inodorus and Curtisia dentata, or Curtisia dentata and Deutzia scabra. When considering transcriptome sequences from all Cornales taxa, alignments showed 26.7-62.3 % variable sites (Fig. 2). However, the range of variable sites was lowered to 19.8-57.5 % when only the four Hydrangeaceae representatives were considered and to 2.8-26.9 % between the two representatives of tribe Hydrangeeae (Fig. 2).Fig. 1


A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea.

Granados Mendoza C, Naumann J, Samain MS, Goetghebeur P, De Smet Y, Wanke S - BMC Evol. Biol. (2015)

Retained potential NSCG after the entire data mining and filtering process. Genes have been ordered by their percent of variability among Cornales representatives. Orange bars denote the percent of variable sites among the six Cornales taxa, whereas green and blue bars represent the percent of variable sites among the four Hydrangeaceae representatives and the two tribe Hydrangeeae taxa, respectively
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4491267&req=5

Fig2: Retained potential NSCG after the entire data mining and filtering process. Genes have been ordered by their percent of variability among Cornales representatives. Orange bars denote the percent of variable sites among the six Cornales taxa, whereas green and blue bars represent the percent of variable sites among the four Hydrangeaceae representatives and the two tribe Hydrangeeae taxa, respectively
Mentions: Our data mining process retrieved 4949 Cornales scaffolds that could be aligned to 546 A. thaliana single-copy gene orthologs. This pool of genes was used to select the most promising and the easiest to handle markers for H. sect. Cornidia. We were aiming for gene alignments where a major part of the gene was covered by at least four of the 1KP Cornales species. This is crucial for estimating phylogenetic utility of the candidate markers, as well as for successful primer design. Among the 546 initial alignments, 444 showed low coverage of Cornales representatives and additional 16 showed low coverage of the two Hydrangeeae taxa (Fig. 1). Therefore these alignments were not considered any further. Multiple scaffold sequences were detected for H. quercifolia in 13 of the remaining alignments and were therefore excluded from further steps. A total of 73 potential NSCG were retained after filtering (Fig. 1). From these alignments, 14 contained the six Cornales representatives, whereas 53 lacked either Curtisia dentata or Deutzia scabra and six did not have either Philadelphus inodorus and Curtisia dentata, or Curtisia dentata and Deutzia scabra. When considering transcriptome sequences from all Cornales taxa, alignments showed 26.7-62.3 % variable sites (Fig. 2). However, the range of variable sites was lowered to 19.8-57.5 % when only the four Hydrangeaceae representatives were considered and to 2.8-26.9 % between the two representatives of tribe Hydrangeeae (Fig. 2).Fig. 1

Bottom Line: Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths.While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution.The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium. carolina.granados@st.ib.unam.mx.

ABSTRACT

Background: Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other "fast" evolving plastid markers.

Results: Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae).

Conclusions: While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales.

Show MeSH