Development of phylogenetic markers from single-copy nuclear genes for multi locus, species level analyses in the mint family (Lamiaceae)

Curto, Manuel; Puppo, Pamela; Ferreira, Diana; Nogueira, Marcos Gomes; Meimberg, Harald

doi:10.1016/j.ympev.2012.02.010

Cited by 32 publications

(34 citation statements)

References 33 publications

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“…Among the markers used in the present study, we detected that the locus O.oni.007 has at least four copies in the Micromeria genome. This is concordant with the observations of excess of heterozygosity reported by Curto et al (2012) and it may explain the lack of resolution of this marker in the individual MJ networks. On the other hand, this lack of resolution may rather be an artifact of haplotype reconstruction that infers that the locus has two paralog sequences rather than the two orthologs.…”

Section: Gene Duplicationsupporting

confidence: 91%

“…For phylogenetic analyses we amplified all 76 samples of Micromeria using eight nuclear loci. These loci were selected from those published by Curto et al (2012) based on sequence quality and variability (number of polymorphisms). Curto et al (2012) identified the loci by comparing EST sequences from several Lamiaceae species to the Arabidopsis thaliana genome and designing primers targeting potential intron regions.…”

Section: Amplification and Sequencingmentioning

confidence: 99%

“…These loci were selected from those published by Curto et al (2012) based on sequence quality and variability (number of polymorphisms). Curto et al (2012) identified the loci by comparing EST sequences from several Lamiaceae species to the Arabidopsis thaliana genome and designing primers targeting potential intron regions. These markers were also used in Puppo et al (2014) and details concerning sequence structure can be found in Table 3.…”

Section: Amplification and Sequencingmentioning

confidence: 99%

“…The sequences used were M. varia sequences taken from Curto et al (2012). To create a whole genome reference, a library with an average insert size of 500 bp was prepared and paired end sequenced on an Illumina HiSeq 2000 (Illumina, San Diego, California, USA) for 100 cycles each end.…”

Section: Gene Duplicationmentioning

confidence: 99%

See 3 more Smart Citations

Molecular phylogenetics of Micromeria (Lamiaceae) in the Canary Islands, diversification and inter-island colonization patterns inferred from nuclear genes

Puppo

Curto

Gusmão-Guedes

et al. 2015

Molecular Phylogenetics and Evolution

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Section: Gene Duplicationsupporting

confidence: 91%

Section: Amplification and Sequencingmentioning

confidence: 99%

Section: Amplification and Sequencingmentioning

confidence: 99%

Section: Gene Duplicationmentioning

confidence: 99%

See 2 more Smart Citations

Molecular phylogenetics of Micromeria (Lamiaceae) in the Canary Islands, diversification and inter-island colonization patterns inferred from nuclear genes

Puppo

Curto

Gusmão-Guedes

et al. 2015

Molecular Phylogenetics and Evolution

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“…133 Curto et al, 2012;Thomson et al, 2008). Curto and colleagues (2012) have shown from their 134 study of Micromeria (Lamiaceae) that this locus can be phylogenetically informative, providing 135 a substantial amount of variation among closely related species.…”

mentioning

confidence: 99%

Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear loci

Roy

Catlin

Garner

et al. 2016

Preprint

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The subfamily Lamioideae (Lamiaceae) comprises ten tribes, of which only Stachydeae and Synandreae include New World members. Previous studies have investigated the phylogenetic relationships among the members of Synandreae based on plastid and nuclear ribosomal DNA loci. In an effort to re-examine the phylogenetic relationships within Synandreae, the current study incorporates data from four low-copy nuclear loci, PHOT1, PHOT2, COR, and PPR. Our results confirm previous studies based on chloroplast and nuclear ribosomal markers in supporting monophyly of tribe Synandreae, as well as sister relationships between Brazoria and Warnockia, and between that pair of genera and a monophyletic Physostegia. However, we observe incongruence in the relationships of Macbridea and Synandra. The placement of Synandreae within Lamioideae is poorly resolved and incongruent among different analyses, and the sister group of Synandreae remains enigmatic. Comparison of the colonization and migration patterns corroborates a single colonization of the New World by Synandreae during the mid-Miocene. This is in contrast to the only other lamioid tribe that includes New World members, Stachydeae, which colonized the New World at least twice-during the mid-Miocene and Pliocene.Edaphic conditions and intolerance of soil acidity may be factors that restricted the distribution of most genera of Synandreae to southeastern and south-central North America, whereas polyploidy could have increased the colonizing capability of the more wide-ranging genus, Physostegia. 19 The subfamily Lamioideae (Lamiaceae) comprises ten tribes, of which only Stachydeae and 20 Synandreae include New World members. Previous studies have investigated the phylogenetic 21 relationships among the members of Synandreae based on plastid and nuclear ribosomal DNA 22 loci. In an effort to re-examine the phylogenetic relationships within Synandreae, the current 23 study incorporates data from four low-copy nuclear loci, PHOT1, PHOT2, COR, and PPR. Our 24 results confirm previous studies based on chloroplast and nuclear ribosomal markers in 25 supporting monophyly of tribe Synandreae, as well as sister relationships between Brazoria and 26 Warnockia, and between that pair of genera and a monophyletic Physostegia. However, we 27 observe incongruence in the relationships of Macbridea and Synandra. The placement of 28 Synandreae within Lamioideae is poorly resolved and incongruent among different analyses, and 29 the sister group of Synandreae remains enigmatic. Comparison of the colonization and migration 30 patterns corroborates a single colonization of the New World by Synandreae during the mid- 31 Miocene. This is in contrast to the only other lamioid tribe that includes New World members, 32 Stachydeae, which colonized the New World at least twice-during the mid-Miocene and 33 Pliocene. Edaphic conditions and intolerance of soil acidity may be factors that restricted the 34 distribution of most genera of Synandreae to southeastern and south-central North America, 35 ...

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Comparison of taxon‐specific versus general locus sets for targeted sequence capture in plant phylogenomics

2018

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Premise of the StudyTargeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single‐copy nuclear loci. Most published studies in plants have used taxon‐specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single‐copy and have orthologs in large clades of plants.MethodsWe identify and compare a taxon‐specific locus set and three general locus sets (conserved ortholog set [COSII], shared single‐copy nuclear [APVO SSC] genes, and pentatricopeptide repeat [PPR] genes) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups. We evaluate their performance in terms of assembly success, sequence variability, and resolution and support of inferred phylogenetic trees.ResultsThe taxon‐specific locus set had the most target loci. Assembly success was high for all locus sets in Buddleja samples. For outgroups, general locus sets had greater assembly success. Taxon‐specific and PPR loci had the highest average variability. The taxon‐specific data set produced the best‐supported tree, but all data sets showed improved resolution over previous non‐sequence capture data sets.DiscussionGeneral locus sets can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.

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Development of phylogenetic markers from single-copy nuclear genes for multi locus, species level analyses in the mint family (Lamiaceae)

Cited by 32 publications

References 33 publications

Molecular phylogenetics of Micromeria (Lamiaceae) in the Canary Islands, diversification and inter-island colonization patterns inferred from nuclear genes

Molecular phylogenetics of Micromeria (Lamiaceae) in the Canary Islands, diversification and inter-island colonization patterns inferred from nuclear genes

Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear loci

Comparison of taxon‐specific versus general locus sets for targeted sequence capture in plant phylogenomics

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