scholarly journals Resolving Recalcitrant Clades in the Pantropical Ochnaceae: Insights From Comparative Phylogenomics of Plastome and Nuclear Genomic Data Derived From Targeted Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Julio V. Schneider ◽  
Juraj Paule ◽  
Tanja Jungcurt ◽  
Domingos Cardoso ◽  
André Márcio Amorim ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
De Novo ◽  
Sequence Data ◽  
Plastid Dna ◽  
Targeted Sequencing ◽  
Recent Analysis ◽  
Target Sequence ◽  
Uniparental Inheritance ◽  
Plastid Genomes ◽  
Nuclear Loci

Plastid DNA sequence data have been traditionally widely used in plant phylogenetics because of the high copy number of plastids, their uniparental inheritance, and the blend of coding and non-coding regions with divergent substitution rates that allow the reconstruction of phylogenetic relationships at different taxonomic ranks. In the present study, we evaluate the utility of the plastome for the reconstruction of phylogenetic relationships in the pantropical plant family Ochnaceae (Malpighiales). We used the off-target sequence read fraction of a targeted sequencing study (targeting nuclear loci only) to recover more than 100 kb of the plastid genome from the majority of the more than 200 species of Ochnaceae and all but two genera using de novo and reference-based assembly strategies. Most of the recalcitrant nodes in the family’s backbone were resolved by our plastome-based phylogenetic inference, corroborating the most recent classification system of Ochnaceae and findings from a phylogenomic study based on nuclear loci. Nonetheless, the phylogenetic relationships within the major clades of tribe Ochnineae, which comprise about two thirds of the family’s species diversity, received mostly low support. Generally, the phylogenetic resolution was lowest at the infrageneric level. Overall there was little phylogenetic conflict compared to a recent analysis of nuclear loci. Effects of taxon sampling were invoked as the most likely reason for some of the few well-supported discords. Our study demonstrates the utility of the off-target fraction of a target enrichment study for assembling near-complete plastid genomes for a large proportion of samples.

scholarly journals Significant cross-species gene flow detected in the Tamias quadrivittatus group of North American chipmunks

2021 ◽  
Author(s):  
Jiayi Ji ◽  
Donavan J. Jackson ◽  
Adam D. Leaché ◽  
Ziheng Yang
Keyword(s):  
Gene Flow ◽  
Sequence Data ◽  
Nuclear Genome ◽  
Likelihood Method ◽  
Recent Analysis ◽  
The Past ◽  
Rapid Speciation ◽  
Full Likelihood ◽  
Nuclear Loci ◽  
Robust Evidence

In the past two decades genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used heuristic methods that analyze summaries of the multilocus sequence data to detect gene flow, which may suffer from low power. Here we use the full likelihood method implemented in the Bayesian program BPP to reanalyze these data. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 65%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. Our analyses highlight the importance of using adequate statistical methods to reach reliable biological conclusions concerning cross-species gene flow.

Phylogenetic relationships in Peniocereus (Cactaceae) inferred from plastid DNA sequence data

2005 ◽  
Vol 118 (5) ◽  
pp. 317-328 ◽  
Author(s):  
Salvador Arias ◽  
Teresa Terrazas ◽  
Hilda J. Arreola-Nava ◽  
Monserrat Vázquez-Sánchez ◽  
Kenneth M. Cameron
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Plastid Dna ◽  
Dna Sequence Data

Phylogenetic relationships in Cyperaceae subfamily Mapanioideae inferred from pollen and plastid DNA sequence data

2003 ◽  
Vol 90 (7) ◽  
pp. 1071-1086 ◽  
Author(s):  
D. A. Simpson ◽  
C. A. Furness ◽  
T. R. Hodkinson ◽  
A. M. Muasya ◽  
M. W. Chase
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Plastid Dna ◽  
Dna Sequence Data

scholarly journals MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes

2020 ◽  
Author(s):  
Zhiqiang Wu ◽  
Gus Waneka ◽  
Amanda K. Broz ◽  
Connor R. King ◽  
Daniel B. Sloan
Keyword(s):  
Candidate Genes ◽  
De Novo ◽  
Point Mutations ◽  
Plastid Dna ◽  
Digital Pcr ◽  
Mutation Rates ◽  
Sequence Evolution ◽  
Small Indels ◽  
Plastid Genomes ◽  
Duplex Sequencing

ABSTRACTMitochondrial and plastid genomes in land plants exhibit some of the slowest rates of sequence evolution observed in any eukaryotic genome, suggesting an exceptional ability to prevent or correct mutations. However, the mechanisms responsible for this extreme fidelity remain unclear. We tested seven candidate genes involved in cytoplasmic DNA replication, recombination, and repair (POLIA, POLIB, MSH1, RECA3, UNG, FPG, and OGG1) for effects on mutation rates in the model angiosperm Arabidopsis thaliana by applying a highly accurate DNA sequencing technique (duplex sequencing) that can detect newly arisen mitochondrial and plastid mutations still at low heteroplasmic frequencies. We find that disrupting MSH1 (but not the other candidate genes) leads to massive increases in the frequency of point mutations and small indels and changes to the mutation spectrum in mitochondrial and plastid DNA. We also used droplet digital PCR to show transmission of de novo heteroplasmies across generations in msh1 mutants, confirming a contribution to heritable mutation rates. This dual-targeted gene is part of an enigmatic lineage within the mutS mismatch repair family that we find is also present outside of green plants in multiple eukaryotic groups (stramenopiles, alveolates, haptophytes, and cryptomonads), as well as certain bacteria and viruses. MSH1 has previously been shown to limit ectopic recombination in plant cytoplasmic genomes. Our results point to a broader role in recognition and correction of errors in plant mitochondrial and plastid DNA sequence, leading to greatly suppressed mutation rates perhaps via initiation of double-stranded breaks and repair pathways based on faithful homologous recombination.

scholarly journals MSH1is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes

2020 ◽  
Vol 117 (28) ◽  
pp. 16448-16455 ◽  
Author(s):  
Zhiqiang Wu ◽  
Gus Waneka ◽  
Amanda K. Broz ◽  
Connor R. King ◽  
Daniel B. Sloan
Keyword(s):  
Candidate Genes ◽  
De Novo ◽  
Point Mutations ◽  
Plastid Dna ◽  
Digital Pcr ◽  
Mutation Rates ◽  
Sequence Evolution ◽  
Small Indels ◽  
Plastid Genomes ◽  
Duplex Sequencing

Mitochondrial and plastid genomes in land plants exhibit some of the slowest rates of sequence evolution observed in any eukaryotic genome, suggesting an exceptional ability to prevent or correct mutations. However, the mechanisms responsible for this extreme fidelity remain unclear. We tested seven candidate genes involved in cytoplasmic DNA replication, recombination, and repair (POLIA,POLIB,MSH1,RECA3,UNG,FPG, andOGG1) for effects on mutation rates in the model angiospermArabidopsis thalianaby applying a highly accurate DNA sequencing technique (duplex sequencing) that can detect newly arisen mitochondrial and plastid mutations even at low heteroplasmic frequencies. We find that disruptingMSH1(but not the other candidate genes) leads to massive increases in the frequency of point mutations and small indels and changes to the mutation spectrum in mitochondrial and plastid DNA. We also used droplet digital PCR to show transmission of de novo heteroplasmies across generations inmsh1mutants, confirming a contribution to heritable mutation rates. This dual-targeted gene is part of an enigmatic lineage within themutSmismatch repair family that we find is also present outside of green plants in multiple eukaryotic groups (stramenopiles, alveolates, haptophytes, and cryptomonads), as well as certain bacteria and viruses.MSH1has previously been shown to limit ectopic recombination in plant cytoplasmic genomes. Our results point to a broader role in recognition and correction of errors in plant mitochondrial and plastid DNA sequence, leading to greatly suppressed mutation rates perhaps via initiation of double-stranded breaks and repair pathways based on faithful homologous recombination.

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