PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data

Cai, Liming; Zhang, Hongrui; Davis, Charles C.

doi:10.1002/aps3.11475

Cited by 16 publications

(14 citation statements)

References 38 publications

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“…Despite a few attempts to use genome skims to recover low copy nuclear loci for direct phylogenetic use ( Besnard et al, 2014 ; Besnard et al, 2018 ; Olofsson et al, 2019 ; Vargas et al, 2019 ; Liu et al, 2021 ; Loiseau et al, 2021 ; Meng et al, 2021 ; Cai, Zhang & Davis, 2022 ), such endeavor remains largely neglected. Causes might include shallow depth of the low copy part of the genome due to libraries with few reads, species with large genomes, and especially, the trade-off between these two, but also might be related to the lack of pipelines for data assembling.…”

Section: Discussionmentioning

confidence: 99%

“…Its main use has been restricted to characterize conserved nuclear loci for primer or probe design for candidate low copy nuclear markers ( Straub et al, 2012 ; Reginato & Michelangeli, 2016 ). Despite some attempts to use low copy nuclear markers from genome skims to base phylogenetic inference ( Besnard et al, 2014 ; Besnard et al, 2018 ; Olofsson et al, 2019 ; Vargas et al, 2019 ; Liu et al, 2021 ; Loiseau et al, 2021 ; Meng et al, 2021 ; Cai, Zhang & Davis, 2022 ), this avenue is still neglected. Two major factors might have hampered the use of genome skims to generate low copy nuclear data: lack of genomic information for the group of interest and shallow sequencing.…”

Section: Introductionmentioning

confidence: 99%

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A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use

Reginato¹

2022

PeerJ

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Background Genome skimming is a popular method in plant phylogenomics that do not include a biased enrichment step, relying on random shallow sequencing of total genomic DNA. From these data the plastome is usually readily assembled and constitutes the bulk of phylogenetic information generated in these studies. Despite a few attempts to use genome skims to recover low copy nuclear loci for direct phylogenetic use, such endeavor remains neglected. Causes might include the trade-off between libraries with few reads and species with large genomes (i.e., missing data caused by low coverage), but also might relate to the lack of pipelines for data assembling. Methods A pipeline and its companion R package designed to automate the recovery of low copy nuclear markers from genome skimming libraries are presented. Additionally, a series of analyses aiming to evaluate the impact of key assembling parameters, reference selection and missing data are presented. Results A substantial amount of putative low copy nuclear loci was assembled and proved useful to base phylogenetic inference across the libraries tested (4 to 11 times more data than previously assembled plastomes from the same libraries). Discussion Critical aspects of assembling low copy nuclear markers from genome skims include the minimum coverage and depth of a sequence to be used. More stringent values of these parameters reduces the amount of assembled data and increases the relative amount of missing data, which can compromise phylogenetic inference, in turn relaxing the same parameters might increase sequence error. These issues are discussed in the text, and parameter tuning through multiple comparisons tracking their effects on support and congruence is highly recommended when using this pipeline. The skimmingLoci pipeline (https://github.com/mreginato/skimmingLoci) might stimulate the use of genome skims to recover nuclear loci for direct phylogenetic use, increasing the power of genome skimming data to resolve phylogenetic relationships, while reducing the amount of sequenced DNA that is commonly wasted.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use

Reginato¹

2022

PeerJ

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“…Applied to genome skims, long reads enable more accurate recovery of mitochondrial genomes with lower sequencing depth. 9 Sample multiplexing, field portability, and the low price of the instrument all reduce cost and enable sequencing by low resource groups. 10 Genome skimming is unbiased in most genomic regions; however, some regions are present in multiple copies and this enrichment will be reflected in the skimmed read dataset.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates

Faulk

2023

Preprint

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Genome skimming is defined as low-pass sequencing below 0.05X coverage and is typically used for mitochondrial genome recovery and species identification. Long read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost genome skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation and transposon assessment. At coverage of just 0.001X, or 30 Mb of reads, accuracy is sub-1%. Biological and technical replicates validate high precision. Skimming 40 vertebrate species reveals conserved patterns of global methylation consistent with whole genome bisulfite sequencing and an average mapping rate above 97%. Genome size directly correlates to global DNA methylation, explaining 44% of its variance. Accurate SINE and LINE transposon methylation in both mouse and primates can be obtained with just 0.0001X coverage, or 3 Mb of reads. Sample multiplexing, field portability, and the low price of this instrument combine to make genome skimming for DNA methylation an accessible method for epigenetic assessment from ecology to epidemiology, and by low resource groups.

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“…Given that high-throughput sequencing technologies now make sequencing of both organellar genomes a relatively easy task, including from “off-target” reads and low coverage genome skimming, it is worth considering whether mitochondrial genomes should be more broadly integrated into plant evolutionary and phylogenomic studies ( Weitemier et al., 2014 ; Cai et al., 2022 ). More fundamentally, the extent of evolutionary concordance between the two organelles remains unknown, not only in terms of their supported phylogenetic topologies, but also in their rates of molecular evolution and sequence composition among genes and across the land plant phylogeny.…”

Section: Introductionmentioning

confidence: 99%

Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants

et al. 2023

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Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles’ evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles’ evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.

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PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data

Cited by 16 publications

References 38 publications

A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use

A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use

Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates

Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants

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