Herbarium genomics: skimming and plastomics from archival specimens

Bakker, Freek T.

doi:10.1080/00837792.2017.1313383

Cited by 59 publications

(62 citation statements)

References 90 publications

(108 reference statements)

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“…connecting type specimens to genetic sequences, and therefore help to resolve longstanding taxonomic issues (Liimatainen et al, 2014). Sánchez Barreiro et al (2017) used a modern genotyping-by-sequencing (GBS) dataset to design RNA baits that were used to enrich for restriction enzyme associated loci in historic herbarium specimens It has also been shown that de novo assembly of genome skimming data is a relatively straightforward approach to generate sequences of high-copy regions like whole plastome sequences and nuclear ribosomal units (Staats et al, 2013;Besnard et al 2014;Zedane et al, 2016;Bakker, 2017). The ongoing PhyloNorway project uses a genome-skimming approach to assemble plastome sequences and aims to complete a reference database for all Norwegian vascular plants, with the majority of the material coming from herbarium collections (Taberlet et al 2018).…”

Section: Mining the Diversity Of Species Genomes Stored In Herbariamentioning

confidence: 99%

Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections

Bieker

Martin

2018

Botany Letters

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Section: Mining the Diversity Of Species Genomes Stored In Herbariamentioning

confidence: 99%

Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections

Bieker

Martin

2018

Botany Letters

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“…Four species of Nicotiana section Suaveolentes (small-medium sized herbs- Figure 1A) were sequenced, for which there were both recently collected silica-dried leaf material (hereafter "fresh") and also herbarium collections of approximately 10 years of age (hereafter "herbarium"). The current consensus is that most damage is done during the initial specimen collection/preservation stage (in particular the heat treatment used in the drying process) (Staats et al, 2011(Staats et al, , 2013Bakker, 2017), hence the young age of specimens chosen here should not confound some conclusions regarding herbarium DNA more broadly. Large variation amplitude of environmental conditions during long-term storage would also contribute to further DNA degradation, but the storage conditions are generally relatively constant in most herbaria.…”

Section: Methodsmentioning

confidence: 99%

“…Provided that patterns of degradation are mostly stochastic (Staats et al, 2011), then the resulting sequence data should be suitable for many studies of genome evolution (including nuclear and organellar). Most studies that have thus far utilized HTS for herbarium specimen sequencing (herbariomics) have focussed on genome skimming (Dodsworth, 2015a) for organellar genome reconstruction, in particular for assembling the plastid genome (Bakker et al, 2016;Bakker, 2017). This is due to several factors, including ease of assembly and the predominance of plastid regions in angiosperm phylogenetics.…”

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confidence: 99%

Potential of Herbariomics for Studying Repetitive DNA in Angiosperms

et al. 2018

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Repetitive DNA has an important role in angiosperm genomes and is relevant to our understanding of genome size variation, polyploidisation and genome dynamics more broadly. Much recent work has harnessed the power of high-throughput sequencing (HTS) technologies to advance the study of repetitive DNA in flowering plants. Herbarium collections provide a useful historical perspective on genome diversity through time, but their value for the study of repetitive DNA has not yet been explored. We propose that herbarium DNA may prove as useful for studies of repetitive DNA content as it has for reconstructed organellar genomes and low-copy nuclear sequence data.Here we present a case study in the tobacco genus (Nicotiana; Solanaceae), showing that herbarium specimens can provide accurate estimates of the repetitive content of angiosperm genomes by direct comparison with recently-collected material. We show a strong correlation between the abundance of repeat clusters, e.g., different types of transposable elements and satellite DNA, in herbarium collections versus recent material for four sets of Nicotiana taxa. These results suggest that herbarium specimen genome sequencing (herbariomics) holds promise for both repeat discovery and analyses that aim to investigate the role of repetitive DNAs in genomic evolution, particularly genome size evolution and/or contributions of repeats to the regulation of gene space.

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“…Of course, the inclusion of paralogous cp genes from the nucleus or mitochondrion cannot be fully ruled out [2]. Another limitation is that highly degraded DNA cannot be used for long-range PCR, which limits its use with herbarium material [61,6]. The method is also unsuitable if larger rearrangements in gene order are to be expected, as have been found for example in Passiflora L. [62].…”

Section: Enrichment Of Chloroplast Dna Using Long-range Pcrmentioning

confidence: 99%

Can we use it? On the utility ofde novoand reference-based assembly of Nanopore data for plant plastome sequencing

Scheunert

Dorfner

Lingl

et al. 2019

Preprint

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The chloroplast genome harbors plenty of valuable information for phylogenetic research.Illumina short-read data is generally used for de novo assembly of whole plastomes. PacBio or Oxford Nanopore long reads are additionally employed in hybrid approaches to enable assembly across the highly similar inverted repeats of a chloroplast genome. Unlike for PacBio, plastome assemblies based solely on Nanopore reads are rarely found, due to their high error rate and non-random error profile. However, the actual quality decline connected to their use has never been quantified. Furthermore, no study has employed reference-based assembly using Nanopore reads, which is common with Illumina data. Using Leucanthemum Mill. as an example, we compared the sequence quality of seven plastome assemblies of the same species, using combinations of two sequencing platforms and three analysis pipelines.In addition, we assessed the factors which might influence Nanopore assembly quality during sequence generation and bioinformatic processing.The consensus sequence derived from de novo assembly of Nanopore data had a sequence identity of 99.59% compared to Illumina short-read de novo assembly. Most of the found errors comprise indels (81.5%), and a large majority of them is part of homopolymer regions.The quality of reference-based assembly is heavily dependent upon the choice of a closeenough reference. Using a reference with 0.83% sequence divergence from the studied species, mapping of Nanopore reads results in a consensus comparable to that from Nanopore de novo assembly, and of only slightly inferior quality compared to a referencebased assembly with Illumina data (0.49% and 0.26% divergence from Illumina de novo). For optimal assembly of Nanopore data, appropriate filtering of contaminants and chimeric sequences, as well as employing moderate read coverage, is essential.Based on these results, we conclude that Nanopore long reads are a suitable alternative to Illumina short reads in plastome phylogenomics. Only few errors remain in the finalized assembly, which can be easily masked in phylogenetic analyses without loss in analytical accuracy. The easily applicable and cost-effective technology might warrant more attention by researchers dealing with plant chloroplast genomes.

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Herbarium genomics: skimming and plastomics from archival specimens

Cited by 59 publications

References 90 publications

Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections

Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections

Potential of Herbariomics for Studying Repetitive DNA in Angiosperms

Can we use it? On the utility ofde novoand reference-based assembly of Nanopore data for plant plastome sequencing

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