The Experts below are selected from a list of 312 Experts worldwide ranked by ideXlab platform
Freek T. Bakker - One of the best experts on this subject based on the ideXlab platform.
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Herbarium Genomics: Plant Archival DNA Explored
Population Genomics, 2018Co-Authors: Freek T. BakkerAbstract:Herbarium genomics, allowing testing of historic biological hypotheses in plant science, is a promising field mainly driven by recent advances in next-generation sequencing (NGS) technology. Herbarium collections represent an enormous botanical repository of both specimens and of phenotypic observations and locality data, of sometimes long-extinct taxa. Herbarium specimens, a large part of which stem from the nineteenth and eighteenth century, are mostly pressed and mounted and were usually heat-treated and poisoned for preservation. Whereas the presence of post-mortem damage in Herbarium DNA has been found to consist of mainly genome fragmentation (single- and double-stranded breaks), damage-derived miscoding lesions appear to be highly limited or even negligible. For organelle genomes and other repetitive genomic compartments, genome skimming appears effective in retrieving sequence data from plant Herbarium specimens, whereas studies addressing Herbarium nuclear-encoded genes and particularly whole genomes are still in minority. High levels of Herbarium genomic fragmentation possibly lead to insert sizes being smaller than Illumina read lengths applied. Using a series of 93 Herbarium DNA samples, representing 10 angiosperm families, near-complete plastomes were assembled for 80% of the specimens, some of which are 146 years old. Overlapping read pairs were found to occur in roughly 80% of all read pairs obtained. After merging such overlapping pairs, the resulting fragments and their distribution can be considered to reflect the ongoing process of genome fragmentation up to the moment of DNA extraction. Fragment length distributions appear to fit gamma distributions with either many small fragments present or an increasing number of longer fragments having accumulated. These distributions appear to differ from usually observed first-order genomic degradation kinetics, possibly due to the nonrepresentative nature of genome skimming samples.
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Herbarium genomics: skimming and plastomics from archival specimens
Webbia, 2017Co-Authors: Freek T. BakkerAbstract:AbstractUsing massive parallel sequencing, which has become known as second-generation sequencing, some of the classic roadblocks to using Herbarium DNA have been overcome. For instance, no longer is the degraded nature of most Herbarium DNA preventing sequencing (because of blocking effective amplification). Instead, several kilobases of genomic sequence can be obtained on a routine basis, especially from high-copy number compartments such as plastomes (chloroplast genomes). With approaches such as genomic skimming a fair coverage of repetitive genome compartments (such as plastomes) can be obtained, enabling fast assembly of associated sequences. Although assembly of complete 150+ kilobase Herbarium plastomes based on skimming still needs more investment, the generation of large contigs spanning several kilo bases is straightforward. It presents an important and cost-effective boost to using Herbarium DNA-sequences in phylogenetic studies at species-level and beyond. At the same time, although Herbarium...
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Herbarium genomics: plastome sequence assembly from a range of Herbarium specimens using an Iterative Organelle Genome Assembly pipeline
Biological Journal of the Linnean Society, 2015Co-Authors: Freek T. Bakker, Di Lei, Setareh Mohammadin, Zhen Wei, Sara J. Van De Kerke, Barbara Gravendeel, Mathijs Nieuwenhuis, Martijn Staats, David E. Alquezar-planasAbstract:Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from Herbarium specimens is feasible, from total DNA extracts and with specimens up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different Angiosperm families, 73 of which were from Herbarium material with ages up to 146 years old. For 84 specimens, a sufficient number of paired-end reads were generated (in total 9.4 × 1012 nucleotides), yielding successful plastome assemblies for 74 specimens. Those derived from Herbarium specimens have lower fractions of plastome-derived reads compared with those from fresh and silica-gel-dried specimens, but total Herbarium assembly lengths are only slightly shorter. Specimens from wet-tropical conditions appear to have a higher number of contigs per assembly and lower N50 values. We find no significant correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from Herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome-enrichment approaches), and can be performed with limited sample destruction.
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DNA Damage in Plant Herbarium Tissue
PloS one, 2011Co-Authors: Martijn Staats, Argelia Cuenca, James E. Richardson, Ria Vrielink Van Ginkel, Gitte Petersen, Ole Seberg, Freek T. BakkerAbstract:Dried plant Herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as Herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative assessment of DNA post-mortem damage is essential to determine the accuracy of molecular data from Herbarium specimens. In this study we present an assessment of DNA damage as miscoding lesions in Herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA. In addition, we assess DNA degradation as a result of strand breaks and other types of polymerase non-bypassable damage by quantitative real-time PCR. Comparing four pairs of fresh and Herbarium specimens of the same individuals we quantitatively assess post-mortem DNA damage, directly after specimen preparation, as well as after long-term Herbarium storage. After specimen preparation we estimate the proportion of gene copy numbers of plastid, mitochondrial, and nuclear DNA to be 2.4-3.8% of fresh control DNA and 1.0-1.3% after long-term Herbarium storage, indicating that nearly all DNA damage occurs on specimen preparation. In addition, there is no evidence of preferential degradation of organelle versus nuclear genomes. Increased levels of CRT/GRA transitions were observed in old Herbarium plastid DNA, representing 21.8% of observed miscoding lesions. We interpret this type of post-mortem DNA damage-derived modification to have arisen from the hydrolytic deamination of cytosine during long-term Herbarium storage. Our results suggest that reliable sequence data can be obtained from Herbarium specimens.
Kush Sharma - One of the best experts on this subject based on the ideXlab platform.
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indian virtual Herbarium project implementing an institutional knowledge repository as a digital archive design development solution architecture and implementation
Journal of Digital Asset Management, 2009Co-Authors: Ramesh Singh, Kush SharmaAbstract:The Indian Virtual Herbarium (IVH) portal is proposed as a customization of the DSpace Digital Library System for archiving. The portal will consist of a user-friendly interface. The classification hierarchy will consist of the Herbariums at the top level, collection plants and then the actual plant image stored in the tiff/jpeg format. The images are assumed to be scanned in an appropriate way with the desired resolution. This paper describes the solution architecture based on the digital library product DSpace, and also outlines the requirements of System Software. The three major missions of this paper are to provide technology services for the IVH, DH and Production Projects; to deal with the standards of information organization; and to build the National Botanical Digital Archives Resource Center. The set up of the collaboration and communication mechanisms involve an integrated searching system; a knowledge management system; and a digital preservation mechanism. Backup services also have to be provided
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Indian Virtual Herbarium Project: Implementing an institutional knowledge repository as a digital archive – Design, development, solution architecture and implementation
Journal of Digital Asset Management, 2009Co-Authors: Ramesh Singh, Kush SharmaAbstract:The Indian Virtual Herbarium (IVH) portal is proposed as a customization of the DSpace Digital Library System for archiving. The portal will consist of a user- friendly interface. The classifi cation hierarchy will consist of the Herbariums at the top level, collection plants and then the actual plant image stored in the tiff/jpeg format. The images are assumed to be scanned in an appropriate way with the desired resolu- tion. This paper describes the solution architecture based on the digital library product DSpace, and also outlines the requirements of System Software. The three major missions of this paper are to provide technology services for the IVH, DH and Produc- tion Projects; to deal with the standards of information organization; and to build the National Botanical Digital Archives Resource Center. The set up of the collaboration and communication mechanisms involve an integrated searching system; a knowledge management system; and a digital preservation mechanism. Backup services also have to be provided
David E. Alquezar-planas - One of the best experts on this subject based on the ideXlab platform.
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Herbarium genomics: plastome sequence assembly from a range of Herbarium specimens using an Iterative Organelle Genome Assembly pipeline
Biological Journal of the Linnean Society, 2015Co-Authors: Freek T. Bakker, Di Lei, Setareh Mohammadin, Zhen Wei, Sara J. Van De Kerke, Barbara Gravendeel, Mathijs Nieuwenhuis, Martijn Staats, David E. Alquezar-planasAbstract:Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from Herbarium specimens is feasible, from total DNA extracts and with specimens up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different Angiosperm families, 73 of which were from Herbarium material with ages up to 146 years old. For 84 specimens, a sufficient number of paired-end reads were generated (in total 9.4 × 1012 nucleotides), yielding successful plastome assemblies for 74 specimens. Those derived from Herbarium specimens have lower fractions of plastome-derived reads compared with those from fresh and silica-gel-dried specimens, but total Herbarium assembly lengths are only slightly shorter. Specimens from wet-tropical conditions appear to have a higher number of contigs per assembly and lower N50 values. We find no significant correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from Herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome-enrichment approaches), and can be performed with limited sample destruction.
Lara D. Shepherd - One of the best experts on this subject based on the ideXlab platform.
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A non-destructive DNA sampling technique for Herbarium specimens.
PloS one, 2017Co-Authors: Lara D. ShepherdAbstract:Herbarium specimens are an important source of DNA for plant research but current sampling methods require the removal of material for DNA extraction. This is undesirable for irreplaceable specimens such as rare species or type material. Here I present the first non-destructive sampling method for extracting DNA from Herbarium specimens. DNA was successfully retrieved from robust leaves and/or stems of Herbarium specimens up to 73 years old.
Ramesh Singh - One of the best experts on this subject based on the ideXlab platform.
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indian virtual Herbarium project implementing an institutional knowledge repository as a digital archive design development solution architecture and implementation
Journal of Digital Asset Management, 2009Co-Authors: Ramesh Singh, Kush SharmaAbstract:The Indian Virtual Herbarium (IVH) portal is proposed as a customization of the DSpace Digital Library System for archiving. The portal will consist of a user-friendly interface. The classification hierarchy will consist of the Herbariums at the top level, collection plants and then the actual plant image stored in the tiff/jpeg format. The images are assumed to be scanned in an appropriate way with the desired resolution. This paper describes the solution architecture based on the digital library product DSpace, and also outlines the requirements of System Software. The three major missions of this paper are to provide technology services for the IVH, DH and Production Projects; to deal with the standards of information organization; and to build the National Botanical Digital Archives Resource Center. The set up of the collaboration and communication mechanisms involve an integrated searching system; a knowledge management system; and a digital preservation mechanism. Backup services also have to be provided
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Indian Virtual Herbarium Project: Implementing an institutional knowledge repository as a digital archive – Design, development, solution architecture and implementation
Journal of Digital Asset Management, 2009Co-Authors: Ramesh Singh, Kush SharmaAbstract:The Indian Virtual Herbarium (IVH) portal is proposed as a customization of the DSpace Digital Library System for archiving. The portal will consist of a user- friendly interface. The classifi cation hierarchy will consist of the Herbariums at the top level, collection plants and then the actual plant image stored in the tiff/jpeg format. The images are assumed to be scanned in an appropriate way with the desired resolu- tion. This paper describes the solution architecture based on the digital library product DSpace, and also outlines the requirements of System Software. The three major missions of this paper are to provide technology services for the IVH, DH and Produc- tion Projects; to deal with the standards of information organization; and to build the National Botanical Digital Archives Resource Center. The set up of the collaboration and communication mechanisms involve an integrated searching system; a knowledge management system; and a digital preservation mechanism. Backup services also have to be provided
