Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline
Explore this paper's citation graph
Summary
It is concluded that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing orplastome-enrichment approaches), and can be performed with limited sample destruction.
- Type
- article
- Published
- 2016-01-01
- Cited by
- 141
- References
- 29
- Access
- Open access
- OpenAlex
- https://openalex.org/W1924760575
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:83639734
Keywords
Herbarium, Chloroplast DNA, Biology, Sequence assembly, Genome
References
- Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico
- Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens
- Reference-Free Comparative Genomics of 174 Chloroplasts
- How to Open the Treasure Chest? Optimising DNA Extraction from Herbarium Specimens
- Mining Herbaria for Plant Pathogen Genomes: Back to the Future
- Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data
- DNA Analysis of Herbarium Specimens of the Grass Weed Alopecurus myosuroides Reveals Herbicide Resistance Pre-Dated Herbicides
- Herbaria are a major frontier for species discovery
- Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke.
- ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
- Versatile and open software for comparing large genomes
- Genome skimming identifies polymorphism in tern populations and species
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- Trimmomatic: a flexible trimmer for Illumina sequence data
- DNA Damage in Plant Herbarium Tissue
- Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics.
- Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach
- When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality
- Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia
- Automatic annotation of organellar genomes with DOGMA
Cited by
- Strategies for complete plastid genome sequencing
- Phylogenetic relationships within Lactuca L. (Asteraceae), including African species, based on chloroplast DNA sequence comparisons
- Collections‐based research in the genomic era
- Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing
- The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae).
- Hybridization and hybrid speciation under global change.
- Telling plant species apart with DNA: from barcodes to genomes
- Mitogenomics of Hesperelaea, an extinct genus of Oleaceae.
- Developmental Control and Plasticity of Fruit and Seed Dimorphism in Aethionema arabicum1[CC-BY]
- Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world's biological collections.
- Museomics resolve the systematics of an endangered grass lineage endemic to north-western Madagascar
- Desiccation tolerance in seeds and plants
- Utilization of complete chloroplast genomes for phylogenetic studies
- Genetic diversity and evolution in Lactuca L. (Asteraceae) : from phylogeny to molecular breeding
- Plant phylogeny as a window on the evolution of hyperdiversity in the tropical rainforest biome.
- From species to trait evolution in Aethionema (Brassicaceae)
- Herbarium genomics: skimming and plastomics from archival specimens
- Correlated evolutionary rates across genomic compartments in Annonaceae.
- Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida
- Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia
Related papers
- Kermit: Guided Long Read Assembly using Coloured Overlap Graphs
- Whole-genome sequence assembly of the water buffalo (Bubalus bubalis)
- Genome Assembly.
- Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
- Bos taurus genome assembly
- WENGAN: Efficient and high quality hybrid de novo assembly of human genomes
- Chromosome-scale assembly comparison of the Korean Reference Genome KOREF from PromethION and PacBio with Hi-C mapping information