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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
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A targeted capture approach to generating reference sequence databases for chloroplast gene regions.

Nicole R Foster1, Kor-Jent van Dijk1, Ed Biffin2

  • 1School of Biological Sciences University of Adelaide Adelaide South Australia Australia.

Ecology and Evolution
|April 18, 2022
PubMed
Summary

Developing comprehensive plant reference databases is crucial for accurate environmental DNA analysis. A new targeted capture method efficiently generates these databases, improving species identification and conservation efforts.

Keywords:
angiospermsbarcodinghybridization captureplastid

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Area of Science:

  • Ecology
  • Conservation Biology
  • Molecular Biology

Background:

  • Metabarcoding advances ecological and conservation studies but relies on accurate reference libraries.
  • Incomplete databases lead to misidentification, impacting species detection and management.
  • Coastal temperate plant taxa are particularly underrepresented in current reference databases.

Purpose of the Study:

  • To develop an efficient targeted capture method for generating plant reference sequence databases.
  • To create a reference database for underrepresented coastal temperate plant species.
  • To assess the efficacy of multiple chloroplast gene regions for plant discrimination.

Main Methods:

  • A targeted capture approach using the OZBaits_CP V1.0 set was employed.
  • Chloroplast gene regions were captured across flowering plant diversity.
  • Pooled samples were used in a single assay for increased efficiency.

Main Results:

  • The targeted capture approach achieved a 92% target gene recovery rate across all specimens.
  • The method demonstrated high efficiency and speed compared to standard barcoding.
  • 80% of samples were accurately discriminated to the family level using the generated database.

Conclusions:

  • Generating comprehensive reference sequences across multiple chloroplast gene regions is essential for robust plant identification.
  • No single genetic locus is sufficient for discriminating all plant groups.
  • The described targeted capture approach offers a viable strategy for advancing reference database creation.