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13:03
Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
Published on: March 8, 2018
Reference-free comparative genomics of 174 chloroplasts.
Chai-Shian Kua1, Jue Ruan, John Harting
1Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan, People's Republic of China.
Plos One
|November 28, 2012
Summary
Analyzing short DNA sequences (kmers) from 174 chloroplast genomes reveals conserved duplication patterns and accelerated evolution in parasitic plants. This method enables comparative genomics without a reference genome.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Comparative genomics traditionally requires complete reference genomes.
- Short read DNA sequencing offers vast data but poses analytical challenges for unassembled genomes.
- Chloroplast genomes exhibit significant size variation and structural differences across plant lineages.
Purpose of the Study:
- To develop a method for direct analysis of unassembled genomic data for comparative genomics.
- To investigate the taxonomic distribution and conservation of short kmers across diverse chloroplast genomes.
- To identify patterns of sequence duplication and evolutionary rates in major plant groups.
Main Methods:
- Analysis of short kmer distribution across 174 chloroplast genomes.
- De novo assembly of contigs centered on informative sequence variation.
- Comparison of duplicated sequence content (inverted repeat regions) and novel sequence across plant clades.
Main Results:
- Approximately 18% of chloroplast DNA was duplicated in the inverted repeat region across a wide range of genome sizes.
- This duplication ratio was conserved across green plants, independent of photosynthesis or genome size change mechanisms.
- Parasitic plants showed accelerated evolution, with hemi-parasitic genomes containing more novel sequence than holo-parasitic ones.
- Legumes exhibited rapid and distinct divergence patterns.
- Small duplicated fragments of rrn23 genes were conserved in seed plants, suggesting a functional role.
Conclusions:
- Direct kmer analysis of unassembled genomic data is a powerful approach for comparative genomics.
- Localized de novo assembly of informative kmers simplifies complex comparative analyses.
- The study reveals conserved and lineage-specific patterns of chloroplast genome evolution, particularly in parasitic plants and legumes.
- The findings facilitate the analysis of previously unstudied genomes and accelerate the discovery of informative genomic regions.
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