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Related Concept Videos

Flow Cytometry01:23

Flow Cytometry

The development of flow cytometry techniques began in 1934 with initial attempts by Andrew Moldavan, a bacteriologist who counted the cells in a flowing capillary system. Moldavan pumped cells through a capillary tube focused under a microscope for visualization. The invention of photometry allowed the measurement of differentially-stained cells, and Louis Kamentsky developed the first multiparameter flow cytometer in 1965 to identify and count the cancer cells in cervical tissue specimens.
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Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses.

Yamkela Mgwatyu1, Allison Anne Stander2, Stephan Ferreira3

  • 1South African National Bioinformatics Institute (SANBI), University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa.

Plants (Basel, Switzerland)
|February 23, 2020
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Summary

Accurate genome size estimation for rooibos (Aspalathus linearis) was achieved using DAPI flow cytometry and k-mer analyses. These genome size data are crucial for advancing rooibos genetic research and breeding programs.

Keywords:
Aspalathus linearisITS regionRooibosflow cytometrygenome sizek-mer analysis

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Area of Science:

  • Plant genomics
  • Bioinformatics
  • Flow cytometry

Background:

  • Plant genomes are vital for understanding biosynthetic pathways of valuable compounds.
  • Accurate genome size estimation is a prerequisite for initiating genome sequencing projects.
  • Rooibos (Aspalathus linearis) is an economically important plant with limited genomic data.

Purpose of the Study:

  • To estimate the genome size of rooibos (Aspalathus linearis) using two complementary methods.
  • To optimize protocols for DAPI flow cytometry of rooibos samples.
  • To evaluate different k-mer analysis tools for genome size estimation in rooibos.

Main Methods:

  • DAPI flow cytometry was performed using radicles from commercial rooibos seedlings and Vicia faba as an internal standard.
  • K-mer analysis was conducted on Illumina paired-end sequencing data from a commercial rooibos genotype.
  • Four k-mer analysis methods (standard formula, BBNorm, GenomeScope, FindGSE) were investigated.

Main Results:

  • Flow cytometry estimated the rooibos genome size at 1.24 ± 0.01 Gbp, consistent across different ecotypes.
  • K-mer analyses, particularly using complete k-mer frequency histograms, estimated the genome size at 1.03 ± 0.04 Gbp.
  • GenomeScope estimates were sensitive to parameter settings (CovMax), while other k-mer methods showed less deviation.

Conclusions:

  • Both flow cytometry and k-mer analyses provide reliable genome size estimates for rooibos.
  • Optimized protocols facilitate accurate genome size determination for rooibos and related species.
  • The established genome size data will support future genomic research and breeding efforts in rooibos.