scholarly journals Novel nuclei isolation buffer for flow cytometric genome size estimation of Zingiberaceae: a comparison with common isolation buffers

2016 ◽  
Vol 118 (6) ◽  
pp. 1057-1070 ◽  
Author(s):  
Abhishek Sadhu ◽  
Sreetama Bhadra ◽  
Maumita Bandyopadhyay
Keyword(s):  
Genome Size ◽  
Size Estimation ◽  
Nuclei Isolation ◽  
Flow Cytometric ◽  
Isolation Buffer

scholarly journals Identification and Genetic Diversity Analysis of Edible and Medicinal Malva Species Using Flow Cytometry and ISSR Molecular Markers

Agronomy ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 650
Author(s):  
Iwona Jedrzejczyk ◽  
Monika Rewers
Keyword(s):  
Flow Cytometry ◽  
Molecular Markers ◽  
Genome Size ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Size Estimation ◽  
Flow Cytometric ◽  
First Choice ◽  
Issr Molecular Markers

The Malva genus contains species that reveal therapeutic properties and are mostly important in medicine and the functional food industry. Its breeding, cultivation, and utilization are based on proper germplasm/plant identification, which is difficult using morphological features. For this reason, we applied flow cytometry and inter simple sequence repeat polymerase chain reaction (ISSR-PCR) for fast and accurate species identification. Genome size estimation by flow cytometry was proposed as the first-choice method for quick accession screening. Out of the 12 tested accessions, it was possible to identify six genotypes based on genome size estimation, whereas all species and varieties were identified using ISSR markers. Flow cytometric analyses revealed that Malva species possessed very small (1.45–2.77 pg/2C), small (2.81–3.80 pg/2C), and intermediate (11.06 pg/2C) genomes, but the majority of accessions possessed very small genomes. Additionally, this is the first report on genome size assessment for eight of the accessions. The relationships between the investigated accessions showed the presence of two clusters representing malvoid and lavateroid group of species. Flow cytometry and ISSR molecular markers can be effectively used in the identification and genetic characterization of Malva species.

scholarly journals Optimized flow cytometric protocol and genome size estimation of Sabah snake grass (Clinacanthus nutans)

2021 ◽  
Vol 15 (12) ◽  
pp. 531-539
Author(s):  
Kandaiah Vidhyaini ◽  
Singaram Nallammai ◽  
Isparan Kandasamy Kodi
Keyword(s):  
Genome Size ◽  
Size Estimation ◽  
Flow Cytometric ◽  
Clinacanthus Nutans

scholarly journals Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 270 ◽  
Author(s):  
Yamkela Mgwatyu ◽  
Allison Anne Stander ◽  
Stephan Ferreira ◽  
Wesley Williams ◽  
Uljana Hesse
Keyword(s):  
Flow Cytometry ◽  
Genome Size ◽  
Internal Standard ◽  
Size Estimation ◽  
Sequencing Data ◽  
Aspalathus Linearis ◽  
Paired End Sequencing ◽  
Size Estimates ◽  
Genome Projects ◽  
Isolation Buffer

Plant genomes provide information on biosynthetic pathways involved in the production of industrially relevant compounds. Genome size estimates are essential for the initiation of genome projects. The genome size of rooibos (Aspalathus linearis species complex) was estimated using DAPI flow cytometry and k-mer analyses. For flow cytometry, a suitable nuclei isolation buffer, plant tissue and a transport medium for rooibos ecotype samples collected from distant locations were identified. When using radicles from commercial rooibos seedlings, Woody Plant Buffer and Vicia faba as an internal standard, the flow cytometry-estimated genome size of rooibos was 1.24 ± 0.01 Gbp. The estimates for eight wild rooibos growth types did not deviate significantly from this value. K-mer analysis was performed using Illumina paired-end sequencing data from one commercial rooibos genotype. For biocomputational estimation of the genome size, four k-mer analysis methods were investigated: A standard formula and three popular programs (BBNorm, GenomeScope, and FindGSE). GenomeScope estimates were strongly affected by parameter settings, specifically CovMax. When using the complete k-mer frequency histogram (up to 9 × 105), the programs did not deviate significantly, estimating an average rooibos genome size of 1.03 ± 0.04 Gbp. Differences between the flow cytometry and biocomputational estimates are discussed.

scholarly journals Flow cytometric analysis using SYBR Green I for genome size estimation in coffee

2011 ◽  
Vol 113 (2) ◽  
pp. 221-225 ◽  
Author(s):  
Wellington Ronildo Clarindo ◽  
Carlos Roberto Carvalho
Keyword(s):  
Genome Size ◽  
Flow Cytometric Analysis ◽  
Sybr Green ◽  
Sybr Green I ◽  
Size Estimation ◽  
Flow Cytometric

scholarly journals Leaves and Seeds as Materials for Flow Cytometric Estimation of the Genome Size of 11 Rosaceae Woody Species Containing DNA-Staining Inhibitors

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Iwona Jedrzejczyk ◽  
Elwira Sliwinska
Keyword(s):  
Genome Size ◽  
Dna Content ◽  
Nuclear Dna ◽  
Nuclear Dna Content ◽  
Woody Species ◽  
Size Estimation ◽  
Flow Cytometric ◽  
Cell Cytosol ◽  
High Concentrations ◽  
First Time

The presence of some secondary metabolites in the cell cytosol can cause a stoichiometric error in the flow cytometric estimation of nuclear DNA content. There is no fully reliable method to completely eliminate the effect of these compounds on nuclei fluorescence, and therefore using plant organs/parts free of staining inhibitors is recommended. Eleven species of Rosaceae with high concentrations of propidium-iodide-staining inhibitors were studied to check the possibility of using seeds instead of leaves for genome size estimation. Despite optimizing the concentration and composition of antioxidants in nuclei-isolation buffer for each species, the effect of cytosolic compounds present in the leaves could not be avoided entirely. None of the seeds of the studied species contained inhibitors, and they produced histograms of good quality. The genome size of the studied species ranged from 1.15 to 3.17 pg/2C; for 10 species the DNA content was estimated for the first time.

scholarly journals Genome Size Diversity in Rare, Endangered, and Protected Orchids in Poland

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 563
Author(s):  
Monika Rewers ◽  
Iwona Jedrzejczyk ◽  
Agnieszka Rewicz ◽  
Anna Jakubska-Busse
Keyword(s):  
Genome Size ◽  
Species Identification ◽  
Dna Content ◽  
Size Estimation ◽  
Orchid Species ◽  
Infraspecific Taxon ◽  
2C Dna Content ◽  
Plant Families ◽  
Liparis Loeselii ◽  
Identification And Characterization

Orchidaceae is one of the largest and the most widespread plant families with many species threatened with extinction. However, only about 1.5% of orchids’ genome sizes have been known so far. The aim of this study was to estimate the genome size of 15 species and one infraspecific taxon of endangered and protected orchids growing wild in Poland to assess their variability and develop additional criterion useful in orchid species identification and characterization. Flow cytometric genome size estimation revealed that investigated orchid species possessed intermediate, large, and very large genomes. The smallest 2C DNA content possessed Liparis loeselii (14.15 pg), while the largest Cypripedium calceolus (82.10 pg). It was confirmed that the genome size is characteristic to the subfamily. Additionally, for four species Epipactis albensis, Ophrys insectifera, Orchis mascula, Orchis militaris and one infraspecific taxon, Epipactis purpurata f. chlorophylla the 2C DNA content has been estimated for the first time. Genome size estimation by flow cytometry proved to be a useful auxiliary method for quick orchid species identification and characterization.

First estimates of genome size in ribbon worms (phylum Nemertea) using flow cytometry and Feulgen image analysis densitometry

2014 ◽  
Vol 92 (10) ◽  
pp. 847-851 ◽  
Author(s):  
Kelly L. Mulligan ◽  
Terra C. Hiebert ◽  
Nicholas W. Jeffery ◽  
T. Ryan Gregory
Keyword(s):  
Flow Cytometry ◽  
Image Analysis ◽  
Body Size ◽  
Genome Size ◽  
Positive Relationship ◽  
Nuclear Dna ◽  
Nuclear Dna Content ◽  
Size Estimation ◽  
Size Diversity ◽  
Size Estimates

Ribbon worms (phylum Nemertea) are among several animal groups that have been overlooked in past studies of genome-size diversity. Here, we report genome-size estimates for eight species of nemerteans, including representatives of the major lineages in the phylum. Genome sizes in these species ranged more than fivefold, and there was some indication of a positive relationship with body size. Somatic endopolyploidy also appears to be common in these animals. Importantly, this study demonstrates that both of the most common methods of genome-size estimation (flow cytometry and Feulgen image analysis densitometry) can be used to assess genome size in ribbon worms, thereby facilitating additional efforts to investigate patterns of variability in nuclear DNA content in this phylum.

Comparative genome size estimation of different life stages of grey mullet, Mugil cephalus Linnaeus, 1758 by flow cytometry

2021 ◽  
Author(s):  
Jani Angel J. Raymond ◽  
Mudagandur Shashi Shekhar ◽  
Vinaya Kumar Katneni ◽  
Ashok Kumar Jangham ◽  
Sudheesh Kommu Prabhudas ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Genome Size ◽  
Mugil Cephalus ◽  
Life Stages ◽  
Size Estimation ◽  
Grey Mullet ◽  
Comparative Genome
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