Coconut genome size determined by flow cytometry: Tall versus Dwarf types

Abstract

ABSTRACT. Coconuts (Cocos nucifera L.) are tropical palm trees that are classified into Tall and Dwarf types based on height, and both types are diploid (2n = 2x = 32 chromosomes). The reproduction mode is autogamous for Dwarf types and allogamous for Tall types. One hypothesis for the origin of the Dwarf coconut suggests that it is a Tall variant that resulted from either mutation or inbreeding, and differences in genome size between the two types would support this hypothesis. In this study, we estimated the genome sizes of 14 coconut accessions (eight Tall and six Dwarf types) using flow cytometry. Nuclei were extracted from leaf discs and stained with propidium iodide, and Pisum sativum (2C = 9.07 pg DNA) was used as an internal standard. Histograms with good resolution and low coefficients of variation (2.5 to 3.2%) were obtained. The 2C DNA content ranged from 5.72 to 5.48 pg for Tall accessions and from 5.58 to 5.52 pg for Dwarf accessions. The mean genome sizes for Tall and Dwarf specimens were 5.59 and 5.55 pg, respectively. Among all accessions, Rennel Island Tall had the highest mean DNA content (5.72 pg), whereas West African Tall had the lowest (5.48 pg). The mean coconut genome size (2C = 5.57 pg, corresponding to 2723.73 Mbp/haploid set) was classified as small. Only small differences in genome size existed among the coconut accessions, suggesting that the Dwarf type did not evolve from the Tall type.

De Novo Genome Sequence Assembly of Dwarf Coconut (Cocos nucifera L. ‘Catigan Green Dwarf’) Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species

“…The calculated ‘CATD’ genome size, however, is lower than the estimated genome size (2.42 Gbp) of the recently sequenced ‘Hainan Tall’ (HAT) coconut variety (Xiao et al 2017) by 280 Mbp. Freitas Neto et al (2016) reported that the genome size variation using flow cytometry method among 14 coconut ‘Tall’ and ‘Dwarf’ varieties is statistically small, and concluded that ‘Dwarf’ types did not really evolve from ‘Tall’ types as previously hypothesized (Perera et al 2016). We suggest otherwise, since there is a large difference between the genome sizes based on k-mer peak analysis between ‘Hainan Tall’ (Xiao et al 2017) and ‘Catigan Green Dwarf’ (this paper) whole genome sequence data.…”

Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance

“…This difference appears to reflect differences in assembling strategies rather than biological differences between CATD and HAIT. In fact, flow cytometry reveals intraspecific variation but to a much lesser extent and tends to yield larger values than does Kmer analysis (around C = 2.9 Gbp 28 or C = 2.7 Gbp 29 ). The CATD assembly also identified 25% more genes, resulting partially from a larger proportion of duplicated genes but also from a larger number of unique genes, especially among the smaller genes (Supplementary Fig.…”

Genome Size: A Novel Predictor of Nut Weight and Nut Size of Walnut Trees

“…are explained in detail by Greilhuber et al (2005). Furthermore, analytical tools such as flow cytometry are a reliable and convenient method to estimate genome size of plant communities such as ornamental plants (Abedi et al, 2015), medicinal plants (Javadian et al, 2017;Mahdavi and Karimzadeh, 2010;Majdi et al, 2010;Sadat Noori et al, 2017;Tarkesh Esfahani et al, 2016;Tavan et al, 2015) and fruit trees such as peach (Baird et al, 1994), olive (Brito et al, 2008;Loureiro et al, 2007b), coconut (Freitas et al, 2015), and Malus species (Hofer and Meister, 2010;Korban et al, 2009;Podwyszy nska et al, 2016). Unlike other fruit trees and plant species, there has been no study on the genome size of different walnut genotypes and cultivars, only flow cytometry is used to determine the ploidy level of walnut samples in in vitro conditions with the aim of identifying haploid plants (Sadat Hosseini Grouh et al, 2011).…”