Determination of the chromosome number and genome size ofGarcinia mangostanaL. via cytogenetics, flow cytometry and k-mer analyses

Abstract

Mangosteen (Garcinia mangostana L.) is one of the most popular tropical fruit of SouthEast Asia. It has considerable economic potential for local and export markets. This paper describes a research work to determine the number of chromosomes and genome size of G. mangostana through chromosome counting, flow cytometry and k-mer analyses. Chromosome count analysis revealed that the chromosome number of G. mangostana varied from 74 to 110. The high number observed could be due to the occurrence of mutation and aneuploidy in G. mangostana. Using flow cytometry with Glycine max cv. Polanka (2C = 2.5 pg) used as standard, G. mangostana genome size was found to be 2C = 6.00 ± 0.17 pg. Meanwhile, a genome survey of G. mangostana was performed using Illumina HiSeq 2000 DNA sequencing; k-mer analysis revealed that the genome size of G. mangostana was approximately 5.92 Gbp, or approximately 6.05 pg (1 pg DNA = 0.9780 × 10 9 bp). Based on the flow cytometry and genome survey, the study concludes that the genome size of G. mangostana is between 6.00 and 6.05 pg.

Effects of Colchicine Treatments on Some Grape Rootstock and Grape Varieties at Cotyledon Stage

“…The numbers of chromosomes vary mainly in two ways. These are changes in euploid (in the chromosome set) and aneuploid (decrease or increase of some chromosomes in the genome) (Park et al, 1999(Park et al, , 2002(Park et al, , 2010Acanda et al, 2013;Maheshwari et al, 2015;Sattler et al, 2016;Lee et al, 2017;Midin et al, 2018).…”

Chromosome count improvement and digitalization of Neolamarckia cadamba

“…The presence of these particles is a major challenge when using ImageJ as a total automated procedure without human intervention to count the chromosomes in N. cadamba. Total automation in chromosome count is still far from perfect as errors and variation in chromosome number exist even within the same species [36,37].…”

“…Two chromosome count studies conducted, utilized computer software to count the chromosomes automatically on micrographs captured by an electronic camera [36,37]. This method uses an image thresholding technique to calibrate the micrograph to identify individual chromosomes, separate overlapped or clumped chromosome and sharpen the images.…”

“…This method uses an image thresholding technique to calibrate the micrograph to identify individual chromosomes, separate overlapped or clumped chromosome and sharpen the images. ImageJ software was used to automatically determine chromosome number yielding a range of different chromosome numbers of a species [37]. However, the mean number of chromosomes was used to determine the chromosome number of the species.…”

“…Automation in chromosome count requires optimization in slide preparation which is tedious, especially when plant material is to be examined such as N. cadamba. The success and accuracy of the automation techniques used would largely depend on the quality of sample preparation that should minimize the occurrence objects other than chromosomes [36,37].…”