Draft genome sequence and SSR mining data of Acacia pachyceras Schwartz

Genetic Diversity of Rhanterium eppaposum Oliv. Populations in Kuwait as Revealed by GBS

“…Previous reports on the use of de novo contigs as a reference for SNP discovery and genotyping on non-model species are available [ 23 , 24 , 26 ]. Genome survey sequencing has been employed previously for a native tree of Kuwait to filter microsatellite motifs [ 19 ]. However, transcriptomes have also been used as a reference for genotyping non-model species avoiding the need for de novo DNA assembly with the advantage of finding SNP sites near selected targets [ 27 ].…”

“…Analogous observations were recorded in Iranian wheat landraces [ 43 ] and wild accessions of H. salicornicum populations [ 15 ]. A highly repetitive genome was also recorded in Acacia pachyceras growing in Kuwait [ 19 ].…”

“…Technological advancement has brought about a paradigm shift in the way of assessing genetic diversity. The conventional morphological markers have been replaced by the use of first-generation molecular markers such as simple sequence repeats (SSRs), amplified fragment length polymorphism (AFLP) and randomly amplified polymorphic DNA (RAPDs) [ 18 , 19 , 20 ]. Due to a further reduction in the costs of next-generation technologies, the second generation of molecular markers based on single nucleotide polymorphisms (SNPs) have now become more common [ 21 ].…”

Comparison and optimization of DNA Isolation protocols for high throughput genomic studies of Acacia pachyceras Schwartz

“…Various molecular methods ranging from the traditional restriction enzyme-based or polymerase chain reaction (PCR) based molecular markers [4] , [5] , [6] to the most advanced next-generation sequencing (NGS) have become valuable tools in all aspects of conservation genetics [7] , [8] , [9] . Where traditional genome analysis relies on relatively small amounts of deoxyribonucleic acid (DNA) of moderate purity, on the other hand, NGS technologies require the input of several micrograms of high molecular weight DNA [10] . Therefore, the extraction of DNA in good qualities and quantities is of utmost importance in developing these studies [11] , [12] , [13] , [14] .…”

“…The species is extremely rich in polysaccharide and polyphenol content, which hampers good quality DNA isolation. The CTAB protocol in this study was used for NGS based genome survey analysis of A. pachyceras [10] . The data generated was mined for thousands of microsatellite motifs that will eventually be used for genetic diversity studies of this endangered species.…”