Types and distributions of microsatellite DNA in the Cotton (Gossypium L.) genome

Production of Cotton (Gossypium L.), which is the most important natural raw material of the rapidly developing textile industry, needs to increase with the increase in the world population and should meet the various needs of people and create employment opportunities with its other by-products. Cotton is grown in approximately 80 countries in the world, including India, China and the USA. While cotton fibers are used as the main source for textiles, its seeds are used for its oil and its cake is used as protein-rich animal feed, so it is an important industrial plant in our country and in the world. Since organisms survive within the framework of their genomes, the structure and function of the genome attract human attention because the structure and functions of genomes are related. Nowadays, especially in the last 10-15 years, many genomes have been sequenced or resequenced with the help of Next Generation Sequencing (NGS) technologies. The cotton genome also benefited from these sequencings. The main objective of this study was to use the whole genome sequences of cultured tetraploid Upland cotton (Gossypium hirsutum L.) and Oriental (Asian) and Peruvian cottons, representatives of the two diploid cottons (G. arboreum L. and G. herbaceum L.) that are the ancestors of Upland cotton. This study was carried out to obtain information regarding the types and distribution of microsatellite (SSR) DNA in species genomes, chromosomes, 5' UTR, 3' UTR, Gene, Upstream, Downstream, Exon, Intron and Intergene sequences. Furthermore, microsatellite analysis of cellulose and cellulose synthase-like genes to obtain more information on the function of microsatellites, phylogenetic studies and protein coding of microsatellite DNA were studied. In the study, reference sequences constructed using whole genome sequences of G. hirsutum, which is an allotetraploid species and commonly called Upland cotton, G. arboreum, which is a diploid species and called Oriental (Asian/Tree) cotton, and G. raimondii, known as Peruvian cotton, were used. Whole genome sequences and files containing genome information were downloaded from the GenBank database in FASTA, GFF and GTF formats, and their microsatellite contents, genomic distributions and types of microsatellites were revealed using PERL-based GMATA and Linux-based software programs. Using GFF/GTF data, positional information of cellulose synthase genes was determined with the help of AWK, SED and GREP scripts. In this study, it was found that the microsatellite contents and repeat types of the genomes, sub-genomes and chromosomes of 3 cotton species were different among the species. It was determined that tri-, tetra-, penta- and hexa-nucleotides were higher in G. hirsutum, while di-nucleotide repeats were higher in G. arboreum and G. raimondii. It was concluded that G. arboreum had more microsatellites than G. raimondii among di nucleotides. Microsatellite numbers vary in each chromosome of the three species. Among species, the highest number of microsatellite values were found in Oriental cotton. When the genic and intergenic SSR frequencies of three cotton species were compared, Peruvian cotton was found to have the highest frequency in terms of genic SSR (SSRs within 5' UTR, 3' UTR, gene, upstream, downstream and exon), followed by Upland cotton and Oriental cotton. In terms of intergenic SSR, Oriental cotton had the highest frequency, followed by Peruvian cotton and Upland cotton. When the frequency and distribution of different SSR types in each cotton chromosome were examined, it was determined that the frequency of SSR loci was not related to chromosome size. It has been revealed that the SSR densities of the three cotton types are different. It was concluded that while genic-SSR and intergenic SSR were more in G. hirsutum, genic and intergenic SSR were less in G. raimondii. This study confirmed that microsatellites are important components of gene elements. In Oriental cotton (A genome) and Upland cotton (AD genome), tri-nucleotide repeats awere more common in coding regions; It was concluded that di-nucleotide repeats were higher in Peruvian cotton. The amino acids encoded by microsatellite sequences in three different reading frames were determined and the amino acid sequences they encoded were identified. It was determined that tri-nucleotide and penta nucleotides code for mono-peptide or di-peptide repeated amino acids, dinucleotide repeats code for di-peptide amino acids, while tetra- and penta-nucleotide repeats code for tetra-peptide amino acids. Cellulose and cellulose synthesis-like genes that synthesize cellulose, the most important polysaccharide of the living kingdom, were grouped as those containing microsatellites and those not containing microsatellites, and it was concluded that microsatellites with cellulose and cellulose synthesis-like genes existed, and they were effective in terms of the functions and phylogenetic positions of the microsatellites they contain. When the numbers of microsatellites in the donor diploid genomes were compared with the numbers in the tetraploid genome, it was determined that some microsatellites were probably lost during the evolution process, but some new microsatellites were formed. In this study, it was also found that by using NGS reference genome information, it is possible to identify all microsatellite types of any organism and compare genic and intergenic microsatellites within and between genomes. In this way, it has been confirmed in this thesis that functional microsatellite (SSR) markers specific to genes and gene regions can be obtained.