The study of ancient DNA (aDNA) is a rapidly evolving field within bioinformatics, offering valuable insights into the genetic diversity, migration, and evolution of past populations. Advances in high-throughput Sequencing technologies have enabled the retrieval of genomic-scale data from archaeological and historical specimens, including subfossil remains. Bioinformatics tools are essential for processing this data, addressing challenges posed by the degradation of aDNA and recovering useful genetic and even epigenetic information. Key bioinformatics applications include sequence alignment, phylogenetic analysis, and identifying genetic relationships between extinct and extant species. These studies have broad interdisciplinary implications in fields such as archaeology, anthropology, human genetics, ecology, and evolutionary biology. aDNA research has contributed to understanding ancient diets, domestication processes, and microbiomes, with samples extracted from sediments, ice cores, and other environmental sources. However, challenges remain: aDNA is often fragmented and chemically altered, and a high proportion of sequenced DNA belongs to non-target species. Effective separation and identification of target DNA rely on tools like BLAST, Bowtie2, and BWA, and on microbial databases, despite their limitations. Furthermore, the preservation conditions, such as temperature, significantly affect DNA survival. Fossils like those of mammoths or Aurochs offer valuable material for genetic studies, though phylogenetic isolation, as seen in saber-toothed cats, can hinder comparative analysis. Nevertheless, ongoing technological progress continues to refine the understanding of ancient genomes.

Background: Dermatophytes are a group of fungi that attack keratinous tissues of the skin, hair, and nail in humans and animals, and cause infections called dermatophytosis (tinea). Since identification of pathogenic fungi at the species level is essential for the detection of the source, control and prevention, and identifying epidemiology of infection, it is necessary to use specific and sensitive diagnostic methods to identify the causes of dermatophytosis. Methods: The clinical samples (skin, nail, and hair) of patients with dermatophytosis in Mashhad City, Iran, were cultured in Mycosyl Agar culture media, and the DNA of obtained dermatophyte colonies were extracted by specific kit. The internal transcribed spacer (ITS) gene was amplified and sequenced by ITS1, ITS4 primers. Finally, the Sequencing results were analyzed using SeqMan software, and were compared with the data of the global genebank. Findings: In this study, 80 dermatophyte isolates were sequenced, which included 9 dermatophyte species as 23 (28. 8%) Trichophyton (T. ) interdigital, 18 (22. 5%) T. tunsorans, 10 (12. 5%) Epidermophyton fluccosum, 10 (12. 5%) of T. mentagrophytes, 8 (10%) Microsporum canis, 4 (5%) T. rubrum, 4 (5%) T. benhamiae, 2 (2. 5%) Nannizzia (N. ) fulvum, 1 (1. 2%) N. persicolor. Conclusion: According to report the rare species of dermatophytes in this study, the use of molecular methods such as Sequencing of the ITS gene can determine the diversity of dermatophytes in a region more precisely than morphological methods.

One of the interdisciplinary approaches which recently had a key role in resolving of archaeological issues, especially domestication process, was Archaeogenetics. Caprines were domesticated in the early Neolithic period and their domestication was a major part of the process that led to the invention of agriculture. Since goat has had a key role in subsistence economy of human societies in different environments hence it became one of the main aims of archeogentics studies. By use of aDNA of goats and archaeogenetics approaches, this paper extracted and analyzed 10 samples of goat aDNA from Neolithic period of Kashan and Qazvin plains and determined their phylogenetic relations with modern domestic and wild goats to shed more light on the life of late Neolithic society of central plateau of Iran. Results show that these samples have closest genetic relations with haplogroup A of wild goats which now live in southeastern of Turkey. Hence archeogenetic evidences show that by 7500 B.P, Neolithic societies of Iran central plateau used goats which were domesticated about 10000 B.P in southeastern Turkey.

Background: Malaria is endemic in southeastern Iran including Jiroft district and in favorite epidemiological condition could threaten the people health. Anopheles fluviatilis complex is a malaria vector in Iran and consists of three species of S, T, and U and 7 genotypes of S, U, T1, T2, Y, X and V which are different in vectorial capacity. The aim of this study was to identify species composition of An.fluviatilis complex using D3 and ITS2 sequences in Jiroft district.Materials and Method: Mosquitoes of An. fluviatilis have been captured using total catch, pit shelter, and human/animal night baits. PCR amplification was done against the 28S D3 and ITS2-rDNA and the products were sequenced. The specimens were identified to species and genotype level using phylogenetic trees and comparison of sequences with entries available in GenBank.Results: Both ITS2 and D3 loci were successfully amplified and produced 514 bp and 376 bp bands respectively.Sequence analysis of ITS2 and D3 regions revealed that the specimens of Jiroft district were matching to the Y and T2 haplotypes of species T of the complex.Conclusion: Anopheles fluviatilis T is the only species in the region and based on the previous studies can be incriminated as the main malaria vector in the region.

DNA Sequencing is one of the most important techniques in biology which determine precise order of nucleotides within a DNA molecule. Old methods such as Sanger DNA Sequencing, are time laboring and expensive methods. Therefore, researchers developed next generation Sequencing (NGS) which are more economical and high-throughput methods comparing with old methods. NGS methods classified into three main generations. These methods are able to fast Sequencing of long fragments of DNA. By means of NGS, whole genome Sequencing, target specific Sequencing, de-novo Sequencing and assembly, RNA Sequencing and investigation of genetically changes are possible. it's so important to consider befits and defects of each method, and choosing a suitable NGS method due to properties of research program.

Extraction and analysis of DNA from ancient remains has numerous applications in archeology and molecular evolution. However, it has become obvious that ancient DNA (aDNA) can be easily contaminated with modern DNA, so it is crucial to detect contamination and to distinguish contaminant from authentic results. In the present study, we report the successful extraction and amplification of aDNA from 3000-3500 year-old human remains excavated from Masjede kabood (Tabriz, North-West of Iran) burial site. To test the authenticity of the extracted aDNA, we have developed a nested PCR/restriction enzyme digestion method for molecular sex determination of the skeletal remains, which their gender was known based on their morphology and belongings (Crown, Sword, Bracelet etc.). A simple and effective modified ethanol precipitation-based protocol was used for DNA extraction from 35 human skeletal remains. A segment of Homologous Amelogenin Gene (AMG), which has different alleles on X and Y-chromosomes, was amplified and analyzed. The obtained data were compared with anthropometric reports as a control for the rate of precision in aDNA analysis. The results showed that reliable aDNA can be extracted and amplified from archeological remains. The presented sex determination procedure could also be used as a reliable control for testing the authenticity of aDNA results