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.

DNA sequencing is an approach exploited to determine the sequence of a DNA molecule. It includes any method or technology used to identify and determine the order of the four bases of adenine, guanine, cytosine, and thymine in a strand of DNA. DNA sequencing might be used to determine the sequence of individual genes, larger genetic regions, full chromosomes, or entire genomes. Traditional sequencing methods are mainly based on the original Sanger sequencing technique which makes them very expensive and low-throughput; thus, they do not meet the needs of researchers. Consequently, with the considerable advances in molecular biology and the high demand for low-cost sequencing has encouraged the development of high-throughput sequencing (or next-generation sequencing) technologies that parallelize the sequencing process, producing thousands or millions of sequences concurrently. Next-generation sequencing enable us to rapidly sequence a large piece of DNA which could span the whole genome with the latest instruments capable of producing gigabases of data in one isolated sequencing run. Next-generation sequencing platforms have a wide variety of applications, such as whole-genome sequencing, de novo sequencing, RNA sequencing (for applications such as transcriptomics and small RNA analysis), methylation analysis, and protein-nucleic acid interaction analysis.

Insertions and deletions (INDELs) are one of the main events contributing to genetic and phenotypic diversity, which have received less attention than SNPs and large structural variations. A total of 287.5 GB of data resulting from whole genome sequencing of six dog and wolf genomes with mean depth and coverage (percentage of mapping to genome reference) of 16X and 99.47, respectively, were analyzed to detect INDELs and assessment of their related functional groups, More than three million INDELs (1-73 bp) were detected. In this study, powerful algorithm (HaplotypeCaller) was used to increase precision and accuracy of detected INDELs. Most of the INDELs (95.179.9%) were smaller than 10bp. Results of INDELs annotation showed that the percentage of INDELs in exon and 3´ utr regions in dog genome was more than that in wolf genome, indicating that the domestication process has targeted the genomic variation in the exon and utr'3 regions.

Egg drop syndrome (EDS) is prevalent in industrial poultry globally. This disease is caused by Duck atadenovirus A or EDS virus (EDSV), a member of the genus Atadenovirus under the family Adenoviridae. The disease is attributed to significant economic losses in the poultry industry worldwide due to a drop in egg production, reduction in egg quality, and failure to reach maximum egg production. Oil‐adjuvant inactivated vaccines, which are widely used in the poultry industry, provide good protection for immunized chickens against EDS. This study aimed to genetically and phylogenetically analyze the full-length genome of an embryonated chicken egg-adapted EDSV strain 127. After extraction of viral DNA from the allantoic fluid, overlapping fragments of the viral genome sequence were generated by polymerase chain reaction (PCR) using 25 pairs of primers. Purified PCR products were subjected to complete genome sequencing by the next-generation sequencing (NGS) approach. The nucleotide homology observed between genomes of the studied strain and that of the original strain 127 (NC_001813) of laying chickens was 99.9%. Its genome was 33,213 bp in length, with a G + C content of 43.01%. A comparison of the genome sequence of the egg-adapted virus with strain 127 revealed only three non-synonymous single-nucleotide polymorphisms (SNPs) between these viral genome sequences. Two mutations of S320G and I62K out of these SNPs were found within the coding regions of fiber and hypothetical proteins which may play a role in the adaptation of EDSV in the embryonated chicken eggs. The full genome sequencing of EDSV using NGS techniques provides insights into the discovery of genetic variants. Moreover, the genome sequence information of the EDSV provides valuable data for vaccine development in near future.

essential, as well as, the first step for designing breeding programs in this species. In this regard, powerful tools such as next-generation sequencing technology have made it possible to decode the genome information in this species. Based on this research motive, the aim of the current study was to identify the genomic runs of homozygosity (ROH) and investigate related genes in dromedary camels using whole genome sequencing data. For this purpose, a total of 12 sequenced genomic data related to Iranian and non-Iranian dromedary camels were used. After bioinformatics analysis including quality assessment, data pre-preprocessing, alignment in the reference genome, and identification of variants, qualitative filter of variants, finally, ROH regions were identified. Based on the obtained results, 549 (137.3 regions per sample) and 1356 (169.5 regions per sample) ROH were identified in the genomes of Iranian dromedary camels and dromedaries from the Arabian Peninsula, respectively. The results of the annotation revealed that some important fertility-related genes such as FSHR and LHCGR are located in the ROH regions of Iranian dromedary camels. Also, investigation of gene ontology results revealed that some important genes including CXCL9, CXCL10 and CXCL11 (immune-related), STBD1 (related to energy metabolism), SCARB2 (related to lipid metabolism and fertility) and SHROOM3 (related to kidney function) are shared between Iranian and non-Iranian camels. Finally, as a summary, it seems that the controlling factor and the reason for the creation of ROHs in the genome of dromedary camels is natural selection to adapt to the desert environment.

Sex determination of sturgeons is one of the most appealing subjects towards both fisheries researchers and fish farmers. Molecular sex identification of these fishes using traditional methods have not had positive results, while due to the new advanced genome sequencing approaches known as NGS, it is now possible to detect and track the sexually divergent regions. Hence, based on the whole genome sequencing approach in two distinct studies, genomic regions harboring sex information in sturgeons were characterized and confirmed the ZZ/ZW sex-determination system in sturgeons. The presence of different sex-specific sequences in sturgeons indicates the presence of different sex-specific genomic regions for sturgeons. In the present paper, in addition to review the conducted studies on sturgeon’s sex identification, an applicable list of newly found genetic markers in sex determination of sturgeons are presented towards the beneficiaries and to improve the aquaculture industry of sturgeons. Furthermore, considering the high-quality results obtained by molecular tools in one hand and non-invasive feature of this method during sampling on the other hand, the usage of new universal markers namely AllWsex2 and SM4 is highly suggested as a novel technique in sturgeons’ sex determination in replace of traditional approaches such as ultrasonography and laparoscopy.

One of the most important approaches in animal breeding is identification of structural variations responsible for economical important traits. Next generation sequencing technologies are provided accurate tools for this purpose. In the present study, Fars province native poultry genome was analyzed using genome sequencing approach. Paired-end sequencing of the whole genome was conducted by Illumina Company in China. Data quality was determined by FastQC software. Short reads of sequences were mapped with the reference genome with the BWA program. Single nucleotide polymorphisms and small deletions and insertions were identified with the GATK program. The short sequences were compared with the reference genome of over 99% and with the mean depth of the X8 coverage. In this study, 8858153 single nucleotide polymorphisms and 895378 small deletions and insertions were identified with the lowest counts in the exon region. Since the results of identifying the variants showed that the most frequent variant is related to single nucleotide polynomials¡ in this study, heterozygous loci were higher than homozygous loci indicating the high diversity of the population under study. Given the history of several thousand years of chicken domestication in Iran, one can expect that adaptation to the environment has occurred in the population studied. As a result of genomic changes in order to adapt to the environment, it has created a diversity in the population.

Bactrian camels are known as one of the resistant species to harsh environmental conditions. The camel’s body temperature may vary from 34 to 41 °C throughout the day. They can survive if they lose body water greater than 25% of total body weight, while, in non-desert mammals, losses of greater than 15% are deadly. Since, Iran is located in one of the most arid regions of the world and water resources shortage, also special capabilities of camels, this species can be a valuable source of protein in the country. The study of genetic diversity is one of the most widely studies in domestic animals and microsatellites are widely used in this field. Microsatellite sequences contain useful information and are widely used to assess genetic diversity within and between populations, as well as to investigate the evolution process between species. The main aim of the present study was to identify the total microsatellites in the genome of Iranian Bactrian camels using whole genome sequencing data and compare them with other mammalians.

This study was carried out to identify genome wide microsatellites on six Bactrian camels from Ardabil province. Blood samples were collected from the jugular vein using 4 ml vacutainer tubes and stored at -20C˚ until use. Illumina HiSeq 2000 technology (Illumina, USA) was used for whole genome sequencing of samples. Sequencing was performed using the paired-end method with 100 bp at both ends of the reads. The quality control of raw sequence reads was performed using FastQC software. The SLIDINGWINDOW (4:20) algorithm of Trimmomatic v0.36 program was used to quality filter of raw reads. After filtration of reads with low quality, reads shorter than 40 bp were discarded. The de novo assembly of trimmed reads from Bactrian camels was done using CLC Genomics Workbench 11 software (CLC Bio, Aarhus, Denmark). The parameters used in this study for de novo assembly of trimmed reads were: 3 for mismatch cost, 3 for deletion and insertion cost, 0.5 for length fraction, and 0.8 for similarity fraction. Assembled genomes were searched for identifying the microsatellites using MISA with motif size ranging from mono-nucleotide to octo-nucleotide. The minimum repeat numbers were defined as 12 for mono-, 6 for di-, 5 for tri- and tetra, 4 for penta- and hexa-, and 3 for hepta- and octo-nucleotide repeat SSRs. Microsatellite motifs that interrupted by 100 nucleotides were considered as compound microsatellites. Also, several mammalians assembled genomes were downloaded and searched for microsatellite loci, including Arabian dromedary camel, Bactrian camel, alpaca, horse, cattle, sheep, and human.

The assembled genome size for the Bactrian camels were ranged from 1.90 for sample one to 1.97 for sample three. Also, the N50 length for the assembled contigs of Iranian Bactrian camels were ranged from 19.1 kb for sample one to 51.5 kb for sample five. The contig N50 length is one of the qualitative measurement parameters of genome assembly and a larger size means better assembly.The total microsatellites loci identified for Iranian Bactrian camels ranged from 136028 for sample two to 539555 for sample three. The results show that the genome of samples one, two, three, four, five and six contained 3.13 Mb, 2.35 Mb, 9.26 Mb, 7.1 Mb, 8.99 Mb and 8.86 Mb microsatellites, respectively. It should be noted that the difference in the microsatellites of SSRs in the Iranian Bactrian camel genomes is due to their different qualities in assembly. In mammals examined in this study, humans with 25.7 Mb and horses with 7.81 Mb had the highest and lowest total size of microsatellites, respectively. The results revealed that the number of microsatellites decreases with increasing in them, repeats, so that, one and two repeats sequences are the most frequent motifs. More than 74% of the identified microsatellites belong to the ten microsatellites with the highest number in all seven species. The motif T is the most frequent motif in the samples one and six Iranian Bactrian camels, Iranian dromedary camels, Bactrian camel, cattle, sheep, horses and humans. In samples two, three, four, five, the non-Iranian dromedary camel and alpaca motif A is the most abundant motif. The finding of this study will be applied as a valuable resource for further studies on camel breeding, especially on Iranian Bactrian camels. A large number of camel’s SSR markers developed in this study established a valuable resource for the investigation of genetic diversity and may improve the development of breeding programs in Iranian Bactrian camels in the future.

This is the first study for discovering genetic variants in Arian line by whole genome sequencing data. The study of Arian line features at genomic level can unravel the genetic background of economic traits such as growth. In this study, the information of three whole genomes of Arian chickens were used. The results of this study indicated that, there were 63866 common variants among samples. 17604 variants Out of 63866 variants were reported as novel variants in this study. Also 604 variants are located in coding regions, which 204 out of them lead to change in the amino acid sequence of the proteins. Considering the importance of dietary protein quality for growth and weight gain for poultry, the results of gene ontology analysis indicated that the pathways of protein catabolism and post-translational modification of proteins, related to growth are considerable. Also candidate genes such as, SMURF2 and SUMO1 was suggested for these biological pathways. Another interesting result of gene ontology was the significance of response to stress pathways. In the Arian line due to intense selection, the existence of stress is inevitable. Therefore, the significance of stress response can indicate the importance of these pathways in relation to the desired performance.