جستجوی مقالات مرتبط با کلیدواژه "توالی یابی کل ژنوم" در نشریات گروه "بیوتکنولوژی و ژنتیک گیاهی"

Iran is considered to be one of the oldest centers of domestication and breeding of livestock and poultry species in the world. Currently, different ecotypes of indigenous sheep are kept in different geographical regions of the country, which have obvious differences from each other in terms of appearance and production characteristics. So far, there has not been a comprehensive study on the whole genome level to identify the genetic diversity of native Iranian sheep. Therefore, the aim of this study is to identify the genomic characteristics of these native reserves in order to organize appropriate programs for their exploitation and protection

In this study, the whole genome sequences of 29 native Iranian sheep were downloaded from the NCBI database and analyzed. Whole genome sequencing of the studied data has been done by Hiseq2000 and Hiseq X Ten sequencer devices. Quality control of raw data sequences was done by FastQC program. To align the sequence data with the sheep reference genome (Oar v.4.0, https://www.ncbi.nlm.nih.gov/assembly/GCF_000298735.2), the BWA-MEM algorithm used in the BWA software package was used. Picard program was used to remove PCR duplicates from mapping outputs. The alignment outputs with the reference genome were processed in two stages, including re-alignment of deletions and small insertions and recalibration of the base quality score using the GATK program. The average coverage depth and alignment percentage for alignment output with the reference genome were calculated using depth and flagstat commands used in samtools software. Single nucleotide polymorphisms (SNPs) were identified by the UnifiedGenotyper tool used in the GATK program. Nucleotide diversity values and genomic inbreeding coefficient were calculated based on homozygous SNPs for each individual using the het command used in the VCFtools program.

The average coverage depth of the used data in this study was 18.39 X. The average percentage of alignment of short sequences with the sheep reference genome was 99.89%. The values of genomic inbreeding coefficient in Iranian native sheep breeds ranged from 0.01 to 0.12. The lowest value of genomic inbreeding coefficient was observed in the genome of Mughani sheep (0.01) and the highest value of inbreeding coefficient was observed in the genome of Afshari sheep. Also, the average values of observed and expected percentage of heterozygosity calculated for single nucleotide polymorphisms in the genome of Iranian native sheep ecotypes ranged from 20.67 to 23.06 and 32.415 to 32.421.

Due to adaptation to environmental conditions, different ecotypes of native goat can be seen in different geographical regions of the country, which are very diverse in terms of appearance and production characteristics. So far, no comprehensive study has been done at the whole genome level to identify the genetic diversity of native goats. Therefore, the aim of this study is to identify the genomic characteristics of these native reserves in order to organize appropriate programs for their exploitation and protection.

In this study, the whole genome sequence of 36 Iranian native goats were downloaded from the NCBI database and analyzed. Whole genome sequencing of the studied data was done by Illumina company and Hiseq2500 and Hiseq2000 sequencing machines. Quality control of raw sequence data was done by FastQC program. The BWA-MEM algorithm applied in the BWA software package was used to align the data sequence with the goat reference genome (ARS1, GCF_001704415.1). The alignment outputs with the reference genome were processed in two steps, including realignment around small deletions and insertions and base quality score recalibration using GATK program.The mean depth for the alignment output with the reference genome was calculated using the depth command applied in the samtools software. Single nucleotide polymorphisms (SNPs) were identified by the UnifiedGenotyper tool used in the GATK program. The values of nucleotide diversity and genomic inbreeding coefficient based on homozygous SNPs for each individual were calculated using the het command used in the VCFtools program.

The mean depth of the used data in this study was 11.25 X. The average number of single nucleotide polymorphisms in the 36 Iranian native goat genomes was 7495554. The genomic inbreeding coefficient values in different ecotypes of Iranian native goat varied from -0.01 to 0.4. The lowest genomic inbreeding coefficient value was observed in the Hamedan native goat genome (-0.01) and the highest genomic inbreeding coefficient value was observed in the Balochi goat ecotype genome of Sistan and Baluchistan. Also, the average of percentage observed and expected of heterozygosity values was calculated for single nucleotide polymorphisms in the o Iranian native goat ecotype genomes varied from 10.27 to 17.75 and from 17.33 to 17.57.

This research shows an important insight about the structural diversity of the Iranian native goat genomes, which have not been evaluated genetically so far. The results obtained from this research can be used in the design of conservation and breeding programs for Iranian native goats.

Pistachio is one of the most important crops that have a large genetic diversity due to its dicotyledonous and high heterozygosity, so identifying these genetic differences is of particular importance for breeding and production of psyllid-resistant pistachio cultivars. Pistachio psyllid is one of the most important pests of the pistachio tree. The nymphs and adult insects of this pest increase the amount of porosity, and reduce yield and lack of laughter, by consuming plant sap. In this study, single nucleotide polymorphisms (SNP) and small indels were investigated in Iranian pistachio sensitive cultivars (Akbari, Kalehghoochi, Ahmad Aghaei, Momtaz) and resistant cultivars (Badami Zarand, Haj Abdollahi, Italian, Sarakhs) to psyllids. The readings were first aligned with the reference genome, and then single-nucleotide polymorphisms and deletions, and small indels were identified by the GATK toolkit. The percentage of alignment of the readings with the reference genome was above 96%, which indicated the high quality of alignment. Sensitive cultivars had 2920688 and 701109 and resistant cultivars had 2919898 and 701000 SNP and small indels, respectively. In general, the results of data analysis showed that the structural and polymorphic diversity of mononucleotides and the small indels are greater in susceptible cultivars than in resistant cultivars.

Evaluation and conservation of native chickensas valuable genomic resources is essential.This is the first study for discovering variants in Lari chicken by whole genome sequencing data. The study of genetic diversity of Lari chicken at genomic level can provide useful information for its preservation and breeding. In this study, genomic diversity of five Lari individuals was investigated using whole genome sequencing technique.

Blood samples were taken from five Lari chickens from cites of Shiraz and Zabol, Iran. Whole genome sequencing (paired end sequencing) was done by Illumina Company) Hiseq 2500). Data quality was determined by FastQC program. Whole genome sequencing datawere aligned with chicken genome reference(Gallus_gallus-5.0/galGal5) using MEM algorithm applied in burrows wheeler aligner program (BWA). Processing of bam files was done in several steps. PCR duplicates were removed using Picard program. The Percentage of alignment with the reference genome and coverage or depth were calculated using the flagstat and depth commands in samtools software. Single nucleotide polymorphisms (SNPs) and small insertions and deletions (INDELs) were identified by the genomic analysis toolkit (GATK)program. Annotation of SNPs and Indels was done using SnpEff program. Genetic diversityof five chicken genomes was calculated with VCFtools.

The mean percentage mapping of short sequences with the reference genome was 99.85% and the mean coverage depth was 7.65 X. In this study, 9.8 million SNPs and 10 million Indels were identified with the most counts of them in the intron and intergenic regions. The mean ofobserved and expected heterozygosity percentages for SNPs in five chicken genomes were 0.30 and 0.35, respectively.

Results from annotation showed that percentage of silentSNPs (74.38%) is higher than that nonsynomous SNPs (missense and nonsense, 25.62%) in Lari chicken genome. The lower observed genetic diversity than the expected genetic diversity, can be due to the forces such as inbreeding in the population of Lari chicken

About half of the human genome is covered by repetitive sequences. These sequences have a large share in the other mammalian genomes, therefore studying this part of the genome can provide researchers valuable information on evolution. The aim of this study was to sequencing and assembly the whole genome of Iranian Bactrian camels to identify transposable elements and their distribution in the genome of this species. In addition, the results of Iranian Bactrian camels were compared with non-Iranian Bactrian camels and dromedary camels.

In this study, the whole genome of six Iranian Bactrian camels was sequenced to transposable elements identification. Iranian Bactrian camel whole genome sequenced using Illumina HiSeq 2000 system in paired-end. FastQC and Trimmomatic software were used to quality control and quality filtering of raw sequencing reads, respectively. CLC Genomics Workbench (CLC Bio, Aarhus, Denmark) was used to de novo assembly of trimmed reads. Also, we used the RepeatMasker program to search for transposable elements using a homology-based method.

Results of the assembling of sequenced genomes showed that the genome size in these samples ranged from 1.9 to 1.97 Gb. In the present study, the percentage of transposable elements for six Iranian Bactrian camels was 29.89% on average of the whole genome. The percentage of LINE sequences for the Iranian Bactrian camel was 17.58% on average. So, these sequences were considered as the largest group of transposable elements in the Bactrian camel in this study. SINE elements showed a lower number in comparison with LINEs. So that, only 3.45% of the total Bactria camel genome length was dedicated to the SINEs. In accordance with the results of Iranian dromedary camels, no Alu element was identified in the genome of Iranian Bactrian camels.

Shortage of genomic and biological information about camels is one of the inhibiting factors in advancing the breeding goals and programs. Although this study is not enough alone, it can be a step towards starting the production of genomic data for camels. Continuing this kind of study and integrating biological and genomic information will provide the ground for the start of modern breeding in Iranian camels.

 Evaluation and conservation of native chickens as future genomic resources are essential. In this study, genomic diversity of four Marandi breeds was investigated using whole genome sequencing technique.  

 Blood samples were taken from four chickens in East Azerbaijan province, Iran. Whole genome sequencing (paired end sequencing) was done by Illumina Company) Hiseq 2500). Data quality control was performed by FastQC program. Whole genome sequencing data were aligned with genome reference (Gallus_gallus-5.0/galGal5) using MEM algorithmimplemented in burrows wheeler aligner program (BWA). Single nucleotide polymorphisms (SNPs) and small insertions and deletions (INDELs) were identified by the GATK program. Annotation of SNPs and Indels was done using SnpEff program. Genetic diversity of 4 chicken genomes was calculated with VCFtools.   

The short sequences were compared with the reference genome of over 99% and with the mean depth of 7X coverage. In this study, 8.7 million SNPs and 9.1 Indels were identified with the most counts of them in the intron and intergenic regions. The mean of observed and expected heterozygosity percentages for SNPs in four chicken genomes were 0.33 and 0.35, respectively.  

Results from annotation showed that percentage of the silent SNPs (74.64%) is higher than that the nonsynomous SNPs (missense and nonsense) in Marandi chicken genome. The results obtained from this research can be useful for Marandichicken breeding and conservation programs.

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.