SlideShare a Scribd company logo
Short Tandem Repeats in plants: Genomic
distributionandfunctionprediction
Presented by: Rana Asif Abbas
Presented to: Dr Munir Ahmad
Course:PBG-514
Introduction
 Tandem repeats are short lengths of DNA that are repeated multiple times within a gene in
eukaryotic organisms.
 They are anywhere from a some to more than a hundred.
 There are three distributions of Tandem Repeats.
 Microsatellite DNA is with base pairs 1-10 is Usually termed STR
 Minisatellite DNA with base pair 10-100 base pair is 2nd distribution
 Longer satellite DNA is with greater then 100 base pairs.
 STRs have different motif types among distantly related species or even among closely
related species.
 STRs are mainly present within noncoding regions
 The STR motif types are affected by GC content with more GC-rich motifs being present
within higher GC content regions.
 Recent STR studies mainly focused on the regulation of human diseases and the 2nd thing
the gene expression .
 The studies focus on different STRs in plants but there is need to study differences among
STR among plants .
 By next-generation sequencing technologies it is possible to study genome wide STRs in
plant
Method for analysis of STR
Sources of genome and CDS sequence
 For this particular research Public literature and genome database used to
obtain the genomic information.
 The 140 plants complete data available and obtained easily from platforms
like (NCBI).
 Plants are divided in to 6 groups for study which are Algae, Ferns,
gymnosperms, Dicots, and Monocots.
STR detection and analysis:
 To detect STR scientist used MISA ( micro satellite identification tool) in
research which is one of best and for correlation analysis Spss 25.0 used.
 MISA help to identify perfect STRs as well as compounds. The MISA setting
for minimum number of repeats for mono-nucleotide is set at 12 while 6 for di-
nucleotide and 4 for tri-nucleotide
 Researchers also analyze the STR motifs and their corresponding
reverse complement Motifs( CAG & GTC).
 By help of well known custom pearl script results from MISA
translated and only nucleotides with A,T,G,C( valid nucleotides)
counted.
 Researchers also find the STR density and GC content in research.
Long STR analysis a function predicted
 The STR with length greater then 500 base pair can be extracted from CDS by
pearl script.
 Long STRs functional role can be studied by translating its sequence by NCBI
ORD(open reading frame).
 PSIPRED 4.0 used to predict the secondary structure of protein while BLASTP
used to investigate the role of long repeating sequences.
 The study used long STRs of Gossypium hirsotum (250bp) and Solanum
tuberosum(200bp)
STR distribution
 In the research 283,867,588 STRs were identified
from the 140 plant species, and their distribution
patterns were characterized in the six taxonomic
groups.
 The STR abundance is correlated with genome
size (GS)(fig 1 part A) and negatively correlated
with STR density(figure 1 part B).
 STR density ranges from 9.3 kb/Mb to 58 kb/Mb
in
 Among the nine gymnosperm species, the highest
STR density is only 19.4 kb/Mb and the average is
15.1 kb/Mb.
Distribution of STR types and motif preference
 The study shows that GC content of the STRs is highly correlated with the genomic
GC content. For example, the genomic GC content of algae ranges from 36.03% to
65.68% and the GC content of STRs ranges from 27.54% to 87.32%.
 By analyzation of top ten motif of each species it is concluded that with a higher GC
content usually has more GC-rich STR motif .
 Sorghum is exception as in Sorghum bicolor genome, despite the fact that most of its
motifs are GC-rich, the GC content of STRs is 40.02%.
 The STR motif distribution patterns of algae were diverse,
 The STR motif distribution patterns of dicots were mainly AT rich.
 Closely related species showed similar types of motifs, and motif preference in the
three mosses was similar to that of dicots.
Genomic patterns of STRs categorized
by motif size
 STRs with hexanucleotides were the most abundant
type in the six groups, ranging from 30% to 64%.
 The frequency of heptanucleotide repeats is second to
that of hexanucleotides except for algae with
trinucleotide repeats second to most.
 The least abundant type of repeat was decanucleotide
accounting for between 0.6% and 2% (Fig. 4)
Conclusion
 It has been concluded that if there is species with Large genome size it provides more
chances for the production of STRs but will have less STR density.
 If look comparatively monocot has higher STR density then dicot and Algae show wide
variation in relative abundance and density of STRs compared with flowering plants.
 STRs also have functional importance in regulating gene expression.
 STRs in eukaryotes are more common in noncoding regions..
 STRs are more likely to be produced in genomes with a high or low GC content .The GC
content of genomes affects the density of GC-rich repeats.
 GC content in Poaceae and some algae is higher than that in other species, possibly due to
gene structure, recombination patterns, and GC-biased gene conversion
 The present research focuses on STR identification and functions on a very broad scale
between plant groups. That help to understand genetics of plant groups but it lack the
comparison of STR impacts between species of same genus and within a species.
 These two studies are most close to breeder interest as he need to study species with in
genus in verity development or with in species.
 There is scope for further studies of STR in species with in genus and between verities of same
species. Example like between cotton and wheat and wheat and rice.
 STR help in DNA finger printing and help in criminological DNA identification and can also be
helpful in plant DNA ancestorial linkage finding and evolution.
Short Tandem Repeats in plants: Genomic distribution and function prediction

More Related Content

What's hot

Microsatellites- Molecular fingerprints
Microsatellites- Molecular fingerprints Microsatellites- Molecular fingerprints
Microsatellites- Molecular fingerprints
Sumana Choudhury
 
Snp
SnpSnp
Pharmacogenomics
PharmacogenomicsPharmacogenomics
Pharmacogenomics
ANAND SAGAR TIWARI
 
Location and mapping of chromosomes using conventional and cytological means.
Location and mapping of chromosomes using conventional and cytological means.Location and mapping of chromosomes using conventional and cytological means.
Location and mapping of chromosomes using conventional and cytological means.
Noor e Mujjassim
 
Gene mapping
Gene mappingGene mapping
Gene mapping
Anurag Raghuvanshi
 
Single nucleotide polymorphism, (SNP)
Single nucleotide polymorphism, (SNP)Single nucleotide polymorphism, (SNP)
Single nucleotide polymorphism, (SNP)
KAUSHAL SAHU
 
Use of SNP-HapMaps in plant breeding
Use of SNP-HapMaps in plant breeding Use of SNP-HapMaps in plant breeding
Use of SNP-HapMaps in plant breeding
Anilkumar C
 
Romero.3C
Romero.3CRomero.3C
Romero.3C
Alicia Romero
 
Gene mapping ppt
Gene mapping pptGene mapping ppt
Gene mapping ppt
prashant tripathi
 
Codon p referance and factor influences it
Codon p referance and factor influences itCodon p referance and factor influences it
Codon p referance and factor influences it
Ahmed Madni
 
Gene mapping
Gene mappingGene mapping
Gene mapping
Laura Melissa Ordonez
 
Gene mapping
Gene mappingGene mapping
Seminar presentation on snp (mulualem & janvier)
Seminar presentation on snp (mulualem & janvier)Seminar presentation on snp (mulualem & janvier)
Seminar presentation on snp (mulualem & janvier)
Mulualem Teshome
 
Single nucleotide polymorphism (sn ps)
Single nucleotide polymorphism (sn ps)Single nucleotide polymorphism (sn ps)
Single nucleotide polymorphism (sn ps)
Bahauddin Zakariya University lahore
 
Genome mapping
Genome mappingGenome mapping
Genome mapping
purvi gosrani
 
Snp and its role in diseases
Snp and its role in diseasesSnp and its role in diseases
Snp and its role in diseases
Ashfaq Ahmad
 
Comparative genomics
Comparative genomicsComparative genomics
Comparative genomics
Athira RG
 
Gene mapping tools
Gene mapping toolsGene mapping tools
Gene mapping tools
Usman Arshad
 
Concept of genome mapping
Concept of genome mappingConcept of genome mapping
Concept of genome mapping
Tenzin t
 
Single nucleotide polymorphism
Single nucleotide polymorphismSingle nucleotide polymorphism
Single nucleotide polymorphism
Bipul Das
 

What's hot (20)

Microsatellites- Molecular fingerprints
Microsatellites- Molecular fingerprints Microsatellites- Molecular fingerprints
Microsatellites- Molecular fingerprints
 
Snp
SnpSnp
Snp
 
Pharmacogenomics
PharmacogenomicsPharmacogenomics
Pharmacogenomics
 
Location and mapping of chromosomes using conventional and cytological means.
Location and mapping of chromosomes using conventional and cytological means.Location and mapping of chromosomes using conventional and cytological means.
Location and mapping of chromosomes using conventional and cytological means.
 
Gene mapping
Gene mappingGene mapping
Gene mapping
 
Single nucleotide polymorphism, (SNP)
Single nucleotide polymorphism, (SNP)Single nucleotide polymorphism, (SNP)
Single nucleotide polymorphism, (SNP)
 
Use of SNP-HapMaps in plant breeding
Use of SNP-HapMaps in plant breeding Use of SNP-HapMaps in plant breeding
Use of SNP-HapMaps in plant breeding
 
Romero.3C
Romero.3CRomero.3C
Romero.3C
 
Gene mapping ppt
Gene mapping pptGene mapping ppt
Gene mapping ppt
 
Codon p referance and factor influences it
Codon p referance and factor influences itCodon p referance and factor influences it
Codon p referance and factor influences it
 
Gene mapping
Gene mappingGene mapping
Gene mapping
 
Gene mapping
Gene mappingGene mapping
Gene mapping
 
Seminar presentation on snp (mulualem & janvier)
Seminar presentation on snp (mulualem & janvier)Seminar presentation on snp (mulualem & janvier)
Seminar presentation on snp (mulualem & janvier)
 
Single nucleotide polymorphism (sn ps)
Single nucleotide polymorphism (sn ps)Single nucleotide polymorphism (sn ps)
Single nucleotide polymorphism (sn ps)
 
Genome mapping
Genome mappingGenome mapping
Genome mapping
 
Snp and its role in diseases
Snp and its role in diseasesSnp and its role in diseases
Snp and its role in diseases
 
Comparative genomics
Comparative genomicsComparative genomics
Comparative genomics
 
Gene mapping tools
Gene mapping toolsGene mapping tools
Gene mapping tools
 
Concept of genome mapping
Concept of genome mappingConcept of genome mapping
Concept of genome mapping
 
Single nucleotide polymorphism
Single nucleotide polymorphismSingle nucleotide polymorphism
Single nucleotide polymorphism
 

Similar to Short Tandem Repeats in plants: Genomic distribution and function prediction

Genome project.pdf
Genome project.pdfGenome project.pdf
Genome project.pdf
ManchikantiDivya
 
Presentation1..gymno..non specific markers n microsatellites..by Nikita Patha...
Presentation1..gymno..non specific markers n microsatellites..by Nikita Patha...Presentation1..gymno..non specific markers n microsatellites..by Nikita Patha...
Presentation1..gymno..non specific markers n microsatellites..by Nikita Patha...
NIKITAPATHANIA
 
Shahbaz Str
Shahbaz StrShahbaz Str
Shahbaz Str
Zahoor Ahmed
 
Shahbaz Str
Shahbaz StrShahbaz Str
Shahbaz Str
Zahoor Ahmed
 
Genomics
GenomicsGenomics
Genomics
Ashfaq Ahmad
 
cytogenomics tools and techniques and chromosome sorting.pptx
cytogenomics tools and techniques and chromosome sorting.pptxcytogenomics tools and techniques and chromosome sorting.pptx
cytogenomics tools and techniques and chromosome sorting.pptx
PABOLU TEJASREE
 
Plant genome project
Plant genome projectPlant genome project
Plant genome project
ANANDALEKSHMIL
 
20150115_JQO_NYAPopulationGenomics
20150115_JQO_NYAPopulationGenomics20150115_JQO_NYAPopulationGenomics
20150115_JQO_NYAPopulationGenomics
Javier Quílez Oliete
 
Plant genomics general overview
Plant genomics general overviewPlant genomics general overview
Plant genomics general overview
KAUSHAL SAHU
 
Transcriptomics and metabolomics
Transcriptomics and metabolomicsTranscriptomics and metabolomics
Transcriptomics and metabolomics
Sukhjinder Singh
 
Karyotype analysis and evolution by Mannat
Karyotype analysis and evolution by MannatKaryotype analysis and evolution by Mannat
Karyotype analysis and evolution by Mannat
MannatAulakh
 
FINAL
FINALFINAL
FINAL
Ehab Zayed
 
Chapter 20 ppt
Chapter 20 pptChapter 20 ppt
Chapter 20 ppt
rehman2009
 
Molecular systematics.pdf
Molecular systematics.pdfMolecular systematics.pdf
Molecular systematics.pdf
Aartisoni17
 
Development of SSR markers in mungbean
Development of SSR markers in mungbeanDevelopment of SSR markers in mungbean
Development of SSR markers in mungbean
Nidhi Singh
 
Bioinformatica 24-11-2011-t6-phylogenetics
Bioinformatica 24-11-2011-t6-phylogeneticsBioinformatica 24-11-2011-t6-phylogenetics
Bioinformatica 24-11-2011-t6-phylogenetics
Prof. Wim Van Criekinge
 
Gutell 120.plos_one_2012_7_e38320_supplemental_data
Gutell 120.plos_one_2012_7_e38320_supplemental_dataGutell 120.plos_one_2012_7_e38320_supplemental_data
Gutell 120.plos_one_2012_7_e38320_supplemental_data
Robin Gutell
 
Tools of Genomics
Tools of GenomicsTools of Genomics
Tools of Genomics
Meghaj Mallick
 
DNA Sequencing in Phylogeny
DNA Sequencing in PhylogenyDNA Sequencing in Phylogeny
DNA Sequencing in Phylogeny
Bikash1489
 
Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in ...
Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in ...Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in ...
Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in ...
Banoth Madhu
 

Similar to Short Tandem Repeats in plants: Genomic distribution and function prediction (20)

Genome project.pdf
Genome project.pdfGenome project.pdf
Genome project.pdf
 
Presentation1..gymno..non specific markers n microsatellites..by Nikita Patha...
Presentation1..gymno..non specific markers n microsatellites..by Nikita Patha...Presentation1..gymno..non specific markers n microsatellites..by Nikita Patha...
Presentation1..gymno..non specific markers n microsatellites..by Nikita Patha...
 
Shahbaz Str
Shahbaz StrShahbaz Str
Shahbaz Str
 
Shahbaz Str
Shahbaz StrShahbaz Str
Shahbaz Str
 
Genomics
GenomicsGenomics
Genomics
 
cytogenomics tools and techniques and chromosome sorting.pptx
cytogenomics tools and techniques and chromosome sorting.pptxcytogenomics tools and techniques and chromosome sorting.pptx
cytogenomics tools and techniques and chromosome sorting.pptx
 
Plant genome project
Plant genome projectPlant genome project
Plant genome project
 
20150115_JQO_NYAPopulationGenomics
20150115_JQO_NYAPopulationGenomics20150115_JQO_NYAPopulationGenomics
20150115_JQO_NYAPopulationGenomics
 
Plant genomics general overview
Plant genomics general overviewPlant genomics general overview
Plant genomics general overview
 
Transcriptomics and metabolomics
Transcriptomics and metabolomicsTranscriptomics and metabolomics
Transcriptomics and metabolomics
 
Karyotype analysis and evolution by Mannat
Karyotype analysis and evolution by MannatKaryotype analysis and evolution by Mannat
Karyotype analysis and evolution by Mannat
 
FINAL
FINALFINAL
FINAL
 
Chapter 20 ppt
Chapter 20 pptChapter 20 ppt
Chapter 20 ppt
 
Molecular systematics.pdf
Molecular systematics.pdfMolecular systematics.pdf
Molecular systematics.pdf
 
Development of SSR markers in mungbean
Development of SSR markers in mungbeanDevelopment of SSR markers in mungbean
Development of SSR markers in mungbean
 
Bioinformatica 24-11-2011-t6-phylogenetics
Bioinformatica 24-11-2011-t6-phylogeneticsBioinformatica 24-11-2011-t6-phylogenetics
Bioinformatica 24-11-2011-t6-phylogenetics
 
Gutell 120.plos_one_2012_7_e38320_supplemental_data
Gutell 120.plos_one_2012_7_e38320_supplemental_dataGutell 120.plos_one_2012_7_e38320_supplemental_data
Gutell 120.plos_one_2012_7_e38320_supplemental_data
 
Tools of Genomics
Tools of GenomicsTools of Genomics
Tools of Genomics
 
DNA Sequencing in Phylogeny
DNA Sequencing in PhylogenyDNA Sequencing in Phylogeny
DNA Sequencing in Phylogeny
 
Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in ...
Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in ...Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in ...
Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in ...
 

More from Rana Asif Abbas

Experimental design
Experimental designExperimental design
Experimental design
Rana Asif Abbas
 
Modern Techniques For Yield Enhancement
Modern Techniques For Yield EnhancementModern Techniques For Yield Enhancement
Modern Techniques For Yield Enhancement
Rana Asif Abbas
 
Breeding Methods for better quality fiber in Jute
Breeding Methods for better quality fiber in JuteBreeding Methods for better quality fiber in Jute
Breeding Methods for better quality fiber in Jute
Rana Asif Abbas
 
OAT “The future Fodder Crop
OAT “The future Fodder CropOAT “The future Fodder Crop
OAT “The future Fodder Crop
Rana Asif Abbas
 
QTL mapping current status and future prospects
QTL mapping current status and future prospectsQTL mapping current status and future prospects
QTL mapping current status and future prospects
Rana Asif Abbas
 
Germplasm Collection activities
Germplasm Collection activitiesGermplasm Collection activities
Germplasm Collection activities
Rana Asif Abbas
 

More from Rana Asif Abbas (6)

Experimental design
Experimental designExperimental design
Experimental design
 
Modern Techniques For Yield Enhancement
Modern Techniques For Yield EnhancementModern Techniques For Yield Enhancement
Modern Techniques For Yield Enhancement
 
Breeding Methods for better quality fiber in Jute
Breeding Methods for better quality fiber in JuteBreeding Methods for better quality fiber in Jute
Breeding Methods for better quality fiber in Jute
 
OAT “The future Fodder Crop
OAT “The future Fodder CropOAT “The future Fodder Crop
OAT “The future Fodder Crop
 
QTL mapping current status and future prospects
QTL mapping current status and future prospectsQTL mapping current status and future prospects
QTL mapping current status and future prospects
 
Germplasm Collection activities
Germplasm Collection activitiesGermplasm Collection activities
Germplasm Collection activities
 

Recently uploaded

How to Manage Your Lost Opportunities in Odoo 17 CRM
How to Manage Your Lost Opportunities in Odoo 17 CRMHow to Manage Your Lost Opportunities in Odoo 17 CRM
How to Manage Your Lost Opportunities in Odoo 17 CRM
Celine George
 
BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...
BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...
BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...
Nguyen Thanh Tu Collection
 
Cognitive Development Adolescence Psychology
Cognitive Development Adolescence PsychologyCognitive Development Adolescence Psychology
Cognitive Development Adolescence Psychology
paigestewart1632
 
Your Skill Boost Masterclass: Strategies for Effective Upskilling
Your Skill Boost Masterclass: Strategies for Effective UpskillingYour Skill Boost Masterclass: Strategies for Effective Upskilling
Your Skill Boost Masterclass: Strategies for Effective Upskilling
Excellence Foundation for South Sudan
 
Natural birth techniques - Mrs.Akanksha Trivedi Rama University
Natural birth techniques - Mrs.Akanksha Trivedi Rama UniversityNatural birth techniques - Mrs.Akanksha Trivedi Rama University
Natural birth techniques - Mrs.Akanksha Trivedi Rama University
Akanksha trivedi rama nursing college kanpur.
 
How to Build a Module in Odoo 17 Using the Scaffold Method
How to Build a Module in Odoo 17 Using the Scaffold MethodHow to Build a Module in Odoo 17 Using the Scaffold Method
How to Build a Module in Odoo 17 Using the Scaffold Method
Celine George
 
RPMS TEMPLATE FOR SCHOOL YEAR 2023-2024 FOR TEACHER 1 TO TEACHER 3
RPMS TEMPLATE FOR SCHOOL YEAR 2023-2024 FOR TEACHER 1 TO TEACHER 3RPMS TEMPLATE FOR SCHOOL YEAR 2023-2024 FOR TEACHER 1 TO TEACHER 3
RPMS TEMPLATE FOR SCHOOL YEAR 2023-2024 FOR TEACHER 1 TO TEACHER 3
IreneSebastianRueco1
 
PCOS corelations and management through Ayurveda.
PCOS corelations and management through Ayurveda.PCOS corelations and management through Ayurveda.
PCOS corelations and management through Ayurveda.
Dr. Shivangi Singh Parihar
 
Community pharmacy- Social and preventive pharmacy UNIT 5
Community pharmacy- Social and preventive pharmacy UNIT 5Community pharmacy- Social and preventive pharmacy UNIT 5
Community pharmacy- Social and preventive pharmacy UNIT 5
sayalidalavi006
 
Pengantar Penggunaan Flutter - Dart programming language1.pptx
Pengantar Penggunaan Flutter - Dart programming language1.pptxPengantar Penggunaan Flutter - Dart programming language1.pptx
Pengantar Penggunaan Flutter - Dart programming language1.pptx
Fajar Baskoro
 
LAND USE LAND COVER AND NDVI OF MIRZAPUR DISTRICT, UP
LAND USE LAND COVER AND NDVI OF MIRZAPUR DISTRICT, UPLAND USE LAND COVER AND NDVI OF MIRZAPUR DISTRICT, UP
LAND USE LAND COVER AND NDVI OF MIRZAPUR DISTRICT, UP
RAHUL
 
How to Add Chatter in the odoo 17 ERP Module
How to Add Chatter in the odoo 17 ERP ModuleHow to Add Chatter in the odoo 17 ERP Module
How to Add Chatter in the odoo 17 ERP Module
Celine George
 
Pride Month Slides 2024 David Douglas School District
Pride Month Slides 2024 David Douglas School DistrictPride Month Slides 2024 David Douglas School District
Pride Month Slides 2024 David Douglas School District
David Douglas School District
 
Walmart Business+ and Spark Good for Nonprofits.pdf
Walmart Business+ and Spark Good for Nonprofits.pdfWalmart Business+ and Spark Good for Nonprofits.pdf
Walmart Business+ and Spark Good for Nonprofits.pdf
TechSoup
 
BBR 2024 Summer Sessions Interview Training
BBR  2024 Summer Sessions Interview TrainingBBR  2024 Summer Sessions Interview Training
BBR 2024 Summer Sessions Interview Training
Katrina Pritchard
 
DRUGS AND ITS classification slide share
DRUGS AND ITS classification slide shareDRUGS AND ITS classification slide share
DRUGS AND ITS classification slide share
taiba qazi
 
The History of Stoke Newington Street Names
The History of Stoke Newington Street NamesThe History of Stoke Newington Street Names
The History of Stoke Newington Street Names
History of Stoke Newington
 
How to Fix the Import Error in the Odoo 17
How to Fix the Import Error in the Odoo 17How to Fix the Import Error in the Odoo 17
How to Fix the Import Error in the Odoo 17
Celine George
 
Life upper-Intermediate B2 Workbook for student
Life upper-Intermediate B2 Workbook for studentLife upper-Intermediate B2 Workbook for student
Life upper-Intermediate B2 Workbook for student
NgcHiNguyn25
 
Liberal Approach to the Study of Indian Politics.pdf
Liberal Approach to the Study of Indian Politics.pdfLiberal Approach to the Study of Indian Politics.pdf
Liberal Approach to the Study of Indian Politics.pdf
WaniBasim
 

Recently uploaded (20)

How to Manage Your Lost Opportunities in Odoo 17 CRM
How to Manage Your Lost Opportunities in Odoo 17 CRMHow to Manage Your Lost Opportunities in Odoo 17 CRM
How to Manage Your Lost Opportunities in Odoo 17 CRM
 
BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...
BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...
BÀI TẬP BỔ TRỢ TIẾNG ANH 8 CẢ NĂM - GLOBAL SUCCESS - NĂM HỌC 2023-2024 (CÓ FI...
 
Cognitive Development Adolescence Psychology
Cognitive Development Adolescence PsychologyCognitive Development Adolescence Psychology
Cognitive Development Adolescence Psychology
 
Your Skill Boost Masterclass: Strategies for Effective Upskilling
Your Skill Boost Masterclass: Strategies for Effective UpskillingYour Skill Boost Masterclass: Strategies for Effective Upskilling
Your Skill Boost Masterclass: Strategies for Effective Upskilling
 
Natural birth techniques - Mrs.Akanksha Trivedi Rama University
Natural birth techniques - Mrs.Akanksha Trivedi Rama UniversityNatural birth techniques - Mrs.Akanksha Trivedi Rama University
Natural birth techniques - Mrs.Akanksha Trivedi Rama University
 
How to Build a Module in Odoo 17 Using the Scaffold Method
How to Build a Module in Odoo 17 Using the Scaffold MethodHow to Build a Module in Odoo 17 Using the Scaffold Method
How to Build a Module in Odoo 17 Using the Scaffold Method
 
RPMS TEMPLATE FOR SCHOOL YEAR 2023-2024 FOR TEACHER 1 TO TEACHER 3
RPMS TEMPLATE FOR SCHOOL YEAR 2023-2024 FOR TEACHER 1 TO TEACHER 3RPMS TEMPLATE FOR SCHOOL YEAR 2023-2024 FOR TEACHER 1 TO TEACHER 3
RPMS TEMPLATE FOR SCHOOL YEAR 2023-2024 FOR TEACHER 1 TO TEACHER 3
 
PCOS corelations and management through Ayurveda.
PCOS corelations and management through Ayurveda.PCOS corelations and management through Ayurveda.
PCOS corelations and management through Ayurveda.
 
Community pharmacy- Social and preventive pharmacy UNIT 5
Community pharmacy- Social and preventive pharmacy UNIT 5Community pharmacy- Social and preventive pharmacy UNIT 5
Community pharmacy- Social and preventive pharmacy UNIT 5
 
Pengantar Penggunaan Flutter - Dart programming language1.pptx
Pengantar Penggunaan Flutter - Dart programming language1.pptxPengantar Penggunaan Flutter - Dart programming language1.pptx
Pengantar Penggunaan Flutter - Dart programming language1.pptx
 
LAND USE LAND COVER AND NDVI OF MIRZAPUR DISTRICT, UP
LAND USE LAND COVER AND NDVI OF MIRZAPUR DISTRICT, UPLAND USE LAND COVER AND NDVI OF MIRZAPUR DISTRICT, UP
LAND USE LAND COVER AND NDVI OF MIRZAPUR DISTRICT, UP
 
How to Add Chatter in the odoo 17 ERP Module
How to Add Chatter in the odoo 17 ERP ModuleHow to Add Chatter in the odoo 17 ERP Module
How to Add Chatter in the odoo 17 ERP Module
 
Pride Month Slides 2024 David Douglas School District
Pride Month Slides 2024 David Douglas School DistrictPride Month Slides 2024 David Douglas School District
Pride Month Slides 2024 David Douglas School District
 
Walmart Business+ and Spark Good for Nonprofits.pdf
Walmart Business+ and Spark Good for Nonprofits.pdfWalmart Business+ and Spark Good for Nonprofits.pdf
Walmart Business+ and Spark Good for Nonprofits.pdf
 
BBR 2024 Summer Sessions Interview Training
BBR  2024 Summer Sessions Interview TrainingBBR  2024 Summer Sessions Interview Training
BBR 2024 Summer Sessions Interview Training
 
DRUGS AND ITS classification slide share
DRUGS AND ITS classification slide shareDRUGS AND ITS classification slide share
DRUGS AND ITS classification slide share
 
The History of Stoke Newington Street Names
The History of Stoke Newington Street NamesThe History of Stoke Newington Street Names
The History of Stoke Newington Street Names
 
How to Fix the Import Error in the Odoo 17
How to Fix the Import Error in the Odoo 17How to Fix the Import Error in the Odoo 17
How to Fix the Import Error in the Odoo 17
 
Life upper-Intermediate B2 Workbook for student
Life upper-Intermediate B2 Workbook for studentLife upper-Intermediate B2 Workbook for student
Life upper-Intermediate B2 Workbook for student
 
Liberal Approach to the Study of Indian Politics.pdf
Liberal Approach to the Study of Indian Politics.pdfLiberal Approach to the Study of Indian Politics.pdf
Liberal Approach to the Study of Indian Politics.pdf
 

Short Tandem Repeats in plants: Genomic distribution and function prediction

  • 1. Short Tandem Repeats in plants: Genomic distributionandfunctionprediction Presented by: Rana Asif Abbas Presented to: Dr Munir Ahmad Course:PBG-514
  • 2. Introduction  Tandem repeats are short lengths of DNA that are repeated multiple times within a gene in eukaryotic organisms.  They are anywhere from a some to more than a hundred.  There are three distributions of Tandem Repeats.  Microsatellite DNA is with base pairs 1-10 is Usually termed STR  Minisatellite DNA with base pair 10-100 base pair is 2nd distribution  Longer satellite DNA is with greater then 100 base pairs.  STRs have different motif types among distantly related species or even among closely related species.  STRs are mainly present within noncoding regions  The STR motif types are affected by GC content with more GC-rich motifs being present within higher GC content regions.
  • 3.  Recent STR studies mainly focused on the regulation of human diseases and the 2nd thing the gene expression .  The studies focus on different STRs in plants but there is need to study differences among STR among plants .  By next-generation sequencing technologies it is possible to study genome wide STRs in plant
  • 4. Method for analysis of STR Sources of genome and CDS sequence  For this particular research Public literature and genome database used to obtain the genomic information.  The 140 plants complete data available and obtained easily from platforms like (NCBI).  Plants are divided in to 6 groups for study which are Algae, Ferns, gymnosperms, Dicots, and Monocots. STR detection and analysis:  To detect STR scientist used MISA ( micro satellite identification tool) in research which is one of best and for correlation analysis Spss 25.0 used.  MISA help to identify perfect STRs as well as compounds. The MISA setting for minimum number of repeats for mono-nucleotide is set at 12 while 6 for di- nucleotide and 4 for tri-nucleotide
  • 5.  Researchers also analyze the STR motifs and their corresponding reverse complement Motifs( CAG & GTC).  By help of well known custom pearl script results from MISA translated and only nucleotides with A,T,G,C( valid nucleotides) counted.  Researchers also find the STR density and GC content in research.
  • 6. Long STR analysis a function predicted  The STR with length greater then 500 base pair can be extracted from CDS by pearl script.  Long STRs functional role can be studied by translating its sequence by NCBI ORD(open reading frame).  PSIPRED 4.0 used to predict the secondary structure of protein while BLASTP used to investigate the role of long repeating sequences.  The study used long STRs of Gossypium hirsotum (250bp) and Solanum tuberosum(200bp)
  • 7. STR distribution  In the research 283,867,588 STRs were identified from the 140 plant species, and their distribution patterns were characterized in the six taxonomic groups.  The STR abundance is correlated with genome size (GS)(fig 1 part A) and negatively correlated with STR density(figure 1 part B).  STR density ranges from 9.3 kb/Mb to 58 kb/Mb in  Among the nine gymnosperm species, the highest STR density is only 19.4 kb/Mb and the average is 15.1 kb/Mb.
  • 8. Distribution of STR types and motif preference  The study shows that GC content of the STRs is highly correlated with the genomic GC content. For example, the genomic GC content of algae ranges from 36.03% to 65.68% and the GC content of STRs ranges from 27.54% to 87.32%.  By analyzation of top ten motif of each species it is concluded that with a higher GC content usually has more GC-rich STR motif .  Sorghum is exception as in Sorghum bicolor genome, despite the fact that most of its motifs are GC-rich, the GC content of STRs is 40.02%.  The STR motif distribution patterns of algae were diverse,  The STR motif distribution patterns of dicots were mainly AT rich.  Closely related species showed similar types of motifs, and motif preference in the three mosses was similar to that of dicots.
  • 9.
  • 10. Genomic patterns of STRs categorized by motif size  STRs with hexanucleotides were the most abundant type in the six groups, ranging from 30% to 64%.  The frequency of heptanucleotide repeats is second to that of hexanucleotides except for algae with trinucleotide repeats second to most.  The least abundant type of repeat was decanucleotide accounting for between 0.6% and 2% (Fig. 4)
  • 11. Conclusion  It has been concluded that if there is species with Large genome size it provides more chances for the production of STRs but will have less STR density.  If look comparatively monocot has higher STR density then dicot and Algae show wide variation in relative abundance and density of STRs compared with flowering plants.  STRs also have functional importance in regulating gene expression.  STRs in eukaryotes are more common in noncoding regions..  STRs are more likely to be produced in genomes with a high or low GC content .The GC content of genomes affects the density of GC-rich repeats.  GC content in Poaceae and some algae is higher than that in other species, possibly due to gene structure, recombination patterns, and GC-biased gene conversion
  • 12.  The present research focuses on STR identification and functions on a very broad scale between plant groups. That help to understand genetics of plant groups but it lack the comparison of STR impacts between species of same genus and within a species.  These two studies are most close to breeder interest as he need to study species with in genus in verity development or with in species.  There is scope for further studies of STR in species with in genus and between verities of same species. Example like between cotton and wheat and wheat and rice.  STR help in DNA finger printing and help in criminological DNA identification and can also be helpful in plant DNA ancestorial linkage finding and evolution.