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.

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.