The document discusses various aspects of bioinformatics in biotechnology, focusing on applications for crop improvement, genome annotation, and comparative genomics. It highlights key databases and tools for sequence analysis, mutation identification, and the role of genome duplication in evolution. Additionally, resources for accessing plant genome data and pathway information are provided.

1. AMBUJ SHAHI
MSc. Biotechnology
4th Semester
DEPARTMENT OF
BIOTECHNOLOGY
DDU GORAKHPUR UNIVERSITY

2. 1. Bioinformatics
2. Applications for crop improvement
3. Plant genome databases
4. NGS based analysis
5. Mutation identification
6. Genome annotation
7. Sequence identity
8. Synteny analysis
9. Comparative genomics
10.Gene pathways databases
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3. 2

4. 3

5. Database contains biological information like nucleic acid and amino sequences.
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The Arabidopsis Information Resource

6. Chart representing the sequenced plant
genomes contains plant species(year wise)
known to have publicly available complete
genome sequences that have been assembled,
annotated and published.
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Source: List of sequenced plant genomes -
Wikipedia
No.
of
plant
genomes
sequenced
Year

7. 6
https://www.1010genome.com/whole-genome-sequencing/

8. 7
To accelerate the mutation
mapping for crop
improvement, several
high-throughput and
novel NGS based forward
genetic approaches are
available.

9. Genome annotation is an in silico approach which
predicts the functional and structural elements within
the nucleotide sequences of genomes.
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i) Nucleotide level annotation ii) Protein level annotation iii) Process level annotation
Genome annotation is classified at three different levels:

10. 9
https://www.mdpi.com/2079-7737/9/9/295/htm
Comparative annotation method :

11. 10
• BLAST
• Phylogenetic
analysis

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Gene and genome duplication
plays a fundamental role in
evolution by providing the
genetic material by which new
traits can arise. Synteny
analysis dealing with genes
having various types of
duplication & decipher the
evolutionary trajectory of
genes and genomes Fig: Synteny analysis of AP genes between grape and Arabidopsis.
G.F. Ejigu et al. 2020

13. 12
PlantDGD (njau.edu.cn)

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Comparative genomics allowing us:
• To link genomic changes to
environmental adaptation
• To transfer knowledge from
model species to others plants
• To trace structural changes within
a genome through time
Programs for comparative
genomics analysis :

15. 14
The Sol Genomics Network (https://solgenomics.net/) is a
database for comparative genomics platform for Solanaceae
species.

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PLAZA, an online platform for plant comparative genomics
(http://bioinformatics.psb.ugent.be/plaza/)

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Pathway information is available through a large number of databases. These
databases can display pathway diagrams, which combine metabolic, genetic,
and signal networks.
KEGG Plant
Exploring the universe of plant
secondary metabolites
PANTHER
Classification system
Pathways analysis tools:

18. Ambuj Shahi
Phone:
+91 8178098368
Email:
shahiambuj98@gmail.com