Information Package / Course Catalogue - Adnan Menderes University

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Phylogenetic Analysis Methods in Plants II

Course Code	: ZBY616
Course Type	: Area Elective
Couse Group	: Third Cycle (Doctorate Degree)
Education Language	: Turkish
Work Placement	: N/A

Theory	: 3
Prt.	: 0
Credit	: 3
Lab	: 0
ECTS	: 8

Objectives of the Course

The aim of this course is to learn DNA sequencing and sequence analysis techniques, nrDNA ITS region, cpDNA trnL-F, matK, psbA-trnH, rpl32-trnL, ndhF, trnQ-rps16, rbcL regions, such as PAUP, MEGA 6.0, CLUSTAL, Phylogeny fr. , MULTALIN, etc. using phylogenetic analysis programs.

Course Content

Obtaining and interpreting phylogenetic tree by PCR amplification of nuclear and chloroplast gene regions together with DNA sequencing techniques and bioinformatic analysis.

Name of Lecturer(s)

Learning Outcomes

1.	Learning the coding and non-coding gene regions used in phylogenetics
2.	Learning various bioinformatics computer programs used in phylogenetics
3.	Evaluation of bioinformatics results
4.	Learning to evaluate phylogenetic data
5.	Learning the interpretation of the phylogenetic tree

Recommended or Required Reading

1.	Evrimsel analiz, Palme Publishing, Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University press, Lemey, P., Salemi, M., Vandamme, A.M. (2009). The Phylogenetic Handbook. Cambridge University press, Genetic (Nobel Academic Publishing) 2010
2.	Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University press, Güler Temizkan and Nazlı Arda, Methods Used in Molecular Biology, Nobel Tıp Kitapevi, İstanbul, 2007, Dale, von Schantz, From Genes to Genomes: Concepts and Applicaitons of DNA Technology, 2nd Edition, John Wiley & Sons, Ltd, USA, 2007

Weekly Detailed Course Contents

Week 1 - Theoretical

DNA sequence analysis techniques

Week 2 - Theoretical

Structure of the core genome

Week 3 - Theoretical

Structure of the organelle genome

Week 4 - Theoretical

nrDNA ITS region

Week 5 - Theoretical

cpDNA trnL-F, matK region

Week 6 - Theoretical

cpDNA rbcL, rps16-trnQ region

Week 7 - Theoretical

cpDNA ndhF, rpl32-trnL region

Week 8 - Theoretical

cpDNA rps-rpl gene region and mtDNA gene regions (Midterm Exam)

Week 9 - Theoretical

Primer design

Week 10 - Theoretical

Use of the NCBI data system

Week 11 - Theoretical

Gen uploading to the NCBI data system

Week 12 - Theoretical

CLUSTAL, Multalin, Phylogeny fr. Etc. use of programs

Week 13 - Theoretical

Using Bioedit, FinchTV, Chromas, Sequencher programs

Week 14 - Theoretical

Using PAUP, MEGA, PHYLIP, DnaSP, GenAlEx programs and Phylogenetic tree interpretation

Assessment Methods and Criteria

Type of Assessment	Count	Percent
Midterm Examination	1	%30
Final Examination	1	%70

Workload Calculation

Activities	Count	Preparation	Time	Total Work Load (hours)
Lecture - Theory	14	10	3	182
Midterm Examination	1	8	1	9
Final Examination	1	8	1	9
TOTAL WORKLOAD (hours)				200

Contribution of Learning Outcomes to Programme Outcomes

	PÇ-1	PÇ-2	PÇ-3	PÇ-4	PÇ-5
OÇ-1	4	4	4	3	4
OÇ-2	5	5	4	4	4
OÇ-3	4	4	4	4	4
OÇ-4	5	4	4	4	5
OÇ-5	4	4	4	3	4

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