Framing an Appropriate Research Question 6b9b26d93da94caf993c038d9efcdedb.pdf
Plang functional genome
1. Biosci 755 Genomics and Gene Expression 9 sessions: 7, 14, 21 & 28 March, 4 April, 2, 9, 16 & 23 May. Lecturers Associate Professor Brian Murray - course coordinator Associate Professor Rob Young Professor Russell Snell Each responsible for three sessions, the first will be an overview lecture of the general area and the second and third will be student seminars. Attendance at ALL sessions is compulsory.
14. Variation in chromosome number and size in the plant family Aloaceae but the karyotypes are always bimodal. This family shows karyotypic orthoselection. From: Brandham and Doherty (1998) Genome size variation in the Aloeaceae, an angiosperm family showing karyotypic orhtoselection. Annals of Botany 82 (Supplement A): 67-73.
15. Karyotypes of these three species from the Commelinaceae are highly diverse, in size, number and shape. From: Jones and Colden (1972) Chromosomes and the classification of the Commelinaceae. Botanical Journal of the Linnean Society 65 : 129-162.
32. From: Lynch M (2007) The Origins of Genome Architecture, Sinauer.
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45. Mechanisms for the initiation of heterochromatin assembly. Grewal and Jia Nature Reviews Genetics 8 , 35 –46 (January 2007) | doi:10.1038/nrg2008 Initiation by recognition of transcription factors (TF) or repetitive DNA, then recruit histone methyltransferase (HMT) and histone deacetylase (HDAC) that modify histone tails and change chromatin conformation. Boundary elements prevent the spread of heterochromatin.
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47. The multiple interactions of heterochromatin with chromosome structure, behaviour and gene activity Grewal and Jia Nature Reviews Genetics 8 , 35 –46 (January 2007) | doi:10.1038/nrg2008
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50. From: KL Adams & JF Wendel (2005) Polyploidy and genome evolution in plants. Current Opinion in Plant Biology 8: 135-141. Inferred polyploidy events during the evolution of angiosperms.
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Editor's Notes
Three plant genomes sequenced in full but many smaller regions of many species have also been sequenced. Need to appreciate that this is a dynamic process and can go in either direction, up or down.
Pre full sequence of Arabidopsis showing that many genes are present in duplicate locations but their order has not been well conserved. Duplicated regions are represented on the different chromosomes in the same colour. Suggestion here of ancient polyploidy in this diploid species.
More recently published sequence in rice also shows extensive segmental duplication .
Duplication events can be dated by looking at the rate of synonymous site substitutions in the duplicated segments. In rice there is a sub-set of more recent duplications.
Can also study retrotransposons and these can also be used to date genomic changes - genome archaeology. Many retrotransposons have long terminal repeats that have the same sequence at insertion. Use molecular clock on number of changes between LTRs to date their insertion. Dot plot alingment of contig with itself. Parallel or perpendicular lines show repeats.
History of the region presented here showing duplication (D), deletion (L) and insertion of transposable elements (T).
Detail of previous figure, gene in grey, Xalas has inserted into Rada in ancestor locus.
Transposons are also important in Triticeae. Also shows that many of the elements are active, not methylated.
Hybrid derived species have 50% more DNA than parents, despite multiple origins hybrid species (except H. deserticola) are constant across range. Natural and synthetic hybrids don’t show increased values of hybrid species.
Similarity of c. 25000 Arabidopsis proteins to c. 52000 proteins from 20 reference genomes. Suggests that c. 4500 Arabidopsis genes were acquired from a cyanobacterial ancestor of plastids. Black bars how many trees homologue shares in common with Arabidopsis, grey bars are number of best matches in genome at different degrees of stringency.
Genome size increase may be counterbalanced by illegitimate recombination, can be identified by finding solo LTRs as in B or clearly different LTRs as in C.
Frequency of a variety of different events observed in the Arabidopsis sequence.
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