The construction of an integrated whole genome HAPPY map of Eimeria tenella

Lim Lik Sin (P41131)

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DC Field	Value	Language
dc.contributor.advisor	Prof. Dr. Wan Kiew Lian
dc.contributor.author	Lim Lik Sin (P41131)
dc.date.accessioned	2023-09-25T09:19:38Z	-
dc.date.available	2023-09-25T09:19:38Z	-
dc.date.issued	2010-12-01
dc.identifier.other	ukmvital:74330
dc.identifier.uri	https://ptsldigital.ukm.my/jspui/handle/123456789/463240	-
dc.description	Eimeria tenella is a protozoan parasite that causes the economically important disease known as coccidiosis in chickens. An effort to sequence the genome of the parasite has been previously initiated and has produced over 4700 contigs assembled from 860,000 randomly generated reads. A genome map will increase the value of these sequence data and aid in the effort to gain a better understanding of the biology of the parasite. The main aim of this study was to construct a whole genome map of E. tenella using the HAPPY mapping approach. An initial study to evaluate the efficiency of this mapping technique was carried out on the two largest contigs from the whole genome assembly, both of which are over 0.5 Mb in size. Thirty three out of 48 markers were successfully typed and linked accordingly to their respective contig. This result indicated that the HAPPY mapping technique was potentially useful for the construction of a whole genome map for this parasite. A total of 1245 contigs representing 70.0% of the whole genome assembly sequences were selected and subjected to marker selection. Subsequently, 2482 markers were developed and typed. Of these, 761 (30.7%) were considered as good markers, 912 (36.7%) as multi-copy markers, 233 (9.4%) as low-copy markers and 576 (23.2%) as failed-PCR markers. The high failure rate in marker development is believed to be largely due to the abundance of multi-copy sequences in the genome. A HAPPY map of the E. tenella genome was successfully constructed, resulting in 65 linkage groups with at least three markers. The HAPPY map was shown to cover ~27.3 Mb of the genome. Markers developed from chromosomally assigned genes were then integrated into the HAPPY map and this aided the assignment of a number of linkage groups to their respective chromosome. Data from BAC end sequences, whole genome sequencing contigs, low-copy markers and chromosomally assigned gene sequences were also integrated to improve and validate the HAPPY map. The number of linkage groups was further reduced to 59, extending the coverage to ~31.0 Mb, which represents approximately half of the estimated 60.0 Mb genome. Further data analysis revealed that most of the contigs with multi-copy markers were linked by BAC end sequences, and these groups of contigs were interspersed with HAPPY map linkage groups, which are mainly made up of unique markers. This observation suggests that the genome of E. tenella is organised in a segmented fashion, with unique regions alternating with multi-copy regions. Analysis of the integrated HAPPY map also showed that approximately half of the E. tenella genome appears to be unique, with the remaining half likely to be represented by multi-copy regions.,Master
dc.language.iso	eng
dc.publisher	UKM, Bangi
dc.relation	Faculty of Science and Technology / Fakulti Sains dan Teknologi
dc.rights	UKM
dc.subject	Construction
dc.subject	Genome HAPPY map
dc.subject	Eimeria tenella
dc.subject	Coccidiosis
dc.title	The construction of an integrated whole genome HAPPY map of Eimeria tenella
dc.type	theses
dc.format.pages	106
dc.identifier.callno	QL368 .C59.L539 2010
dc.identifier.barcode	000442
Appears in Collections:	Faculty of Science and Technology / Fakulti Sains dan Teknologi

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