Isolation characterization and mapping of expressed sequence tags (ESTs) from pineapple fruit cDNA library

Pineapple (Ananas comosus var. comosus), is an important tropical non-climacteric fruit with high commercial potential. Understanding the phenomena behind fruit ripening with a focus on improving fruit quality traits such as flavor, texture, appearance and sweetness may be possible through gene expr...

Full description

Saved in:

Bibliographic Details
Format:	Thesis
Language:	English English
Published:	2011
Subjects:	QK900-989 Plant ecology
Online Access:	https://eprints.ums.edu.my/id/eprint/38640/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/38640/2/FULLTEXT.pdf
Tags:	Add Tag No Tags, Be the first to tag this record!

id	my-ums-ep.38640
record_format	uketd_dc
spelling	my-ums-ep.386402024-05-10T02:53:16Z Isolation characterization and mapping of expressed sequence tags (ESTs) from pineapple fruit cDNA library 2011 QK900-989 Plant ecology Pineapple (Ananas comosus var. comosus), is an important tropical non-climacteric fruit with high commercial potential. Understanding the phenomena behind fruit ripening with a focus on improving fruit quality traits such as flavor, texture, appearance and sweetness may be possible through gene expression profiling of pineapple fruit transcriptome. As such, the objectives of this project are to, firstly, construct and sequenced mature green pineapple cDNA and de novo assembly of paired-end Solexa reads. Secondly, to characterize and functionally annotate the transcripts through similarity search and mapping against Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database respectively. Finally, to develop a database of Expressed Sequence Tags containing Simple Sequence Repeats (EST-SSRs) using the newly obtained transcripts and/or through pineapple ESTs that are available in GenBank. The results show that both the unique transcripts (UT) assembled pineapple sequences and contigs from de novo assembly generated a total of 28,896 transcripts being generated with length ranges from 100 bp to 3.8 kb. A search for sequence similarity with NCBI's nonredundant database identified about 17,049 transcripts which were found to be associated with primary metabolisms, amino acid synthesis and processing, membrane and transport, cell division, cytoskeleton, cell wall and metabolism, RNA related gene expression, signal transduction, defense and stress related protein and also secondary metabolisms. Out of these transcripts, 71 % returned GO terms with the distribution among the ontologies given as such: 35.8% in molecular function, 33.5% in cellular component and 30.7% in biological process. Annotation against the KEGG database pathways on the other hand, enabled the assignment of 542 enzyme commissions to 13,598 transcripts. The enzymes were further categorized into a total of 126 pathways with 122 pathways being involved in pineapple metabolism. The metabolic and cellular processes points out that there are tremendous changes in metabolic activities during pineapple fruit maturation as seen by the large numbers of the annotated transcripts. Data mining of the pineapple transcripts EST-SSRs showed that only 4% of the pineapple transcripts contained SSRs. Dinucleotide SSR (49.5%) was the most abundant followed by trinucleotide SSR (46.8%). The least abundant was tetranucleotide SSR (3.7%). Out of these, about 40% of the pineapple transcripts were found to have suitable flanking sites to enable the design of the upstream and downstream primers for future PCR amplification. This research cataloged the first pineapple fruit transcriptome. The transcripts will be subsequently useful to develop microarray chips for future gene expression studies among different plant tissue and development stages of the fruit. Further validation and/or relevant use of the ESTSSRs found will be useful in comparative mapping and genome mapping and gene tagging in pineapple. 2011 Thesis https://eprints.ums.edu.my/id/eprint/38640/ https://eprints.ums.edu.my/id/eprint/38640/1/24%20PAGES.pdf text en public https://eprints.ums.edu.my/id/eprint/38640/2/FULLTEXT.pdf text en validuser masters Universiti Malaysia Sabah Institut Penyelidikan Bioteknologi
institution	Universiti Malaysia Sabah
collection	UMS Institutional Repository
language	English English
topic	QK900-989 Plant ecology
spellingShingle	QK900-989 Plant ecology Isolation characterization and mapping of expressed sequence tags (ESTs) from pineapple fruit cDNA library
description	Pineapple (Ananas comosus var. comosus), is an important tropical non-climacteric fruit with high commercial potential. Understanding the phenomena behind fruit ripening with a focus on improving fruit quality traits such as flavor, texture, appearance and sweetness may be possible through gene expression profiling of pineapple fruit transcriptome. As such, the objectives of this project are to, firstly, construct and sequenced mature green pineapple cDNA and de novo assembly of paired-end Solexa reads. Secondly, to characterize and functionally annotate the transcripts through similarity search and mapping against Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database respectively. Finally, to develop a database of Expressed Sequence Tags containing Simple Sequence Repeats (EST-SSRs) using the newly obtained transcripts and/or through pineapple ESTs that are available in GenBank. The results show that both the unique transcripts (UT) assembled pineapple sequences and contigs from de novo assembly generated a total of 28,896 transcripts being generated with length ranges from 100 bp to 3.8 kb. A search for sequence similarity with NCBI's nonredundant database identified about 17,049 transcripts which were found to be associated with primary metabolisms, amino acid synthesis and processing, membrane and transport, cell division, cytoskeleton, cell wall and metabolism, RNA related gene expression, signal transduction, defense and stress related protein and also secondary metabolisms. Out of these transcripts, 71 % returned GO terms with the distribution among the ontologies given as such: 35.8% in molecular function, 33.5% in cellular component and 30.7% in biological process. Annotation against the KEGG database pathways on the other hand, enabled the assignment of 542 enzyme commissions to 13,598 transcripts. The enzymes were further categorized into a total of 126 pathways with 122 pathways being involved in pineapple metabolism. The metabolic and cellular processes points out that there are tremendous changes in metabolic activities during pineapple fruit maturation as seen by the large numbers of the annotated transcripts. Data mining of the pineapple transcripts EST-SSRs showed that only 4% of the pineapple transcripts contained SSRs. Dinucleotide SSR (49.5%) was the most abundant followed by trinucleotide SSR (46.8%). The least abundant was tetranucleotide SSR (3.7%). Out of these, about 40% of the pineapple transcripts were found to have suitable flanking sites to enable the design of the upstream and downstream primers for future PCR amplification. This research cataloged the first pineapple fruit transcriptome. The transcripts will be subsequently useful to develop microarray chips for future gene expression studies among different plant tissue and development stages of the fruit. Further validation and/or relevant use of the ESTSSRs found will be useful in comparative mapping and genome mapping and gene tagging in pineapple.
format	Thesis
qualification_level	Master's degree
title	Isolation characterization and mapping of expressed sequence tags (ESTs) from pineapple fruit cDNA library
title_short	Isolation characterization and mapping of expressed sequence tags (ESTs) from pineapple fruit cDNA library
title_full	Isolation characterization and mapping of expressed sequence tags (ESTs) from pineapple fruit cDNA library
title_fullStr	Isolation characterization and mapping of expressed sequence tags (ESTs) from pineapple fruit cDNA library
title_full_unstemmed	Isolation characterization and mapping of expressed sequence tags (ESTs) from pineapple fruit cDNA library
title_sort	isolation characterization and mapping of expressed sequence tags (ests) from pineapple fruit cdna library
granting_institution	Universiti Malaysia Sabah
granting_department	Institut Penyelidikan Bioteknologi
publishDate	2011
url	https://eprints.ums.edu.my/id/eprint/38640/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/38640/2/FULLTEXT.pdf
_version_	1804890335394922496

Isolation characterization and mapping of expressed sequence tags (ESTs) from pineapple fruit cDNA library

Similar Items