Discovery, target prediction and expression of micrornas in pineapple (Ananas comosus var. comosus)
Pineapple (Ananas comosusvar. comosus) is a non-climacteric fruit, of which the underlying mechanism of fruit ripening is still unknown. The non-ethylene induced ripening of non-climacteric fruitis very much different from climacteric ripening as revealed by the model organism of flesh-fruit i.e....
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| Format: | Thesis |
| Language: | English |
| Published: |
2012
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| Online Access: | https://eprints.ums.edu.my/id/eprint/19288/1/Discovery%2C%20target%20prediction%20and%20expression.pdf |
| _version_ | 1825713364696825856 |
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| author | Noor Hydayaty Md. Yusuf |
| author_facet | Noor Hydayaty Md. Yusuf |
| author_sort | Noor Hydayaty Md. Yusuf |
| collection | UMS |
| description | Pineapple (Ananas comosusvar. comosus) is a non-climacteric fruit, of which the
underlying mechanism of fruit ripening is still unknown. The non-ethylene induced
ripening of non-climacteric fruitis very much different from climacteric ripening as
revealed by the model organism of flesh-fruit i.e. tomato. Recently discovered
gene regulators, i.e. miRNAs, are known to silence the translation of mRNA
transcripts, leading to a silencing effect on proteins and affecting various phenotype
changes in plants throughout plant development. Thus, this study aims to
determine the mechanism of non-climacteric ripening through the differential
expression of miRNA genes. Orthologous miRNAs were first amplified through
stem-loop RT -PCR to prove for the existence of the presence of miRNAs in
pineapples. Large scale mining of miRNA from small RNA libraries (fruit and leaf)
constructed through the use of high-throughput Solexa technology was then
carried out and the target mRNA transcripts were subsequently predicted. For this
purpose, the miRNA registry (miRBase) and EST database (NCBI) were referred to
and a bioinformatics pipeline was developed and utilized. The regulation of miRNAs
in regulation of fruit ripening was postulated through correlating the target protein
predicted with the pattern of expression of miRNAs during pineapple ripening
obtained through stem-loop RT-qPCR. As a result, 12 orthologous miRNAs were
amplified and showed the presence of miRNAs in pineapple, while finding of 153
miRNAs, 41 miRNA families, 20 miRNA*s, and 20 target transcripts obtained
showed the conservation of miRNAs in pineapple. The miRNAs were then
characterized. Finally, differential regulation was postulated where 7 miRNAs
(miR16S, miR166, miRl64, miR171, miR444, miR1088, and miR396) are believed
to be involved in fruit development and 4 miRNAs (miR172, miR1S6, miRS3S,
miR319) in phase transition from flowering to senescence. Besides that,
throughout pineapple development,5 miRNAs (miR159, miR167, miR390, miR393
and miR394) control hormone Signaling, 4 miRNAs (miR39S, miR397, miR399, and
miR893) control nutrient uptake and homeostasis, and 2 miRNAs (miR162 and
miR168) control the overall homeostasis of miRNAs. Thus, the preliminary putative
of pineapple regulated by miRNAs is postulated and revealed. |
| first_indexed | 2024-03-06T02:55:26Z |
| format | Thesis |
| id | ums.eprints-19288 |
| institution | Universiti Malaysia Sabah |
| language | English |
| last_indexed | 2024-03-06T02:55:26Z |
| publishDate | 2012 |
| record_format | dspace |
| spelling | ums.eprints-192882018-03-22T02:07:24Z https://eprints.ums.edu.my/id/eprint/19288/ Discovery, target prediction and expression of micrornas in pineapple (Ananas comosus var. comosus) Noor Hydayaty Md. Yusuf QP Physiology Pineapple (Ananas comosusvar. comosus) is a non-climacteric fruit, of which the underlying mechanism of fruit ripening is still unknown. The non-ethylene induced ripening of non-climacteric fruitis very much different from climacteric ripening as revealed by the model organism of flesh-fruit i.e. tomato. Recently discovered gene regulators, i.e. miRNAs, are known to silence the translation of mRNA transcripts, leading to a silencing effect on proteins and affecting various phenotype changes in plants throughout plant development. Thus, this study aims to determine the mechanism of non-climacteric ripening through the differential expression of miRNA genes. Orthologous miRNAs were first amplified through stem-loop RT -PCR to prove for the existence of the presence of miRNAs in pineapples. Large scale mining of miRNA from small RNA libraries (fruit and leaf) constructed through the use of high-throughput Solexa technology was then carried out and the target mRNA transcripts were subsequently predicted. For this purpose, the miRNA registry (miRBase) and EST database (NCBI) were referred to and a bioinformatics pipeline was developed and utilized. The regulation of miRNAs in regulation of fruit ripening was postulated through correlating the target protein predicted with the pattern of expression of miRNAs during pineapple ripening obtained through stem-loop RT-qPCR. As a result, 12 orthologous miRNAs were amplified and showed the presence of miRNAs in pineapple, while finding of 153 miRNAs, 41 miRNA families, 20 miRNA*s, and 20 target transcripts obtained showed the conservation of miRNAs in pineapple. The miRNAs were then characterized. Finally, differential regulation was postulated where 7 miRNAs (miR16S, miR166, miRl64, miR171, miR444, miR1088, and miR396) are believed to be involved in fruit development and 4 miRNAs (miR172, miR1S6, miRS3S, miR319) in phase transition from flowering to senescence. Besides that, throughout pineapple development,5 miRNAs (miR159, miR167, miR390, miR393 and miR394) control hormone Signaling, 4 miRNAs (miR39S, miR397, miR399, and miR893) control nutrient uptake and homeostasis, and 2 miRNAs (miR162 and miR168) control the overall homeostasis of miRNAs. Thus, the preliminary putative of pineapple regulated by miRNAs is postulated and revealed. 2012 Thesis NonPeerReviewed text en https://eprints.ums.edu.my/id/eprint/19288/1/Discovery%2C%20target%20prediction%20and%20expression.pdf Noor Hydayaty Md. Yusuf (2012) Discovery, target prediction and expression of micrornas in pineapple (Ananas comosus var. comosus). Masters thesis, Universiti Malaysia Sabah. |
| spellingShingle | QP Physiology Noor Hydayaty Md. Yusuf Discovery, target prediction and expression of micrornas in pineapple (Ananas comosus var. comosus) |
| title | Discovery, target prediction and expression of micrornas in pineapple (Ananas comosus var. comosus) |
| title_full | Discovery, target prediction and expression of micrornas in pineapple (Ananas comosus var. comosus) |
| title_fullStr | Discovery, target prediction and expression of micrornas in pineapple (Ananas comosus var. comosus) |
| title_full_unstemmed | Discovery, target prediction and expression of micrornas in pineapple (Ananas comosus var. comosus) |
| title_short | Discovery, target prediction and expression of micrornas in pineapple (Ananas comosus var. comosus) |
| title_sort | discovery target prediction and expression of micrornas in pineapple ananas comosus var comosus |
| topic | QP Physiology |
| url | https://eprints.ums.edu.my/id/eprint/19288/1/Discovery%2C%20target%20prediction%20and%20expression.pdf |
| work_keys_str_mv | AT noorhydayatymdyusuf discoverytargetpredictionandexpressionofmicrornasinpineappleananascomosusvarcomosus |