A preliminary transcriptomic analysis of lichen Dirinaria sp.

A. R Siti Nurhani, Abdul Munir Abd. Murad, S. Mohd Wahid, A. B Farah Diba

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

Lichen is a slow-growing symbiotic organism that consists of a fungus and a photobiont, comprising either an algae or a cyanobacterium living together in a single composite body, known as a thallus. Lichens have a remarkable ability to survive in extreme environmental conditions on earth that makes them a great biological indicator of air quality. The primary goal of this study is to discover the genes that may unravel the mechanism behind the tolerance of this lichen towards air pollution. Lichen samples of Dirinaria sp. were collected from two sites-Jerantut (J) as having a relatively good air quality and Klang (K), an area of bad air quality. Total RNA extraction was carried out, followed by sample preparation prior to transcriptomic sequencing. Altogether 21.7 million and 30.5 million high quality sequence reads from samples J and K, respectively were de novo assembled into 106884 and 88116 transcripts. The assembled sequences were annotated by BLASTX comparison against a non-redundant protein sequence database with 59403 sequences (67.4%) of sample K and 68972 sequences (64.5%) of sample J had a match in the database with a cut-off value of 1e-06. A total of 42175 sequences (47.8%) of sample K and 25648 sequences (24%) of sample J had a Gene Ontology term match. The sequences were assigned to Kyoto Encyclopedia of Genes and Genome (KEGG) pathways, resulting in 129 KEGG pathways generated from sample K, whilst 123 KEGG pathways were produced from sample J.

Original languageEnglish
Title of host publicationAIP Conference Proceedings
Pages258-263
Number of pages6
Volume1571
DOIs
Publication statusPublished - 2013
Event2013 UKM Faculty of Science and Technology Post-Graduate Colloquium - Selangor
Duration: 3 Jul 20134 Jul 2013

Other

Other2013 UKM Faculty of Science and Technology Post-Graduate Colloquium
CitySelangor
Period3/7/134/7/13

Fingerprint

lichens
genes
air quality
genome
air pollution
sequencing
fungi
algae
organisms
cut-off
proteins

Keywords

  • Dirinaria sp.
  • Functional annotation
  • Lichen
  • Transcriptomic sequencing

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Cite this

Nurhani, A. R. S., Abd. Murad, A. M., Wahid, S. M., & Diba, A. B. F. (2013). A preliminary transcriptomic analysis of lichen Dirinaria sp. In AIP Conference Proceedings (Vol. 1571, pp. 258-263) https://doi.org/10.1063/1.4858665

A preliminary transcriptomic analysis of lichen Dirinaria sp. / Nurhani, A. R Siti; Abd. Murad, Abdul Munir; Wahid, S. Mohd; Diba, A. B Farah.

AIP Conference Proceedings. Vol. 1571 2013. p. 258-263.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Nurhani, ARS, Abd. Murad, AM, Wahid, SM & Diba, ABF 2013, A preliminary transcriptomic analysis of lichen Dirinaria sp. in AIP Conference Proceedings. vol. 1571, pp. 258-263, 2013 UKM Faculty of Science and Technology Post-Graduate Colloquium, Selangor, 3/7/13. https://doi.org/10.1063/1.4858665
Nurhani ARS, Abd. Murad AM, Wahid SM, Diba ABF. A preliminary transcriptomic analysis of lichen Dirinaria sp. In AIP Conference Proceedings. Vol. 1571. 2013. p. 258-263 https://doi.org/10.1063/1.4858665
Nurhani, A. R Siti ; Abd. Murad, Abdul Munir ; Wahid, S. Mohd ; Diba, A. B Farah. / A preliminary transcriptomic analysis of lichen Dirinaria sp. AIP Conference Proceedings. Vol. 1571 2013. pp. 258-263
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