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A preliminary transcriptomic analysis of lichen Dirinaria sp

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...

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Main Authors:	Nurhani A R Siti, Abdul, Munir A M, Mohd, Wahid S, Farah, Diba A B
Format:	Conference Proceeding
Language:	English
Subjects:	Air pollution Air quality Encyclopedias Gene sequencing Genes Lichens Outdoor air quality Proteins Ribonucleic acid RNA
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creator	Nurhani A R Siti Abdul, Munir A M Mohd, Wahid S Farah, Diba A B
description	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.
doi_str_mv	10.1063/1.4858665
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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. 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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. 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source	American Institute of Physics:Jisc Collections:Transitional Journals Agreement 2021-23 (Reading list)
subjects	Air pollution Air quality Encyclopedias Gene sequencing Genes Lichens Outdoor air quality Proteins Ribonucleic acid RNA
title	A preliminary transcriptomic analysis of lichen Dirinaria sp
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