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Generating small mammals mitogenome reference dataset for Malaysian species

Malaysia’s biological diversity is among the richest in the world but rapidly declining due to various human activities and climate change. Despite the continuous loss in biodiversity with the most recent death of our last Sumatran Rhino in May 2019, Malaysia's biodiversity data is still poorly...

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Main Author: Jahari, Puteri Nur Syahzanani
Format: Thesis
Language:English
Published: 2019
Subjects:
Q Science (General)
Online Access:http://eprints.utm.my/id/eprint/101827/1/PuteriNurSyahzananiMFS2019.pdf.pdf
http://eprints.utm.my/id/eprint/101827/
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spelling my.utm.1018272023-07-10T09:34:04Z http://eprints.utm.my/id/eprint/101827/ Generating small mammals mitogenome reference dataset for Malaysian species Jahari, Puteri Nur Syahzanani Q Science (General) Malaysia’s biological diversity is among the richest in the world but rapidly declining due to various human activities and climate change. Despite the continuous loss in biodiversity with the most recent death of our last Sumatran Rhino in May 2019, Malaysia's biodiversity data is still poorly characterized and systematically documented. Most species data have limited visibility with very abysmal publications which are mostly restricted to morphological traits and lack genomic data. As in line with the country’s National Policy on Biological Diversity 2016- 2025 to combat biodiversity loss and global effort to sequence all life by 2028 (Earth Biogenome Project), this study has focused on generating Malaysian small mammals mitogenome reference dataset. The genomic DNA of two fresh tissue samples (Balionycteris maculata and Callosciurus notatus) were extracted, fragmented to 300 bp, and further constructed into Illumina-compatible libraries using BEST protocol. Next, about 15 amplification cycles during library indexing was used to produce maximum data output with high complexity, and low clonality suggesting the rare variants could be easily detected. Prior to sequencing using BGISEQ-500 platform, the 3-indexed libraries (including extraction blanks) with approximately 300-400 bp were pooled to equimolar DNA (<12,000 pmol/L). Approximately 5 gigabases raw sequence data per sample were generated comprising of the whole genome data (mitochondrial DNA and nuclear DNA). The new high quality mitogenomes has been successfully assembled using MITOBIM and PALEOMIX with an average size of 16-17 Kbp and an average depth of coverage of 140.27x. The detailed pipeline and challenges on mitogenome assembly for species with and without reference genome in Genbank was discussed. The mitogenomes were further annotated to its 37 designated genes via MitoZ. The robust pipeline of mitogenome sequence generation established in this work could be applied to generate more genomic data from thousands of tissue samples available from local biodiversity key players such as Perbadanan Taman Negara Johor, FRIM and PERHILITAN. The further enrichment of DNA reference database will strongly magnify species detection in invertebrate-derived DNA (iDNA) research for biodiversity assessment, wildlife forensics to monitor illegal trade of endangered species in this region, as well as population genetic studies. 2019 Thesis NonPeerReviewed application/pdf en http://eprints.utm.my/id/eprint/101827/1/PuteriNurSyahzananiMFS2019.pdf.pdf Jahari, Puteri Nur Syahzanani (2019) Generating small mammals mitogenome reference dataset for Malaysian species. Masters thesis, Universiti Teknologi Malaysia. http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:146182
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
language English
topic Q Science (General)
spellingShingle Q Science (General)
Jahari, Puteri Nur Syahzanani
Generating small mammals mitogenome reference dataset for Malaysian species
description Malaysia’s biological diversity is among the richest in the world but rapidly declining due to various human activities and climate change. Despite the continuous loss in biodiversity with the most recent death of our last Sumatran Rhino in May 2019, Malaysia's biodiversity data is still poorly characterized and systematically documented. Most species data have limited visibility with very abysmal publications which are mostly restricted to morphological traits and lack genomic data. As in line with the country’s National Policy on Biological Diversity 2016- 2025 to combat biodiversity loss and global effort to sequence all life by 2028 (Earth Biogenome Project), this study has focused on generating Malaysian small mammals mitogenome reference dataset. The genomic DNA of two fresh tissue samples (Balionycteris maculata and Callosciurus notatus) were extracted, fragmented to 300 bp, and further constructed into Illumina-compatible libraries using BEST protocol. Next, about 15 amplification cycles during library indexing was used to produce maximum data output with high complexity, and low clonality suggesting the rare variants could be easily detected. Prior to sequencing using BGISEQ-500 platform, the 3-indexed libraries (including extraction blanks) with approximately 300-400 bp were pooled to equimolar DNA (<12,000 pmol/L). Approximately 5 gigabases raw sequence data per sample were generated comprising of the whole genome data (mitochondrial DNA and nuclear DNA). The new high quality mitogenomes has been successfully assembled using MITOBIM and PALEOMIX with an average size of 16-17 Kbp and an average depth of coverage of 140.27x. The detailed pipeline and challenges on mitogenome assembly for species with and without reference genome in Genbank was discussed. The mitogenomes were further annotated to its 37 designated genes via MitoZ. The robust pipeline of mitogenome sequence generation established in this work could be applied to generate more genomic data from thousands of tissue samples available from local biodiversity key players such as Perbadanan Taman Negara Johor, FRIM and PERHILITAN. The further enrichment of DNA reference database will strongly magnify species detection in invertebrate-derived DNA (iDNA) research for biodiversity assessment, wildlife forensics to monitor illegal trade of endangered species in this region, as well as population genetic studies.
format Thesis
author Jahari, Puteri Nur Syahzanani
author_facet Jahari, Puteri Nur Syahzanani
author_sort Jahari, Puteri Nur Syahzanani
title Generating small mammals mitogenome reference dataset for Malaysian species
title_short Generating small mammals mitogenome reference dataset for Malaysian species
title_full Generating small mammals mitogenome reference dataset for Malaysian species
title_fullStr Generating small mammals mitogenome reference dataset for Malaysian species
title_full_unstemmed Generating small mammals mitogenome reference dataset for Malaysian species
title_sort generating small mammals mitogenome reference dataset for malaysian species
publishDate 2019
url http://eprints.utm.my/id/eprint/101827/1/PuteriNurSyahzananiMFS2019.pdf.pdf
http://eprints.utm.my/id/eprint/101827/
http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:146182
_version_ 1772811119077883904
score 13.211869

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