Whole Genome Sequencing For Establishment Of Phylogenetic Position And Discovery Of Miniaturization And Lipid Metabolism Genes In Paedocypris

Paedocypris is the world’s smallest vertebrate with a total length of ≤ 20 mm restricted to acidic freshwater peat swamp environments. The anatomy of Paedocypris is highly modified with developmental truncated characters. The unique miniature phenotypes make the Paedocypris a good model fish to stud...

Full description

Saved in:

Bibliographic Details
Main Author:	Sam, Ka Kei
Format:	Thesis
Language:	English
Published:	2022
Subjects:	QH1 Natural history (General - Including nature conservation geographical distribution)
Online Access:	http://eprints.usm.my/59992/1/SAM%20KA%20KEI%20-%20TESIS24.pdf
Tags:	Add Tag No Tags, Be the first to tag this record!

id	my-usm-ep.59992
record_format	uketd_dc
spelling	my-usm-ep.599922024-02-23T08:42:03Z Whole Genome Sequencing For Establishment Of Phylogenetic Position And Discovery Of Miniaturization And Lipid Metabolism Genes In Paedocypris 2022-05 Sam, Ka Kei QH1 Natural history (General - Including nature conservation, geographical distribution) Paedocypris is the world’s smallest vertebrate with a total length of ≤ 20 mm restricted to acidic freshwater peat swamp environments. The anatomy of Paedocypris is highly modified with developmental truncated characters. The unique miniature phenotypes make the Paedocypris a good model fish to study development and evolution. Three Paedocypris species have been described, including P. micromegethes from Sarawak and another two species, P. progenetica and P. carbunculus from Indonesia. Thus far, Paedocypris has no chromosome-scale genome, with only a draft genome with scaffold N50 ~59-61 kb. In this study, a high-quality chromosome level genome assembly for the P. micromegethes was generated with improved scaffold N50 of 29.8 Mb using a combination of Illumina, PacBio and Hi-C sequencing technologies. Meanwhile, the draft genome for the P. carbunculus was improved with N50 scaffold length of 125 Kb. This study revealed that the small and compact genome sizes of miniature Paedocypris are characterized by a low repeat content, short introns, and a lack of recent genome duplications. Additionally, this study discovered gene loss from the improved genome assemblies, such as fgf8b, mtmr14, scpp3a, scpp3b, scpp6, scpp7 scpp8, gsp37, spp2, and tbx22. Phylogenetic analysis to resolve the contentious taxonomy position of miniaturized cyprinids using mitochondrial 13 protein-coding genes (PCGs) and two ribosomal RNA genes (rRNAs) showed improved supportive values for the sister-group relationship for Paedocypris and Sundadanio to the Danionidae family. 2022-05 Thesis http://eprints.usm.my/59992/ http://eprints.usm.my/59992/1/SAM%20KA%20KEI%20-%20TESIS24.pdf application/pdf en public phd doctoral Universiti Sains Malaysia Pusat Pengajian Sains Kajihayat
institution	Universiti Sains Malaysia
collection	USM Institutional Repository
language	English
topic	QH1 Natural history (General - Including nature conservation geographical distribution)
spellingShingle	QH1 Natural history (General - Including nature conservation geographical distribution) Sam, Ka Kei Whole Genome Sequencing For Establishment Of Phylogenetic Position And Discovery Of Miniaturization And Lipid Metabolism Genes In Paedocypris
description	Paedocypris is the world’s smallest vertebrate with a total length of ≤ 20 mm restricted to acidic freshwater peat swamp environments. The anatomy of Paedocypris is highly modified with developmental truncated characters. The unique miniature phenotypes make the Paedocypris a good model fish to study development and evolution. Three Paedocypris species have been described, including P. micromegethes from Sarawak and another two species, P. progenetica and P. carbunculus from Indonesia. Thus far, Paedocypris has no chromosome-scale genome, with only a draft genome with scaffold N50 ~59-61 kb. In this study, a high-quality chromosome level genome assembly for the P. micromegethes was generated with improved scaffold N50 of 29.8 Mb using a combination of Illumina, PacBio and Hi-C sequencing technologies. Meanwhile, the draft genome for the P. carbunculus was improved with N50 scaffold length of 125 Kb. This study revealed that the small and compact genome sizes of miniature Paedocypris are characterized by a low repeat content, short introns, and a lack of recent genome duplications. Additionally, this study discovered gene loss from the improved genome assemblies, such as fgf8b, mtmr14, scpp3a, scpp3b, scpp6, scpp7 scpp8, gsp37, spp2, and tbx22. Phylogenetic analysis to resolve the contentious taxonomy position of miniaturized cyprinids using mitochondrial 13 protein-coding genes (PCGs) and two ribosomal RNA genes (rRNAs) showed improved supportive values for the sister-group relationship for Paedocypris and Sundadanio to the Danionidae family.
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Sam, Ka Kei
author_facet	Sam, Ka Kei
author_sort	Sam, Ka Kei
title	Whole Genome Sequencing For Establishment Of Phylogenetic Position And Discovery Of Miniaturization And Lipid Metabolism Genes In Paedocypris
title_short	Whole Genome Sequencing For Establishment Of Phylogenetic Position And Discovery Of Miniaturization And Lipid Metabolism Genes In Paedocypris
title_full	Whole Genome Sequencing For Establishment Of Phylogenetic Position And Discovery Of Miniaturization And Lipid Metabolism Genes In Paedocypris
title_fullStr	Whole Genome Sequencing For Establishment Of Phylogenetic Position And Discovery Of Miniaturization And Lipid Metabolism Genes In Paedocypris
title_full_unstemmed	Whole Genome Sequencing For Establishment Of Phylogenetic Position And Discovery Of Miniaturization And Lipid Metabolism Genes In Paedocypris
title_sort	whole genome sequencing for establishment of phylogenetic position and discovery of miniaturization and lipid metabolism genes in paedocypris
granting_institution	Universiti Sains Malaysia
granting_department	Pusat Pengajian Sains Kajihayat
publishDate	2022
url	http://eprints.usm.my/59992/1/SAM%20KA%20KEI%20-%20TESIS24.pdf
_version_	1794024072998289408

Whole Genome Sequencing For Establishment Of Phylogenetic Position And Discovery Of Miniaturization And Lipid Metabolism Genes In Paedocypris

Similar Items