Use of emerging complete organelle DNA reference database in the diet analysis of the herbivorous wood grouse, western capercaillies (Tetrao urogallus)

Physilia Ying Shi Chua

Abstract

Diet analysis is an important tool in conservation biology, where it can provide information on species’ resource use and habitat requirements. Environmental DNA (eDNA) is a valuable source for diet reconstruction, but the use of reference databases comprising short DNA sequence markers can limit the resolution for accurate species identification. We explore how the optimal use of emerging complete organelle DNA reference databases such as PhyloNorway, may lead to better taxonomic identification of plants in animal diet. We collected faecal samples from eight individual western
capercaillies located in Norway. We used shotgun sequencing to obtain 150bp paired reads and diet information was retrieved by blasting to both GenBank and the PhyloNorway reference database. Our preliminary results suggest that when using PhyloNorway as a reference database, we were able to retrieve at least 160 times more reads assigned to the species-level.

Original language	English
Publication date	2019
Publication status	In preparation - 2019
Event	8th International Barcode of Life Conference 2019 - Trondheim, Norway, Trondheim, Norway Duration: 17 Jun 2019 → 20 Jun 2019 http://dnabarcodes2019.org/

Conference

Conference	8th International Barcode of Life Conference 2019
Location	Trondheim, Norway
Country/Territory	Norway
City	Trondheim
Period	17/06/2019 → 20/06/2019
Internet address	http://dnabarcodes2019.org/

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@conference{60e22143c9ca4ada9cbdcabc941ea4f2,

title = "Use of emerging complete organelle DNA reference database in the diet analysis of the herbivorous wood grouse, western capercaillies (Tetrao urogallus)",

abstract = "Diet analysis is an important tool in conservation biology, where it can provide information on species{\textquoteright} resource use and habitat requirements. Environmental DNA (eDNA) is a valuable source for diet reconstruction, but the use of reference databases comprising short DNA sequence markers can limit the resolution for accurate species identification. We explore how the optimal use of emerging complete organelle DNA reference databases such as PhyloNorway, may lead to better taxonomic identification of plants in animal diet. We collected faecal samples from eight individual westerncapercaillies located in Norway. We used shotgun sequencing to obtain 150bp paired reads and diet information was retrieved by blasting to both GenBank and the PhyloNorway reference database. Our preliminary results suggest that when using PhyloNorway as a reference database, we were able to retrieve at least 160 times more reads assigned to the species-level.",

author = "Chua, {Physilia Ying Shi}",

year = "2019",

language = "English",

note = "8th International Barcode of Life Conference 2019, iBOL2019 ; Conference date: 17-06-2019 Through 20-06-2019",

url = "http://dnabarcodes2019.org/",

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TY - ABST

T1 - Use of emerging complete organelle DNA reference database in the diet analysis of the herbivorous wood grouse, western capercaillies (Tetrao urogallus)

AU - Chua, Physilia Ying Shi

PY - 2019

Y1 - 2019

N2 - Diet analysis is an important tool in conservation biology, where it can provide information on species’ resource use and habitat requirements. Environmental DNA (eDNA) is a valuable source for diet reconstruction, but the use of reference databases comprising short DNA sequence markers can limit the resolution for accurate species identification. We explore how the optimal use of emerging complete organelle DNA reference databases such as PhyloNorway, may lead to better taxonomic identification of plants in animal diet. We collected faecal samples from eight individual westerncapercaillies located in Norway. We used shotgun sequencing to obtain 150bp paired reads and diet information was retrieved by blasting to both GenBank and the PhyloNorway reference database. Our preliminary results suggest that when using PhyloNorway as a reference database, we were able to retrieve at least 160 times more reads assigned to the species-level.

AB - Diet analysis is an important tool in conservation biology, where it can provide information on species’ resource use and habitat requirements. Environmental DNA (eDNA) is a valuable source for diet reconstruction, but the use of reference databases comprising short DNA sequence markers can limit the resolution for accurate species identification. We explore how the optimal use of emerging complete organelle DNA reference databases such as PhyloNorway, may lead to better taxonomic identification of plants in animal diet. We collected faecal samples from eight individual westerncapercaillies located in Norway. We used shotgun sequencing to obtain 150bp paired reads and diet information was retrieved by blasting to both GenBank and the PhyloNorway reference database. Our preliminary results suggest that when using PhyloNorway as a reference database, we were able to retrieve at least 160 times more reads assigned to the species-level.

M3 - Conference abstract for conference

T2 - 8th International Barcode of Life Conference 2019

Y2 - 17 June 2019 through 20 June 2019

ER -

Use of emerging complete organelle DNA reference database in the diet analysis of the herbivorous wood grouse, western capercaillies (Tetrao urogallus)

Abstract

Conference

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