Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding
DNA metabarcoding was employed to identify plant-derived food resources for the Japanese rock ptarmigan ( Lagopus muta japonica ), which is registered as a natural living monument in Japan, in the Northern Japanese Alps in Toyama Prefecture, Japan, in July to October, 2015–2018. DNA metabarcoding us...
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crplos:10.1371/journal.pone.0252632 2024-05-19T07:39:45+00:00 Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding Fujii, Taichi Ueno, Kaoru Shirako, Tomoyasu Nakamura, Masatoshi Minami, Motoyasu Šiler, Branislav T. JSPS Grant in Aid for Scientific Research Chubu University Grant DAIKO FOUNDATION 2022 http://dx.doi.org/10.1371/journal.pone.0252632 https://dx.plos.org/10.1371/journal.pone.0252632 en eng Public Library of Science (PLoS) http://creativecommons.org/licenses/by/4.0/ PLOS ONE volume 17, issue 3, page e0252632 ISSN 1932-6203 journal-article 2022 crplos https://doi.org/10.1371/journal.pone.0252632 2024-05-01T07:06:37Z DNA metabarcoding was employed to identify plant-derived food resources for the Japanese rock ptarmigan ( Lagopus muta japonica ), which is registered as a natural living monument in Japan, in the Northern Japanese Alps in Toyama Prefecture, Japan, in July to October, 2015–2018. DNA metabarcoding using high-throughput sequencing (HTS) of rbcL and ITS2 sequences from alpine plants found in ptarmigan fecal samples collected in the study area. The obtained sequences were analyzed using a combination of a constructed local database and the National Center for Biotechnology Information (NCBI) database, revealed that a total of 53 plant taxa were food plant resources for ptarmigans. Of these plant taxa, 49 could be assigned to species (92.5%), three to genus (5.7%), and one to family (1.9%). Of the 23 plant families identified from the 105 fecal samples collected, the dominant families throughout all collection periods were Ericaceae (99.0% of 105 fecal samples), followed by Rosaceae (42.9%), Apiaceae (35.2%), and Poaceae (21.0%). In all of the fecal samples examined, the most frequently encountered plant species were Vaccinium ovalifolium var. ovalifolium (69.5%), followed by Empetrum nigrum var. japonicum (68.6%), Kalmia procumbens (42.9%), Tilingia ajanensis (34.3%) and V . uliginosum var. japonicum (34.3%). A rarefaction analysis for each collection period in the study revealed that the food plant resources found in the study area ranged from a minimum of 87.0% in July to a maximum of 97.5% in September, and that 96.4% of the food plant taxa were found throughout the study period. The findings showed that DNA metabarcoding using HTS to construct a local database of rbcL and ITS2 sequences in conjunction with rbcL and ITS2 sequences deposited at the NCBI, as well as rarefaction analysis, are well suited to identifying the dominant food plants in the diet of Japanese rock ptarmigans. In the windswept alpine dwarf shrub community found in the study area, dominant taxa in the Ericaceae family were the major food plant ... Article in Journal/Newspaper Empetrum nigrum Lagopus muta rock ptarmigan PLOS PLOS ONE 17 3 e0252632 |
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English |
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DNA metabarcoding was employed to identify plant-derived food resources for the Japanese rock ptarmigan ( Lagopus muta japonica ), which is registered as a natural living monument in Japan, in the Northern Japanese Alps in Toyama Prefecture, Japan, in July to October, 2015–2018. DNA metabarcoding using high-throughput sequencing (HTS) of rbcL and ITS2 sequences from alpine plants found in ptarmigan fecal samples collected in the study area. The obtained sequences were analyzed using a combination of a constructed local database and the National Center for Biotechnology Information (NCBI) database, revealed that a total of 53 plant taxa were food plant resources for ptarmigans. Of these plant taxa, 49 could be assigned to species (92.5%), three to genus (5.7%), and one to family (1.9%). Of the 23 plant families identified from the 105 fecal samples collected, the dominant families throughout all collection periods were Ericaceae (99.0% of 105 fecal samples), followed by Rosaceae (42.9%), Apiaceae (35.2%), and Poaceae (21.0%). In all of the fecal samples examined, the most frequently encountered plant species were Vaccinium ovalifolium var. ovalifolium (69.5%), followed by Empetrum nigrum var. japonicum (68.6%), Kalmia procumbens (42.9%), Tilingia ajanensis (34.3%) and V . uliginosum var. japonicum (34.3%). A rarefaction analysis for each collection period in the study revealed that the food plant resources found in the study area ranged from a minimum of 87.0% in July to a maximum of 97.5% in September, and that 96.4% of the food plant taxa were found throughout the study period. The findings showed that DNA metabarcoding using HTS to construct a local database of rbcL and ITS2 sequences in conjunction with rbcL and ITS2 sequences deposited at the NCBI, as well as rarefaction analysis, are well suited to identifying the dominant food plants in the diet of Japanese rock ptarmigans. In the windswept alpine dwarf shrub community found in the study area, dominant taxa in the Ericaceae family were the major food plant ... |
author2 |
Šiler, Branislav T. JSPS Grant in Aid for Scientific Research Chubu University Grant DAIKO FOUNDATION |
format |
Article in Journal/Newspaper |
author |
Fujii, Taichi Ueno, Kaoru Shirako, Tomoyasu Nakamura, Masatoshi Minami, Motoyasu |
spellingShingle |
Fujii, Taichi Ueno, Kaoru Shirako, Tomoyasu Nakamura, Masatoshi Minami, Motoyasu Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding |
author_facet |
Fujii, Taichi Ueno, Kaoru Shirako, Tomoyasu Nakamura, Masatoshi Minami, Motoyasu |
author_sort |
Fujii, Taichi |
title |
Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding |
title_short |
Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding |
title_full |
Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding |
title_fullStr |
Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding |
title_full_unstemmed |
Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding |
title_sort |
identification of lagopus muta japonica food plant resources in the northern japan alps using dna metabarcoding |
publisher |
Public Library of Science (PLoS) |
publishDate |
2022 |
url |
http://dx.doi.org/10.1371/journal.pone.0252632 https://dx.plos.org/10.1371/journal.pone.0252632 |
genre |
Empetrum nigrum Lagopus muta rock ptarmigan |
genre_facet |
Empetrum nigrum Lagopus muta rock ptarmigan |
op_source |
PLOS ONE volume 17, issue 3, page e0252632 ISSN 1932-6203 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1371/journal.pone.0252632 |
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PLOS ONE |
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17 |
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3 |
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e0252632 |
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