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 usin...
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ftdoajarticles:oai:doaj.org/article:71a7ff53d9ba46d1aaf1627b7b28fefb 2023-05-15T16:06:06+02:00 Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding. Taichi Fujii Kaoru Ueno Tomoyasu Shirako Masatoshi Nakamura Motoyasu Minami 2022-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0252632 https://doaj.org/article/71a7ff53d9ba46d1aaf1627b7b28fefb EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pone.0252632 https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0252632 https://doaj.org/article/71a7ff53d9ba46d1aaf1627b7b28fefb PLoS ONE, Vol 17, Iss 3, p e0252632 (2022) Medicine R Science Q article 2022 ftdoajarticles https://doi.org/10.1371/journal.pone.0252632 2022-12-31T00:49:27Z 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 s ... Article in Journal/Newspaper Empetrum nigrum Lagopus muta rock ptarmigan Directory of Open Access Journals: DOAJ Articles PLOS ONE 17 3 e0252632 |
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Medicine R Science Q Taichi Fujii Kaoru Ueno Tomoyasu Shirako Masatoshi Nakamura Motoyasu Minami Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding. |
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Medicine R Science Q |
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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 s ... |
format |
Article in Journal/Newspaper |
author |
Taichi Fujii Kaoru Ueno Tomoyasu Shirako Masatoshi Nakamura Motoyasu Minami |
author_facet |
Taichi Fujii Kaoru Ueno Tomoyasu Shirako Masatoshi Nakamura Motoyasu Minami |
author_sort |
Taichi Fujii |
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 |
https://doi.org/10.1371/journal.pone.0252632 https://doaj.org/article/71a7ff53d9ba46d1aaf1627b7b28fefb |
genre |
Empetrum nigrum Lagopus muta rock ptarmigan |
genre_facet |
Empetrum nigrum Lagopus muta rock ptarmigan |
op_source |
PLoS ONE, Vol 17, Iss 3, p e0252632 (2022) |
op_relation |
https://doi.org/10.1371/journal.pone.0252632 https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0252632 https://doaj.org/article/71a7ff53d9ba46d1aaf1627b7b28fefb |
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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