A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding

The diversity of macroinvertebrates, the structure of their communities in Bolshiye Koty Bay (Lake Baikal) was studied by a DNA metabarcoding approach using an Illumina MiSeq system. Internal primer mlCOIintF in combination with jgHCO2198 of the Folmer fragment of the COI gene were used for macroinv...

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Main Authors: L. S. Kravtsova, T. E. Peretolchina, T. I. Triboy, I. A. Nebesnykh, A. E. Tupikin, M. R. Kabilov, Л. С. Кравцова, Т. Е. Перетолчина, Т. И. Трибой, И. А. Небесных, А. Е. Тупикин, М. Р. Кабилов
Other Authors: The work was supported by the project of the Russian Foundation for Basic Research No. 19-05-00398_a. Collection and analysis of samples was partially carried out within the state-funded project conducted by LIN SB RAS No. 121032300196-8, bioinformatics analysis was partially supported by the state-funded project conducted by LIN SB RAS No. 121031300042-1
Format: Article in Journal/Newspaper
Language:English
Published: Institute of Cytology and Genetics of Siberian Branch of the RAS 2023
Subjects:
Байкал
diversity
DNA metabarcoding
COI
high-throughput sequencing technologies
Lake Baikal
разнообразие
ДНК метабаркодинг
СОI
высокопроизводительное секвенирование
Bay Lake
Folmer
Arctic
Online Access:https://vavilov.elpub.ru/jour/article/view/3941
https://doi.org/10.18699/VJGB-23-80
id ftjvavilov:oai:oai.vavilov.elpub.ru:article/3941
record_format openpolar
institution Open Polar
collection Vavilov Journal of Genetics and Breeding
op_collection_id ftjvavilov
language English
topic Байкал
diversity
DNA metabarcoding
COI
high-throughput sequencing technologies
Lake Baikal
разнообразие
ДНК метабаркодинг
СОI
высокопроизводительное секвенирование
spellingShingle Байкал
diversity
DNA metabarcoding
COI
high-throughput sequencing technologies
Lake Baikal
разнообразие
ДНК метабаркодинг
СОI
высокопроизводительное секвенирование
L. S. Kravtsova
T. E. Peretolchina
T. I. Triboy
I. A. Nebesnykh
A. E. Tupikin
M. R. Kabilov
Л. С. Кравцова
Т. Е. Перетолчина
Т. И. Трибой
И. А. Небесных
А. Е. Тупикин
М. Р. Кабилов
A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding
topic_facet Байкал
diversity
DNA metabarcoding
COI
high-throughput sequencing technologies
Lake Baikal
разнообразие
ДНК метабаркодинг
СОI
высокопроизводительное секвенирование
description The diversity of macroinvertebrates, the structure of their communities in Bolshiye Koty Bay (Lake Baikal) was studied by a DNA metabarcoding approach using an Illumina MiSeq system. Internal primer mlCOIintF in combination with jgHCO2198 of the Folmer fragment of the COI gene were used for macroinvertebrate metabarcoding. A total of 118009 reads of the COI gene fragment (at least 313 bp in length) were obtained. The correlation of the Spearman coefficient (S = 0.6, p < 0.05) with the abundance of macroinvertebrates in the samples before DNA extraction showed that the number of reads can serve as an indirect characteristic of the abundance of a species (operational taxonomic unit, OTU). 115 OTUs belonging to the higher taxa of macroinvertebrates were identified: Porifera, 1; Platyhelminthes, 3; Annelida, 38; Arthropoda, 55; Mollusca, 18. At a high level of resolution (with homology with GenBank reference sequences ≥ 95 %, coverage ≥ 90 %), 46 taxa of macroinvertebrates comprising three communities were registered: one dominated by molluscs (Choanomphalus conf. maacki) and two dominated by chironomids (Orthocladius grega rius Linev., Sergentia baicalensis Tshern.). Communities are characterized by low species diversity according to Shannon (from 0.7 to 1.2 bits), high concentration of dominance according to Simpson (from 0.5 to 0.7) and low evenness according to Pielou (from 0.3 to 0.4). Dominants and subdominants in the communities account for 91 to 96 % of COI gene fragment reads. The spatial distribution of the dominant species identified in the communities is influenced by the geomorphological features of the bottom and the composition of sediments in the area studied. The approach proposed for studying the structure of macroinvertebrate communities based on DNA metabarcoding and next generation sequencing can be recommended for express assessment of the state of aquatic ecosystems in the monitoring. Приводятся сведения о разнообразии макробеспозвоночных животных, структуре их сообществ в бухте Большие ...
author2 The work was supported by the project of the Russian Foundation for Basic Research No. 19-05-00398_a. Collection and analysis of samples was partially carried out within the state-funded project conducted by LIN SB RAS No. 121032300196-8
bioinformatics analysis was partially supported by the state-funded project conducted by LIN SB RAS No. 121031300042-1
format Article in Journal/Newspaper
author L. S. Kravtsova
T. E. Peretolchina
T. I. Triboy
I. A. Nebesnykh
A. E. Tupikin
M. R. Kabilov
Л. С. Кравцова
Т. Е. Перетолчина
Т. И. Трибой
И. А. Небесных
А. Е. Тупикин
М. Р. Кабилов
author_facet L. S. Kravtsova
T. E. Peretolchina
T. I. Triboy
I. A. Nebesnykh
A. E. Tupikin
M. R. Kabilov
Л. С. Кравцова
Т. Е. Перетолчина
Т. И. Трибой
И. А. Небесных
А. Е. Тупикин
М. Р. Кабилов
author_sort L. S. Kravtsova
title A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding
title_short A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding
title_full A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding
title_fullStr A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding
title_full_unstemmed A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding
title_sort study of macroinvertebrate communities in bolshiye koty bay of lake baikal using dna metabarcoding
publisher Institute of Cytology and Genetics of Siberian Branch of the RAS
publishDate 2023
url https://vavilov.elpub.ru/jour/article/view/3941
https://doi.org/10.18699/VJGB-23-80
long_lat ENVELOPE(-100.964,-100.964,56.759,56.759)
ENVELOPE(12.601,12.601,64.648,64.648)
geographic Bay Lake
Folmer
geographic_facet Bay Lake
Folmer
genre Arctic
genre_facet Arctic
op_source Vavilov Journal of Genetics and Breeding; Том 27, № 6 (2023); 694-702
Вавиловский журнал генетики и селекции; Том 27, № 6 (2023); 694-702
2500-3259
op_relation https://vavilov.elpub.ru/jour/article/view/3941/1755
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https://vavilov.elpub.ru/jour/article/view/3941
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op_doi https://doi.org/10.18699/VJGB-23-8010.3391/ai.2008.3.2.1210.1371/journal.pone.009052910.2307/146832210.1111/j.1365­2486.2007.01375.x10.1111/j.13652427.2007.0110.1007/s00442­0060542­910.1371/journal.pone.001371610.2307/122112210.1093/bioinformatics/btq4611
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spelling ftjvavilov:oai:oai.vavilov.elpub.ru:article/3941 2023-12-03T10:15:15+01:00 A study of macroinvertebrate communities in Bolshiye Koty Bay of Lake Baikal using DNA metabarcoding Исследование сообществ макробеспозвоночных животных в бухте Большие Коты озера Байкал с использованием ДНК метабаркодинга L. S. Kravtsova T. E. Peretolchina T. I. Triboy I. A. Nebesnykh A. E. Tupikin M. R. Kabilov Л. С. Кравцова Т. Е. Перетолчина Т. И. Трибой И. А. Небесных А. Е. Тупикин М. Р. Кабилов The work was supported by the project of the Russian Foundation for Basic Research No. 19-05-00398_a. Collection and analysis of samples was partially carried out within the state-funded project conducted by LIN SB RAS No. 121032300196-8 bioinformatics analysis was partially supported by the state-funded project conducted by LIN SB RAS No. 121031300042-1 2023-11-02 application/pdf https://vavilov.elpub.ru/jour/article/view/3941 https://doi.org/10.18699/VJGB-23-80 eng eng Institute of Cytology and Genetics of Siberian Branch of the RAS https://vavilov.elpub.ru/jour/article/view/3941/1755 Arbačiauskas K., Semenchenko V., Grabovski M., Leuven R., Paunović M., Son M., Csanyi B., Gumuliauskaitè S., Konopacka A., Nehring S., van der Velde G., Vezhnovetz V., Panov V. Assessment of biocontamination of benthic macroinvertebrate communities in European inland waterways. Aquat. Invasions. 2008;3(2):211­230. DOI:10.3391/ai.2008.3.2.12. Aylagas E., Borja A., Rodríguez­Ezpeleta N. Environmental status assessment using DNA metabarcoding: towards a genetics based marine biotic index (gAMBI). 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DOI:10.1111/j.2041­-210X.2012.00198.x. https://vavilov.elpub.ru/jour/article/view/3941 doi:10.18699/VJGB-23-80 Authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access). 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Vavilov Journal of Genetics and Breeding; Том 27, № 6 (2023); 694-702 Вавиловский журнал генетики и селекции; Том 27, № 6 (2023); 694-702 2500-3259 Байкал diversity DNA metabarcoding COI high-throughput sequencing technologies Lake Baikal разнообразие ДНК метабаркодинг СОI высокопроизводительное секвенирование info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 2023 ftjvavilov https://doi.org/10.18699/VJGB-23-8010.3391/ai.2008.3.2.1210.1371/journal.pone.009052910.2307/146832210.1111/j.1365­2486.2007.01375.x10.1111/j.13652427.2007.0110.1007/s00442­0060542­910.1371/journal.pone.001371610.2307/122112210.1093/bioinformatics/btq4611 2023-11-07T18:15:22Z The diversity of macroinvertebrates, the structure of their communities in Bolshiye Koty Bay (Lake Baikal) was studied by a DNA metabarcoding approach using an Illumina MiSeq system. Internal primer mlCOIintF in combination with jgHCO2198 of the Folmer fragment of the COI gene were used for macroinvertebrate metabarcoding. A total of 118009 reads of the COI gene fragment (at least 313 bp in length) were obtained. The correlation of the Spearman coefficient (S = 0.6, p < 0.05) with the abundance of macroinvertebrates in the samples before DNA extraction showed that the number of reads can serve as an indirect characteristic of the abundance of a species (operational taxonomic unit, OTU). 115 OTUs belonging to the higher taxa of macroinvertebrates were identified: Porifera, 1; Platyhelminthes, 3; Annelida, 38; Arthropoda, 55; Mollusca, 18. At a high level of resolution (with homology with GenBank reference sequences ≥ 95 %, coverage ≥ 90 %), 46 taxa of macroinvertebrates comprising three communities were registered: one dominated by molluscs (Choanomphalus conf. maacki) and two dominated by chironomids (Orthocladius grega rius Linev., Sergentia baicalensis Tshern.). Communities are characterized by low species diversity according to Shannon (from 0.7 to 1.2 bits), high concentration of dominance according to Simpson (from 0.5 to 0.7) and low evenness according to Pielou (from 0.3 to 0.4). Dominants and subdominants in the communities account for 91 to 96 % of COI gene fragment reads. The spatial distribution of the dominant species identified in the communities is influenced by the geomorphological features of the bottom and the composition of sediments in the area studied. The approach proposed for studying the structure of macroinvertebrate communities based on DNA metabarcoding and next generation sequencing can be recommended for express assessment of the state of aquatic ecosystems in the monitoring. Приводятся сведения о разнообразии макробеспозвоночных животных, структуре их сообществ в бухте Большие ... Article in Journal/Newspaper Arctic Vavilov Journal of Genetics and Breeding Bay Lake ENVELOPE(-100.964,-100.964,56.759,56.759) Folmer ENVELOPE(12.601,12.601,64.648,64.648)

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