Development of species-specific primers with potential for amplifying eDNA from imperilled freshwater unionid mussels

被引:11
作者
Cho, Anna [1 ]
Morris, Todd [2 ]
Wilson, Chris [3 ]
Freeland, Joanna [1 ]
机构
[1] Trent Univ, Dept Biol, Peterborough, ON, Canada
[2] Canada Ctr Inland Waters, Dept Fisheries & Oceans, Burlington, ON, Canada
[3] Trent Univ, Ontario Minist Resources & Forestry, Peterborough, ON, Canada
基金
加拿大自然科学与工程研究理事会;
关键词
eDNA; cytochrome oxidase I; mtDNA; unionidae; freshwater mussels; ENVIRONMENTAL DNA; UNIONOIDA; NORTH;
D O I
10.1139/gen-2015-0196
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Environmental DNA (eDNA) is emerging as a potentially powerful tool for inferring species' presence, and hence occupancy, from DNA that is shed into environmental samples such as water. Although eDNA screening has been used to detect DNA from a variety of taxonomic groups, it has not yet been used to identify DNA from species with numerous potentially sympatric confamilial species, a situation that may preclude the development of species-specific markers. There are 41 native freshwater mussel species (Unionidae) in Ontario, Canada. Many of these are potentially sympatric, and 14 species have been formally assessed as endangered, threatened, or special concern. We investigated whether there was sufficient variation within the cytochrome oxidase region (COI) to develop species-specific eDNA markers for at-risk unionids. We developed 32 COI markers for eight unionid species, and tested each of these on the target species plus 29 potentially sympatric unionid taxa. Six of these markers amplified DNA only from the intended target species. We then extracted and amplified mussel eDNA from rearing-tank water samples. We conclude that despite high species diversity, it should be possible to develop eDNA COI markers and screen water samples for habitat occupancy by unionid mussels.
引用
收藏
页码:1141 / 1149
页数:9
相关论文
共 30 条
[1]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[2]   Improving efficiency and reliability of environmental DNA analysis for silver carp [J].
Amberg, Jon J. ;
McCalla, S. Grace ;
Monroe, Emy ;
Lance, Richard ;
Baerwaldt, Kelly ;
Gaikowski, Mark P. .
JOURNAL OF GREAT LAKES RESEARCH, 2015, 41 (02) :367-373
[3]   ENDOBENTHIC AND EPIBENTHIC DISTRIBUTION OF THE UNIONID MOLLUSK ELLIPTIO-COMPLANATA [J].
AMYOT, JP ;
DOWNING, JA .
JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY, 1991, 10 (03) :280-285
[4]   A DNA-barcoding approach to identifying juvenile freshwater mussels (Bivalvia:Unionidae) recovered from naturally infested fishes [J].
Boyer, Sarah L. ;
Howe, Alexander A. ;
Juergens, Nathan W. ;
Hove, Mark C. .
JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY, 2011, 30 (01) :182-194
[5]   Combining species-specific COI primers with environmental DNA analysis for targeted detection of rare freshwater species [J].
Bronnenhuber, Jennifer E. ;
Wilson, Chris C. .
CONSERVATION GENETICS RESOURCES, 2013, 5 (04) :971-975
[6]   Identification of 'extinct' freshwater mussel species using DNA barcoding [J].
Campbell, David C. ;
Johnson, Paul D. ;
Williams, James D. ;
Rindsberg, Andrew K. ;
Serb, Jeanne M. ;
Small, Kory K. ;
Lydeard, Charles .
MOLECULAR ECOLOGY RESOURCES, 2008, 8 (04) :711-724
[7]  
COSEWIC, 2014, CAN WILDL SPEC RISK
[8]   Distribution of Pfiesteria piscicida cyst populations in sediments of the Delaware Inland Bays, USA [J].
Coyne, Kathryn J. ;
Hare, Clinton E. ;
Popels, Linda C. ;
Hutchins, David A. ;
Cary, S. Craig .
HARMFUL ALGAE, 2006, 5 (04) :363-373
[9]   Cryptic lineages and hybridization in freshwater mussels of the genus Pyganodon (Unionidae) in northeastern North America [J].
Cyr, Frederic ;
Paquet, Annie ;
Martel, Andre L. ;
Angers, Bernard .
CANADIAN JOURNAL OF ZOOLOGY, 2007, 85 (12) :1216-1227
[10]   Development and Validation of Environmental DNA (eDNA) Markers for Detection of Freshwater Turtles [J].
Davy, Christina M. ;
Kidd, Anne G. ;
Wilson, Chris C. .
PLOS ONE, 2015, 10 (07)