Genome‐ and transcriptome‐assisted development of nuclear insertion/deletion markers for C alanus species ( C opepoda: C alanoida) identification
Abstract Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear mar...
Saved in:
| Published in | Molecular ecology resources Vol. 14; no. 5; pp. 1072 - 1079 |
|---|---|
| Main Authors | , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
01.09.2014
|
| Online Access | Get full text |
Cover
Loading…
| Abstract | Abstract
Copepods of the genus
Calanus
are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among
Calanus
species highlights the need for diagnostic nuclear markers to efficiently identify parental species and hybrids. Using next‐generation sequencing analysis of both the genome and transcriptome from two sibling species,
C
alanus finmarchicus
and
C
alanus glacialis
, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species‐specific amplicon length. Furthermore, most of the markers were successfully amplified in other
C
alanus
species, allowing the molecular identification of
C
alanus helgolandicus
,
C
alanus hyperboreus
and
C
alanus marshallae
. |
|---|---|
| AbstractList | Abstract
Copepods of the genus
Calanus
are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among
Calanus
species highlights the need for diagnostic nuclear markers to efficiently identify parental species and hybrids. Using next‐generation sequencing analysis of both the genome and transcriptome from two sibling species,
C
alanus finmarchicus
and
C
alanus glacialis
, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species‐specific amplicon length. Furthermore, most of the markers were successfully amplified in other
C
alanus
species, allowing the molecular identification of
C
alanus helgolandicus
,
C
alanus hyperboreus
and
C
alanus marshallae
. |
| Author | Hoarau, G. Castellani, C. Kollias, S. Lindeque, P. Poortvliet, M. Smolina, I. Nielsen, T. G. Blanco‐Bercial, L. Møller, E. F. |
| Author_xml | – sequence: 1 givenname: I. surname: Smolina fullname: Smolina, I. organization: Faculty of Biosciences and Aquaculture University of Nordland 8049 Bodø Norway – sequence: 2 givenname: S. surname: Kollias fullname: Kollias, S. organization: Faculty of Biosciences and Aquaculture University of Nordland 8049 Bodø Norway – sequence: 3 givenname: M. surname: Poortvliet fullname: Poortvliet, M. organization: Faculty of Biosciences and Aquaculture University of Nordland 8049 Bodø Norway – sequence: 4 givenname: T. G. surname: Nielsen fullname: Nielsen, T. G. organization: National Institute of Aquatic Resources Section of Oceanography and Climate Technical University of Denmark Kavalergården 6 2920 Charlottenlund Denmark, Greenland Climate Research Centre Greenland Institute of Natural Resources Nuuk Greenland – sequence: 5 givenname: P. surname: Lindeque fullname: Lindeque, P. organization: Plymouth Marine Laboratory Prospect Place The Hoe Plymouth PL1 3DH UK – sequence: 6 givenname: C. surname: Castellani fullname: Castellani, C. organization: Sir Alister Hardy Foundation for Ocean Sciences Citadel Hill Plymouth UK – sequence: 7 givenname: E. F. surname: Møller fullname: Møller, E. F. organization: Department of Bioscience Aarhus University Frederiksborgvej 399 4000 Roskilde Denmark – sequence: 8 givenname: L. orcidid: 0000-0003-0658-7183 surname: Blanco‐Bercial fullname: Blanco‐Bercial, L. organization: Department of Marine Sciences University of Connecticut 1080 Shennecossett Rd Groton 06340 CT USA – sequence: 9 givenname: G. surname: Hoarau fullname: Hoarau, G. organization: Faculty of Biosciences and Aquaculture University of Nordland 8049 Bodø Norway |
| BookMark | eNo9kLFOwzAQhi1UJNrCzOoRhrR27MQxG6qgIFVi6cAWXeKLZEjtyE6R2HgEFl6QJyGhVW-5X99Jv07fjEycd0jINWcLPsySqyxLmNbFgqep5GdkeiKTUy5eL8gsxjfGcqaVnJKfNTq_w9-vbwrO0D6Ai3WwXX-AEKONPRpq8ANb3-3Q9dQ31O3rFiFQ6yKG3nq3NNjiGOgOwjuGSBsf6IpCC24faeywthjpzYB8h503cHe8emvgllozNNvG1jCWXJLzBtqIV8c9J9vHh-3qKdm8rJ9X95ukLnKeFJXkygjW5FKLDCopqkJp2egcC1axSueMp5mUEkHoistUGc5knSslQYBgYk6Wh9o6-BgDNmUX7PD_Z8lZOUotR23lqLD8lyr-AHs-by4 |
| CitedBy_id | crossref_primary_10_1002_lno_11583 crossref_primary_10_1093_plankt_fbac070 crossref_primary_10_1098_rsbl_2017_0588 crossref_primary_10_1038_s41598_020_79165_6 crossref_primary_10_1007_s00227_023_04309_x crossref_primary_10_1002_lno_11931 crossref_primary_10_1080_23802359_2017_1361357 crossref_primary_10_1002_ece3_1330 crossref_primary_10_1002_lom3_10240 crossref_primary_10_1016_j_margen_2022_100981 crossref_primary_10_1002_ece3_6997 crossref_primary_10_1007_s12526_017_0774_4 crossref_primary_10_3354_meps13820 crossref_primary_10_1007_s00300_018_2294_5 crossref_primary_10_3354_meps11398 crossref_primary_10_3389_fmars_2022_877904 crossref_primary_10_1098_rstb_2019_0446 crossref_primary_10_3354_meps14307 crossref_primary_10_1002_lno_11725 crossref_primary_10_3389_fmars_2021_609480 crossref_primary_10_1007_s00227_014_2419_5 crossref_primary_10_1038_s41597_020_00751_4 crossref_primary_10_3389_fmars_2022_877910 crossref_primary_10_1038_s41598_023_40131_7 |
| Cites_doi | 10.1093/plankt/25.1.1 10.1007/s002270050446 10.1038/nrg2626 10.1093/icesjms/fst147 10.1016/j.dsr2.2007.08.006 10.1080/17451000802512267 10.1007/BF00349301 10.1371/journal.pone.0049794 10.1186/1471-2164-13-341 10.1016/S0305-0491(00)00233-9 10.1007/s00227‐014‐2419‐5 10.1016/S0079-6611(03)00111-3 10.1007/978-3-540-48514-8_9 10.1111/j.1471-8286.2007.01889.x 10.1093/bioinformatics/btm091 10.1111/j.1365-2486.2010.02311.x 10.1093/plankt/fbi115 10.1007/s10059-013-2347-0 10.1016/j.pocean.2012.10.004 10.1111/j.1461-0248.2006.00889.x 10.1007/s11033-013-2521-7 10.3390/ijms14034793 10.1093/plankt/fbm068 10.3732/ajb.1200077 10.1111/1755-0998.12075 10.1186/1471-2156-9-8 10.1016/j.aquaculture.2004.05.027 10.1007/BF02772677 10.1046/j.1365-2664.2003.00841.x 10.1093/nar/gks596 10.1126/science.1071329 10.4319/lo.2012.57.4.1057 10.2144/000113608 10.1093/plankt/fbr072 10.1016/j.dsr2.2008.05.024 10.1007/s00300-012-1202-7 10.1111/j.1365-294X.2004.02396.x 10.1111/j.0014-3820.2004.tb01606.x 10.1111/j.1755-0998.2010.02969.x 10.1007/s002270100548 10.1007/BF00297174 10.1016/j.pocean.2012.11.002 |
| ContentType | Journal Article |
| DBID | AAYXX CITATION |
| DOI | 10.1111/1755-0998.12241 |
| DatabaseName | CrossRef |
| DatabaseTitle | CrossRef |
| DatabaseTitleList | CrossRef |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Ecology |
| EISSN | 1755-0998 |
| EndPage | 1079 |
| ExternalDocumentID | 10_1111_1755_0998_12241 |
| GroupedDBID | --- .3N .GA .Y3 05W 0R~ 10A 123 1OC 31~ 33P 36B 3SF 4.4 50Y 50Z 51W 51X 52M 52N 52O 52P 52S 52T 52U 52W 52X 53G 5HH 5LA 5VS 702 7PT 8-0 8-1 8-3 8-4 8-5 8UM 930 A03 AAESR AAEVG AAHBH AAHHS AANLZ AAONW AASGY AAXRX AAYXX AAZKR ABCQN ABCUV ABEML ABJNI ABPVW ACAHQ ACBWZ ACCFJ ACCZN ACGFO ACGFS ACNCT ACPOU ACPRK ACSCC ACXBN ACXQS ADBBV ADEOM ADIZJ ADKYN ADMGS ADOZA ADXAS ADZMN AEEZP AEGXH AEIGN AEIMD AENEX AEQDE AEUQT AEUYR AFBPY AFFPM AFGKR AFPWT AFRAH AFZJQ AHBTC AIAGR AITYG AIURR AIWBW AJBDE AJXKR ALAGY ALMA_UNASSIGNED_HOLDINGS ALUQN AMBMR AMYDB ATUGU AUFTA AZBYB AZFZN AZVAB BAFTC BDRZF BFHJK BHBCM BMNLL BMXJE BNHUX BROTX BRXPI BY8 CAG CITATION COF CS3 D-E D-F DCZOG DPXWK DR2 DRFUL DRSTM EBS ECGQY EJD ESX F00 F01 F04 FEDTE G-S G.N GODZA H.T H.X HF~ HGLYW HVGLF HZI HZ~ IHE IX1 J0M K48 LATKE LC2 LC3 LEEKS LH4 LITHE LOXES LP6 LP7 LUTES LW6 LYRES MEWTI MK4 MRFUL MRSTM MSFUL MSSTM MXFUL MXSTM N04 N05 N9A NF~ O66 O9- OIG P2P P2W P2X P4D Q.N Q11 QB0 R.K ROL RX1 SUPJJ UB1 V8K W8V W99 WBKPD WIH WIK WNSPC WOHZO WQJ WRC WXSBR WYISQ XG1 ~IA ~WT |
| ID | FETCH-LOGICAL-c861-8b417d30f64935ab43b8794f96e80b0b960125444ea39b1427d104c6774a3a303 |
| ISSN | 1755-098X |
| IngestDate | Fri Aug 23 03:54:55 EDT 2024 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 5 |
| Language | English |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-c861-8b417d30f64935ab43b8794f96e80b0b960125444ea39b1427d104c6774a3a303 |
| ORCID | 0000-0003-0658-7183 |
| PageCount | 8 |
| ParticipantIDs | crossref_primary_10_1111_1755_0998_12241 |
| PublicationCentury | 2000 |
| PublicationDate | 2014-09-00 |
| PublicationDateYYYYMMDD | 2014-09-01 |
| PublicationDate_xml | – month: 09 year: 2014 text: 2014-09-00 |
| PublicationDecade | 2010 |
| PublicationTitle | Molecular ecology resources |
| PublicationYear | 2014 |
| References | Hirche H (e_1_2_6_18_1) 1994; 14 e_1_2_6_32_1 e_1_2_6_10_1 e_1_2_6_31_1 e_1_2_6_30_1 e_1_2_6_19_1 e_1_2_6_13_1 e_1_2_6_36_1 e_1_2_6_14_1 e_1_2_6_35_1 e_1_2_6_11_1 e_1_2_6_34_1 e_1_2_6_12_1 e_1_2_6_33_1 e_1_2_6_17_1 e_1_2_6_39_1 e_1_2_6_15_1 e_1_2_6_38_1 e_1_2_6_16_1 e_1_2_6_37_1 e_1_2_6_42_1 e_1_2_6_43_1 e_1_2_6_21_1 e_1_2_6_20_1 e_1_2_6_41_1 e_1_2_6_40_1 e_1_2_6_9_1 e_1_2_6_8_1 e_1_2_6_5_1 e_1_2_6_4_1 e_1_2_6_7_1 e_1_2_6_6_1 e_1_2_6_25_1 e_1_2_6_24_1 e_1_2_6_3_1 e_1_2_6_23_1 e_1_2_6_2_1 e_1_2_6_22_1 e_1_2_6_29_1 e_1_2_6_44_1 e_1_2_6_28_1 e_1_2_6_27_1 e_1_2_6_26_1 |
| References_xml | – ident: e_1_2_6_21_1 doi: 10.1093/plankt/25.1.1 – ident: e_1_2_6_22_1 doi: 10.1007/s002270050446 – ident: e_1_2_6_27_1 doi: 10.1038/nrg2626 – ident: e_1_2_6_8_1 doi: 10.1093/icesjms/fst147 – ident: e_1_2_6_17_1 doi: 10.1016/j.dsr2.2007.08.006 – ident: e_1_2_6_13_1 doi: 10.1080/17451000802512267 – ident: e_1_2_6_5_1 doi: 10.1007/BF00349301 – ident: e_1_2_6_28_1 doi: 10.1371/journal.pone.0049794 – ident: e_1_2_6_39_1 doi: 10.1186/1471-2164-13-341 – ident: e_1_2_6_6_1 doi: 10.1016/S0305-0491(00)00233-9 – ident: e_1_2_6_30_1 doi: 10.1007/s00227‐014‐2419‐5 – ident: e_1_2_6_15_1 doi: 10.1016/S0079-6611(03)00111-3 – ident: e_1_2_6_12_1 doi: 10.1007/978-3-540-48514-8_9 – ident: e_1_2_6_38_1 doi: 10.1111/j.1471-8286.2007.01889.x – ident: e_1_2_6_20_1 doi: 10.1093/bioinformatics/btm091 – ident: e_1_2_6_44_1 doi: 10.1111/j.1365-2486.2010.02311.x – ident: e_1_2_6_23_1 doi: 10.1093/plankt/fbi115 – ident: e_1_2_6_7_1 doi: 10.1007/s10059-013-2347-0 – ident: e_1_2_6_26_1 doi: 10.1016/j.pocean.2012.10.004 – ident: e_1_2_6_40_1 doi: 10.1111/j.1461-0248.2006.00889.x – ident: e_1_2_6_34_1 doi: 10.1007/s11033-013-2521-7 – ident: e_1_2_6_19_1 doi: 10.3390/ijms14034793 – ident: e_1_2_6_10_1 doi: 10.1093/plankt/fbm068 – ident: e_1_2_6_29_1 doi: 10.3732/ajb.1200077 – ident: e_1_2_6_31_1 doi: 10.1111/1755-0998.12075 – ident: e_1_2_6_43_1 doi: 10.1186/1471-2156-9-8 – ident: e_1_2_6_24_1 doi: 10.1016/j.aquaculture.2004.05.027 – ident: e_1_2_6_9_1 doi: 10.1007/BF02772677 – ident: e_1_2_6_2_1 doi: 10.1046/j.1365-2664.2003.00841.x – ident: e_1_2_6_42_1 doi: 10.1093/nar/gks596 – ident: e_1_2_6_3_1 doi: 10.1126/science.1071329 – ident: e_1_2_6_33_1 doi: 10.4319/lo.2012.57.4.1057 – ident: e_1_2_6_35_1 doi: 10.2144/000113608 – ident: e_1_2_6_32_1 doi: 10.1093/plankt/fbr072 – ident: e_1_2_6_41_1 doi: 10.1016/j.dsr2.2008.05.024 – ident: e_1_2_6_14_1 doi: 10.1007/s00300-012-1202-7 – volume: 14 start-page: 491 year: 1994 ident: e_1_2_6_18_1 article-title: The northeast water Polynya, Greenland Sea. 3. Mesozooplankton and macrozooplankton distribution and production of dominant herbivorous copepods during spring publication-title: Polar Biology contributor: fullname: Hirche H – ident: e_1_2_6_37_1 doi: 10.1111/j.1365-294X.2004.02396.x – ident: e_1_2_6_36_1 doi: 10.1111/j.0014-3820.2004.tb01606.x – ident: e_1_2_6_11_1 doi: 10.1111/j.1755-0998.2010.02969.x – ident: e_1_2_6_16_1 doi: 10.1007/s002270100548 – ident: e_1_2_6_25_1 doi: 10.1007/BF00297174 – ident: e_1_2_6_4_1 doi: 10.1016/j.pocean.2012.11.002 |
| SSID | ssj0060974 |
| Score | 2.1249094 |
| Snippet | Abstract
Copepods of the genus
Calanus
are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species... |
| SourceID | crossref |
| SourceType | Aggregation Database |
| StartPage | 1072 |
| Title | Genome‐ and transcriptome‐assisted development of nuclear insertion/deletion markers for C alanus species ( C opepoda: C alanoida) identification |
| Volume | 14 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9NAEF6FVkhcqvISpQXtgUORZePHemNzQ1FpVYkK0SD1Fu3aXimH2lVIeuDET-iF38adX8LMvrKtALW9WPHYGiWZT_Owv5kh5E0jOcSNpo5lK4qYScZjqaSKxwyLgUwokWJz8qcTfvSVHZ-VZ6PRr4C1tFrKpPn-176S-1gVZGBX7JK9g2W9UhDAZ7AvHMHCcLyVjQ-7HrecO76CYUNi8NGuILwEKTLas3VNUo4C0OM4Y6Ep6Uiw1nkgrsbRqDhH6s5CD2yIJhFyIFffImzNnJtntSAcLiCBb_V-H3PHMIezvI7mraUhrS3v9ka5hbxR15gBUAv7CsGn96fnepWQ9l-JDwk4Pty0n5164ecByodLyKMN68TLT-YY883m5SQ6TMKHGxnz7C3nj8dlCTK9fRjCVSgzy6u9E2cBWMvAI0N5mwfRHU7r_0QOrzvRbxzXQdIRA27ETs9odLUUKpihgplW8IBs5uABNX_gi59rxtNajwf3v87OnEKK2Y1vEKRLQd4z3SZbtmChHwz6HpNR1z8hDw-M6Z6SnwaDv39cUUAfvYY-EDrc0QB3dFDU4o563L1zqKMWdRRQRyfUoI5a1NF9EFnMvbdXEXFv6XW8PSPTjwfTyVFsV33ETcWzuJIsG7dFqjiri1JIVsgKAoWqeVelMpVQZmc4S491oqjxseW4zVLWcKhdRCEgC3tONvqh714QykUDOXybpkpAgpbLqs27jINiVYtKyWyH7Ls_dHZhBrrM_mG8l7e_dZc8WsN3j2wsF6vuFWSrS_laW_4PlGWTgg |
| link.rule.ids | 315,783,787,27936,27937 |
| linkProvider | Wiley-Blackwell |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Genome%E2%80%90+and+transcriptome%E2%80%90assisted+development+of+nuclear+insertion%2Fdeletion+markers+for+C+alanus+species+%28+C+opepoda%3A+C+alanoida%29+identification&rft.jtitle=Molecular+ecology+resources&rft.au=Smolina%2C+I.&rft.au=Kollias%2C+S.&rft.au=Poortvliet%2C+M.&rft.au=Nielsen%2C+T.+G.&rft.date=2014-09-01&rft.issn=1755-098X&rft.eissn=1755-0998&rft.volume=14&rft.issue=5&rft.spage=1072&rft.epage=1079&rft_id=info:doi/10.1111%2F1755-0998.12241&rft.externalDBID=n%2Fa&rft.externalDocID=10_1111_1755_0998_12241 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1755-098X&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1755-098X&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1755-098X&client=summon |