Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009–31 July 2009
Abstract
This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.
This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) genotyping primers to the Molecular Ecology Resources Database. Table 1 contains information on the focal species, the number of loci developed, any other species the loci were tested in and the accession numbers for the loci in both the Molecular Ecology Resources Database and GenBank. The authors responsible for each set of loci are listed in the final column. Table 2 presents information on SNP genotyping resources added to the MER database, and presents data on the focal species, the number of sequencing primer pairs, the observed number of SNPs, other species the loci were tested in, and the number of allele specific primers or probes. The MER database and Genbank accession numbers and the authors responsible are also listed. A full description of the development protocol for the loci presented here can be found on the Molecular Ecology Resources Database (http://tomato.biol.trinity.edu/). [Correction added on 23 December 2020, after first online publication: The Molecular Ecology Resources Database is no longer active. Readers may continue to access the microsatellite marker loci and Single Nucleotide Polymorphism (SNP) sequencing primers via the GenBank accession numbers listed in Table 1 and Table 2, respectively.]
| Species | No. of primers developed | Other species tested | MER database no. | GenBank Accession no. | Authors |
|---|---|---|---|---|---|
| Alcippe morrisonia morrisonia | 15 | n/a | 37424–3743137433–37438 | DQ858940–DQ858948, DQ858950–DQ858953, FJ716585,FJ716586 | Rong-Chien Lin, Chuan-Chin Huang, Shou-Hsien Li, Cheng-Te Yao |
| Bashania fangiana | 25 | n/a | 37708–37732 | GQ281353–GQ281377 | Xiangjiang Zhan, Fuwen Wei, Michael W. Bruford |
| Bashania fargesii | 17 | n/a | 37691–37707 | GQ267715–GQ267731 | Xiangjiang Zhan, Lifeng Zhu, Yongqiang Gao, Fuwen Wei, Michael W. Bruford |
| Chaetodon vagabundus | 15 | Chaetodon baronessa | 37840–37854 | GQ281437–GQ281451 | Michael L. Berumen, Elisabeth Rochel, Glenn R. Almany, Simon R. Thorrold, Geoffrey P. Jones, Morgan S. Pratchett, Craig Syms, Serge Planes |
| Colletes floralis | 9 | n/a | 37651–37659 | FJ041148- FJ041150, EF137744–EF137749 | Tomás E. Murray, Emily S. Davis Robert J. Paxton |
| Coluber constrictor flaviventris | 12 | n/a | 37758–37769 | GQ371177–GQ371188 | Page E. Klug, Kimberly A. With, Samantha M. Wisely |
| Coptotermes gestroi | 11 | n/a | 37779–37789 | GQ412733–GQ412743 | Beng-Keok Yeap, Ahmad Sofiman Othman, Chow-Yang Lee |
| Crotophaga major | 12 | n/a | 37778, 37790–37800 | GQ144418–GQ144429 | C. Riehl S. M. Bogdanowicz |
| Cyprinella lutrensis | 29 | n/a | 37521–37549 | GQ169555–GQ169567 | PJ Monnahan, Grose, MJ, Landis, JB, Wiley, EO, Hudman, SP |
| Danaus plexippus | 12 | n/a | 37855–37866 | FJ649210, FJ649212–FJ649223 | Helen M McCormick, Olivia A Patty, Richard J Wilkins |
| Fagus grandifolia | 10 | n/a | 37406–37415 | GO248754–GO248763 | T. Kubisiak, D. Carey, C. Burdine, J. Koch |
| Falco tinnunculus | 10 | F. columbarius, F. eleonorae, F. naumanni, F. peregrinus, F. subbuteo | 37310-37319 | FJ842386–FJ842395 | P.J.G. de Nova, J.A. Dávila, P. Vergara, J.A. Fargallo |
| Fletcherimyia fletcheri | 12 | n/a | 37679–37690 | GQ300842–GQ300853 | Gordana Rasic, Nusha Keyghobadi |
| Fusarium oxysporum f. sp. Lycopersici F. oxysporum f. sp. radicis-lycopersici | 27 | F. oxysporum f. sp. radicis-lycopersici, Fusarium oxysporum f. sp. Lycopersici | 38143–38117 | FJ882019–FJ882025 | C. H. Huang, L. E. Datnoff, L. R. Gale P. D. Roberts |
| Hydrilla verticillata | 8 | n/a | 37770–37777 | FJ907306–FJ907313 | Amber M. Grajczyk, W.A. Overholt, J.P. Cuda, S.D. Brown, D.A. Williams |
| Laterallus jamaicensis coturniculus | 19 | n/a | 37660–37678 | FJ997575–FJ997593 | Philippe Girard, Steven R. Beissinger |
| Leavenworthia alabamica | 12 | n/a | 37161–37172 | FJ860908, FJ860911–FJ860913, FJ860915, FJ860918, FJ860920, FJ860921, FJ860926, FJ860928, FJ860930, FJ860933 | Jeremiah W. Busch William J. Werner |
| Marmosops incanus | 15 | Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis and Monodelphis americana | 37173–37187 | FJ793928–FJ793937,AJ270097, AY386653, AY386655,AY386664,EF486346 | Simone Sommer, Anke Schmidt, Fabiano Fernandes, Thomas Püttker, Renata Pardini |
| Miichthys miiuy | 15 | n/a | 37801–37815 | FJ754034–FJ754048 | Ru Zhao, W.C.Liu, M. Liu, S. Y. Zhang, R X Wang |
| Nasua nasua | 15 | n/a | 37498–37512 | FJ914573–FJ914587 | Mirian Tieko Nunes Tsuchiya-Jerep, Cladinara Roberts Sarturi, Eduardo Eizirik |
| Noturus exilis | 25 | n/a | 37733–37757 | EU760354-EU760378 | SP Hudman, MJ Grose, JB Landis, EO Wiley |
| Odontesthes bonariensis | 17 | O. hatcheri | 37559–37575 | AB375407-AB375410,AB375412–AB375419,AB375421- AB375423,AB375425,AB375426,AB375428 | Eriko Koshimizu, Carlos Augusto Strüssmann, Eugenio Daniel Tejedor, Nobuaki Okamoto, Hideo Fukuda, Takashi Sakamoto |
| Quadrula fragosa | 9 | n/a | 37301- 37309 | FJ785629- FJ785636, FJ785639 | Amanda H. Hemmingsen, Kevin J. Roe, Jeanne M. Serb |
| Pinctada maxima | 16 | n/a | 37867–37882 | FJ607747–FJ607749, FJ607751,FJ607753–FJ607756, FJ607759–FJ607760,FJ607762, FJ607764,FJ607767, FJ607768, FJ607770,FJ607774 | Yan Wang, Na Liu, Yaohua Shi, Zhifeng Gu, Aimin Wang |
| Pseudaletia separata | 8 | n/a | 37292–37295,37297- 37300 | FJ896055–FJ896062 | Guo-Yan Zhang, Bao-Ping Zhai |
| Pseudoperonospora cubensis | 8 | n/a | 37513–37520 | FJ764997–FJ765004 | Loukas Kanetis, Xinwang Wang, Phillip A. Wadl, Katie Neufeld, Gerald Holmes, Peter S. Ojiambo, Marc A. Cubeta, Robert N. Trigiano |
| Podocarpus elatus | 9 | P. grayi, P. lawrencei, P. smithii. | 37550–37558 | FJ935795–FJ935803 | Rohan Mellick, Carolyn Porter, Maurizio Rossetto |
| Portunus trituberculatus | 17 | P. pelagicus | 37634–37650 | AF410872 FJ660922 FJ660923-FJ660929GE342670GE342703GE342919GE468057GE468081GE468082GE468121GE468190 | Zhaoxia Cui, Hongxia Wang, Feng Tan, Danhua Wu, Yuan Liu, Weisha Luan Qianqian Li |
| Rhagoletis cerasi | 13 | R. cingulata, R. completa, R. mendax, R. pomonella | 37816–37828 | GQ149111–GQ149123 | Wolfgang Arthofer, Susanne Krumböck, Hannes Schuler, Bilal Rasool, Markus Riegler, Kirsten Köppler, Christian Stauffer |
| Rhinella schneideri | 11 | n/a | 37594–37604 | FJ847928,FJ847930,FJ847931,FJ847933–FJ847940 | Maurício P. de Arruda, Eliana Morielle-Versute, Artur Silva, Maria Paula Cruz Schneider, Evonnildo C. Gonçalves |
| Sarracenia alata | 9 | n/a | 37585–37593 | GQ219717–GQ219725 | Margaret M. Koopman,Elizabeth Gallagher, Bryan C. Carstens |
| Skeletonema marinoi | 8 | n/a | 37621–37626,37628–37629 | EU855763,EU855769–EU855771,EU855775,EU855777,GQ250935, GQ250937 | Anna Godhe, Karolina Härnström, V. Saravanan, Christer Halldén, Iddya Karunasagar, Indrani Karunasagar |
| Sminthurus viridis | 14 | n/a | 37914–37927 | FJ971060–FJ971073 | John M. K. Roberts, Andrew R. Weeks |
| Syngnathus abaster | 9 | S. acus, S. typhle | 37576–37584 | GQ168557-GQ168565 | Onno E. Diekmann, Licinia Gouveia, Ester T. A. Serrão, Mirjam S. van de Vliet |
| Uroteuthis (Photololigo) chinensis | 12 | Uroteuthis (Photololigo) edulis Uroteuthis (Photololigo) duvauceli | 37954–37965 | FJ980010–FJ980021 | Y. W. Sin, K. H. Chu, Cynthia Yau |
| Verticillium dahliae | 22 | V. albo-atrum | 37063-37084 | FJ851470 FJ851474 FJ851480 FJ851483 GQ160902 FJ851489 FJ851494 FJ851499 FJ851504 FJ851508 FJ851511 FJ851514 FJ851519 FJ851521 GQ160903 FJ851523 FJ851527 FJ851530 FJ851534 FJ851538 FJ851541 FJ851545 | Z. K. Atallah, K. K. Maruthachalam, R. M. Davis, S. J. Klosterman, K. V. Subbarao |
| Wasmannia auropunctata | 21 | W. rochai, W. sigmoidea, A. decemarticulatus, L. humile, S. saevissima, B. spp | 37234–37255 | FJ970003–FJ970023 | O. Rey, A. Loiseau |
| Zygochlamys patagonica | 11 | n/a | 38059–38069 | FJ937726–FJ937736 | Ian G Paterson, María I Trucco, Mario L Lasta, Daniel E Ruzzante |
| Species | No. primer pairs | No. SNPs in sequence | Others species tested | No. Allele specific primers/ probes | Target gene(s) | MER database numbers | Genbank Accession no. | Authors |
|---|---|---|---|---|---|---|---|---|
| Oncorhynchus mykiss/Oncorhynchus tshawytscha | 9/9 | 87/68 | O. mykiss/O. tshawytscha | 16 | heat shock proteins | 37605–37620 | FJ772745–FJ772915, FJ772947–FJ773066, FJ773092–FJ772525 | Nathan R. Campbell, Shawn R. Narum |
