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Background: Next-generation sequencing technology has allowed for the rapid development of microsatellites, neutral polymorphic markers that can be used for the analysis of population structure.

Methods and Results: In this study, we performed whole-genome sequencing using the Illumina MiSeq system and de novo assembly to design microsatellite primers for Triops granarius populations in Qatar. The developed microsatellites are suitable for future studies of genetic structuring among geographically isolated freshwater pools. A total of 23 different primer pairs produced typical microsatellite results, with each pair successfully amplified in up to 40 individuals. Only five of the loci produced a significant departure from Hardy-Weinberg equilibrium.

Conclusions: Some of the underlying mechanisms regarding the few loci that deviated from HWE may be further investigated to determine the source of deviation. As T. granarius is the most widely distributed species of the family, the development of these molecular markers would be useful for conducting population genetics and biogeographical studies broadly.

Titel:	Development and characterization of microsatellite primers for Triops granarius (Branchiopoda: Notostraca) using MiSeq technology.
Autor/in / Beteiligte Person:	Ahmed, L ; Al-Najjar, Y ; Cramer, ERA ; Thareja, G ; Suhre, K ; Chen, KC
Link:	View record at Springer (Volltext)
Zeitschrift:	Molecular biology reports, Jg. 49 (2022-10-01), Heft 10, S. 10121-10125
Veröffentlichung:	Dordrecht, Boston, Reidel., 2022
Medientyp:	academicJournal
ISSN:	1573-4978 (electronic)
DOI:	10.1007/s11033-022-07804-4
Schlagwort:	Animals Crustacea genetics High-Throughput Nucleotide Sequencing methods Humans Technology Genetics, Population Microsatellite Repeats genetics
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Publication Type: Journal Article Language: English [Mol Biol Rep] 2022 Oct; Vol. 49 (10), pp. 10121-10125. <i>Date of Electronic Publication: </i>2022 Sep 04. MeSH Terms: Genetics, Population* ; Microsatellite Repeats* / genetics ; Animals ; Crustacea / genetics ; High-Throughput Nucleotide Sequencing / methods ; Humans ; Technology References: Kardousha MM (2017) New records of freshwater crustaceans from vernal pools of Qatar including large branchiopods and a mysid shrimp, a natural resource of economic importance for the aquaculture industry. Arab World Geogr 20(2–3):237–251. https://doi.org/10.5555/1480-6800.20.2.237. (PMID: 10.5555/1480-6800.20.2.237) ; Longhurst AR (1955) A review of the Notostraca. Bull Br Mus Nat Hist Zool 3(1):1–57. ; Vieira MLC, Santini L, Diniz AL, de Munhoz C F (2016) Microsatellite markers: what they mean and why they are so useful. Genet Mol Biol 39(3):312–328. https://doi.org/10.1590/1678-4685-gmb-2016-0027. (PMID: 10.1590/1678-4685-gmb-2016-0027275611125004837) ; Lin L-H, Mao L-X, Luo X, Qu Y-F, Ji X (2011) Isolation and characterization of microsatellite loci in the Chinese cobra Naja atra (Elapidae). Int J Mol Sci 12(7):4435–4440. https://doi.org/10.3390/ijms12074435. (PMID: 10.3390/ijms12074435218450873155360) ; Chang Y-C, Li S-H, Chang M-H, Chen S-L (2014) Isolation and characterization of 18 microsatellite loci for an endangered freshwater crocodile Tomistoma schlegelii. Conserv Genet Resour 6(2):495–498. https://doi.org/10.1007/s12686-013-0139-7. (PMID: 10.1007/s12686-013-0139-7) ; Nowak C, Zuther S, Leontyev SV, Geismar J (2013) Rapid development of microsatellite markers for the critically endangered Saiga (Saiga tatarica) using Illumina® MiSeq next generation sequencing technology. Conserv Genet Resour 6(1):159–162. https://doi.org/10.1007/s12686-013-0033-3. (PMID: 10.1007/s12686-013-0033-3) ; López-Márquez V, García-Jiménez R, Templado J, Machordom A (2016) Development and characterization of 26 novel microsatellite loci for the trochid gastropod Gibbula divaricata (Linnaeus, 1758), using Illumina MiSeq next generation sequencing technology. PeerJ 4, e1789. https://doi.org/10.7717/peerj.1789. ; Korn M, Rabet N, Ghate Hv, Marrone F, Hundsdoerfer AK (2013) Molecular phylogeny of the Notostraca. Mol Phylogenetics Evol 69(3):1159–1171. https://doi.org/10.1016/j.ympev.2013.08.006. (PMID: 10.1016/j.ympev.2013.08.006) ; Meglecz E, Pech N, Gilles A, Dubut V, Hingamp P, Trilles A, Martin JF (2014) QDD version 3.1: a user-friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate. Mol Ecol Resour 14(6):1302–1313. doi: https://doi.org/10.1111/1755-0998.12271. (PMID: 10.1111/1755-0998.1227124785154) ; Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinform 26(6):841–842. https://doi.org/10.1093/bioinformatics/btq033. (PMID: 10.1093/bioinformatics/btq033) ; Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234. (PMID: 10.1038/7270810657137) ; Stoeckle BC, Cowley DE, Schaack Y, MacDonald KS, Sallenave R, Kuehn R (2013) Microsatellites for North American species of Triops (Branchiopoda: Notostraca). J Crustacean Biology 33(1):48–55. https://doi.org/10.1163/1937240X-00002118. (PMID: 10.1163/1937240X-00002118) ; Peakall R, Smouse PE (2012) GenAIEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinform 28(19):2537–2539. https://doi.org/10.1093/bioinformatics/bts460. (PMID: 10.1093/bioinformatics/bts460) ; Morin P, Leduc R, Archer F, Martien K, Huebinger R, Bickham J, Taylor B (2009) Significant deviations from Hardy–Weinberg equilibrium caused by low levels of microsatellite genotyping errors. Mol Ecol Resour 9(2):498–504. https://doi.org/10.1111/j.1755-0998.2008.02502.x. (PMID: 10.1111/j.1755-0998.2008.02502.x21564679) ; Karlsson S, Mork J (2005) Deviation from Hardy–Weinberg equilibrium, and temporal instability in allele frequencies at microsatellite loci in a local population of Atlantic cod. ICES J Marin Sci 62(8):1588–1596. https://doi.org/10.1016/j.icesjms.2005.05.009. (PMID: 10.1016/j.icesjms.2005.05.009) Grant Information: SRMP-002-01 Weill Cornell Medicine - Qatar Contributed Indexing: Keywords: MiSeq; Microsatellite; Primer development; Qatar; Triops granarius Entry Date(s): Date Created: 20220904 Date Completed: 20220929 Latest Revision: 20221201 Update Code: 20231215 PubMed Central ID: PMC9515016

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Development and characterization of microsatellite primers for Triops granarius (Branchiopoda: Notostraca) using MiSeq technology.