Comprehensive Characterization of Simple Sequence Repeats in Eggplant ( L.) Genome and Construction of a Web Resource

Overview

Journal Front Plant Sci

Date 2018 Apr 13

PMID 29643862

Citations 22

Authors

Ezio Portis

Sergio Lanteri

Lorenzo Barchi

Flavio Portis

Luisa Valente

Laura Toppino

Giuseppe L Rotino

Alberto Acquadro

Affiliations

Soon will be listed here.

Abstract

We have characterized the simple sequence repeat (SSR) markers of the eggplant () using a recent high quality sequence of its whole genome. We found nearly 133,000 perfect SSRs, a density of 125.5 SSRs/Mbp, and also about 178,400 imperfect SSRs. Of the perfect SSRs, 15.6% were complex, with two stretches of repeats separated by an intervening block of <100 nt. Di- and trinucleotide SSRs accounted, respectively, for 43 and 37% of the total. The SSRs were classified according to their number of repeats and overall length, and were assigned to their linkage group. We found 2,449 of the perfect SSRs in 2,086 genes, with an overall density of 18.5 SSRs/Mbp across the gene space; 3,524 imperfect SSRs were present in 2,924 genes at a density of 26.7 SSRs/Mbp. Putative functions were assigned via ontology to genes containing at least one SSR. Using this data we developed an "Eggplant Microsatellite DataBase" () which permits identification of SSR markers in terms of their location on the genome, type of repeat (perfect vs. imperfect), motif type, sequence, repeat number and genomic/gene context. It also suggests forward and reverse primers. We employed an PCR analysis to validate these SSR markers, using as templates two CDS sets and three assembled transcriptomes obtained from diverse eggplant accessions.

Citing Articles

Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb.

Rabeh K, Mghazli N, Gaboun F, Filali-Maltouf A, Sbabou L, Belkadi B Database (Oxford). 2024; 2024.

PMID: 39602824 PMC: 11602033. DOI: 10.1093/database/baae118.

Identification of New Cultivar and Different Provenances of (Poaceae: Bambusoideae) Using Simple Sequence Repeats Developed from the Whole Genome.

Geng R, Xu J, Jiang J, Cheng Z, Sun M, Xia N Plants (Basel). 2024; 13(20).

PMID: 39458856 PMC: 11511551. DOI: 10.3390/plants13202910.

Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.

Geethanjali S, Kadirvel P, Anumalla M, Hemanth Sadhana N, Annamalai A, Ali J Plants (Basel). 2024; 13(18).

PMID: 39339594 PMC: 11435353. DOI: 10.3390/plants13182619.

TriticeaeSSRdb: a comprehensive database of simple sequence repeats in .

Li T, Cai S, Cai Z, Fu Y, Liu W, Zhu X Front Plant Sci. 2024; 15:1412953.

PMID: 38841284 PMC: 11150838. DOI: 10.3389/fpls.2024.1412953.

CoreSNP: an efficient pipeline for core marker profile selection from genome-wide SNP datasets in crops.

Dou T, Wang C, Ma Y, Chen Z, Zhang J, Guo G BMC Plant Biol. 2023; 23(1):580.

PMID: 37986037 PMC: 10662547. DOI: 10.1186/s12870-023-04609-w.

References

Brouwer J, Willemsen R, Oostra B . Microsatellite repeat instability and neurological disease. Bioessays. 2009; 31(1):71-83. PMC: 4321794. DOI: 10.1002/bies.080122. View

Li Y, Korol A, Fahima T, Nevo E . Microsatellites within genes: structure, function, and evolution. Mol Biol Evol. 2004; 21(6):991-1007. DOI: 10.1093/molbev/msh073. View

Cheng J, Zhao Z, Li B, Qin C, Wu Z, Trejo-Saavedra D . A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum. Sci Rep. 2016; 6:18919. PMC: 4703971. DOI: 10.1038/srep18919. View

Jurka J, Pethiyagoda C . Simple repetitive DNA sequences from primates: compilation and analysis. J Mol Evol. 1995; 40(2):120-6. DOI: 10.1007/BF00167107. View

Stagel A, Portis E, Toppino L, Rotino G, Lanteri S . Gene-based microsatellite development for mapping and phylogeny studies in eggplant. BMC Genomics. 2008; 9:357. PMC: 2527019. DOI: 10.1186/1471-2164-9-357. View

Subramanian S, Mishra R, Singh L . Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol. 2003; 4(2):R13. PMC: 151303. DOI: 10.1186/gb-2003-4-2-r13. View

Weber J . Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics. 1990; 7(4):524-30. DOI: 10.1016/0888-7543(90)90195-z. View

Varshney R, Graner A, Sorrells M . Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 2005; 23(1):48-55. DOI: 10.1016/j.tibtech.2004.11.005. View

Sawaya S, Bagshaw A, Buschiazzo E, Kumar P, Chowdhury S, Black M . Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements. PLoS One. 2013; 8(2):e54710. PMC: 3566118. DOI: 10.1371/journal.pone.0054710. View

10.

Liu W, Jia X, Liu Z, Zhang Z, Wang Y, Liu Z . Development and Characterization of Transcription Factor Gene-Derived Microsatellite (TFGM) Markers in Medicago truncatula and Their Transferability in Leguminous and Non-Leguminous Species. Molecules. 2015; 20(5):8759-71. PMC: 6272326. DOI: 10.3390/molecules20058759. View

11.

Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P . Genome sequence and analysis of the tuber crop potato. Nature. 2011; 475(7355):189-95. DOI: 10.1038/nature10158. View

12.

Cavagnaro P, Senalik D, Yang L, Simon P, Harkins T, Kodira C . Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics. 2010; 11:569. PMC: 3091718. DOI: 10.1186/1471-2164-11-569. View

13.

Gramazio P, Blanca J, Ziarsolo P, Herraiz F, Plazas M, Prohens J . Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding. BMC Genomics. 2016; 17:300. PMC: 4841963. DOI: 10.1186/s12864-016-2631-4. View

14.

Morgante M, Hanafey M, Powell W . Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet. 2002; 30(2):194-200. DOI: 10.1038/ng822. View

15.

Hurtado M, Vilanova S, Plazas M, Gramazio P, Fonseka H, Fonseka R . Diversity and relationships of eggplants from three geographically distant secondary centers of diversity. PLoS One. 2012; 7(7):e41748. PMC: 3407184. DOI: 10.1371/journal.pone.0041748. View

16.

Hirakawa H, Shirasawa K, Miyatake K, Nunome T, Negoro S, Ohyama A . Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. DNA Res. 2014; 21(6):649-60. PMC: 4263298. DOI: 10.1093/dnares/dsu027. View

17.

Kujur A, Bajaj D, Saxena M, Tripathi S, Upadhyaya H, Gowda C . Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping. DNA Res. 2013; 20(4):355-74. PMC: 3738162. DOI: 10.1093/dnares/dst015. View

18.

Toth G, Gaspari Z, Jurka J . Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 2000; 10(7):967-81. PMC: 310925. DOI: 10.1101/gr.10.7.967. View

19.

Behura S, Severson D . Motif mismatches in microsatellites: insights from genome-wide investigation among 20 insect species. DNA Res. 2014; 22(1):29-38. PMC: 4379975. DOI: 10.1093/dnares/dsu036. View

20.

Barchi L, Lanteri S, Portis E, Vale G, Volante A, Pulcini L . A RAD tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation. PLoS One. 2012; 7(8):e43740. PMC: 3422253. DOI: 10.1371/journal.pone.0043740. View