Detection and Application of Novel SSR Markers from Transcriptome Data for Astronium Fraxinifolium Schott, a Threatened Brazilian Tree Species

Overview

Journal Mol Biol Rep

Specialty Molecular Biology

Date 2021 Apr 18

PMID 33866490

Citations 1

Authors

Maiara R Cornacini

Ricardo O Manoel

Marcelo A M Alcantara

Mario L T Moraes

Edvaldo A A Silva

Leonel G Pereira Neto

Alexandre M Sebbenn

Bruno C Rossini

Celso L Marino

Affiliations

Soon will be listed here.

Abstract

Astronium fraxinifolium is an endangered tree species from Brazil. Due to its significance in environmental reforestation, as well as the continued exploitation of its wood, it is necessary to develop management programs that support the conservation of the species. Simple sequence repeats (SSR) or microsatellite markers are widely used in population genetic studies across a range of diverse organisms. In this study, we present the first SSR markers developed for A. fraxinifolium as well as their frequency and distribution based on transcriptome data. From transcriptome data, we identified more than 100 thousand sequences presenting microsatellites, with a predominant distribution of trinucleotide repeats. From the initial screening, we selected 20 microsatellite loci which were validated and evaluated for genetic indices in two natural populations. All loci were polymorphic, ranging from four to 11 alleles per locus. The observed and expected heterozygosities ranged from 0 to 1.0 and from 0.533 to 1.0, respectively, while the genetic differentiation (G = 0.363) was greater within than between populations. The developed SSR loci from RNA-Seq data provides a foundation for future studies on genetic diversity and population structure, mating system, and gene flow for A. fraxinifolium populations and related species, aiming at conservation and management.

Citing Articles

Landscape barriers to pollen and seed flow in the dioecious tropical tree Astronium fraxinifolium in Brazilian savannah.

Manoel R, Rossini B, Cornacini M, Moraes M, Cambuim J, Alcantara M PLoS One. 2021; 16(8):e0255275.

PMID: 34339479 PMC: 8336915. DOI: 10.1371/journal.pone.0255275.

References

Gonzalez-Castellano I, Perina A, Gonzalez-Tizon A, Torrecilla Z, Martinez-Lage A . Isolation and characterization of 21 polymorphic microsatellite loci for the rockpool shrimp Palaemon elegans using Illumina MiSeq sequencing. Sci Rep. 2018; 8(1):17197. PMC: 6249324. DOI: 10.1038/s41598-018-35408-1. View

Souza D, Rossini B, de Souza F, Sebbenn A, Marino C, de Moraes M . Development of microsatellite markers for Myracrodruon urundeuva (F.F. & M.F. Allemão), a highly endangered species from tropical forest based on next-generation sequencing. Mol Biol Rep. 2017; 45(1):71-75. DOI: 10.1007/s11033-017-4142-z. View

Fraga D, de Carvalho A, Santana R, Machado M, Lacorte G . Development of microsatellite markers for the threatened species Coleocephalocereus purpureus (Cactaceae) using next-generation sequencing. Mol Biol Rep. 2019; 47(2):1485-1489. DOI: 10.1007/s11033-019-05213-8. View

Hou M, Du G, Zhao Z . Development of genomic microsatellite markers for Aconitum gymnandrum (Ranunculaceae) by next generation sequencing (NGS). Mol Biol Rep. 2019; 47(1):727-729. DOI: 10.1007/s11033-019-05160-4. View

Zheng X, Pan C, Diao Y, You Y, Yang C, Hu Z . Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae). BMC Genomics. 2013; 14:490. PMC: 3737116. DOI: 10.1186/1471-2164-14-490. View

Zhou T, Li Z, Bai G, Feng L, Chen C, Wei Y . Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae). Molecules. 2016; 21(3):166. PMC: 6272838. DOI: 10.3390/molecules21030166. View

Lu Q, Gao J, Wu J, Zhou X, Wu X, Li M . Development of 19 novel microsatellite markers of lily-of-the-valley (Convallaria, Asparagaceae) from transcriptome sequencing. Mol Biol Rep. 2020; 47(4):3041-3047. DOI: 10.1007/s11033-020-05376-9. View

Miller M, Knaus B, Mullins T, Haig S . SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data. J Hered. 2013; 104(6):881-5. DOI: 10.1093/jhered/est056. View

Gotz S, Garcia-Gomez J, Terol J, Williams T, Nagaraj S, Nueda M . High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008; 36(10):3420-35. PMC: 2425479. DOI: 10.1093/nar/gkn176. View

10.

Schuelke M . An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol. 2000; 18(2):233-4. DOI: 10.1038/72708. View

11.

Kalinowski S, Taper M, Marshall T . Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol. 2007; 16(5):1099-106. DOI: 10.1111/j.1365-294X.2007.03089.x. View

12.

Jombart T, Ahmed I . adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. 2011; 27(21):3070-1. PMC: 3198581. DOI: 10.1093/bioinformatics/btr521. View

13.

Evanno G, Regnaut S, Goudet J . Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005; 14(8):2611-20. DOI: 10.1111/j.1365-294X.2005.02553.x. View

14.

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

15.

Mrazek J, Guo X, Shah A . Simple sequence repeats in prokaryotic genomes. Proc Natl Acad Sci U S A. 2007; 104(20):8472-7. PMC: 1895974. DOI: 10.1073/pnas.0702412104. View

16.

Cai K, Zhu L, Zhang K, Li L, Zhao Z, Zeng W . Development and Characterization of EST-SSR Markers From RNA-Seq Data in . Front Plant Sci. 2019; 10:50. PMC: 6367221. DOI: 10.3389/fpls.2019.00050. View

17.

Sanchez-Gomez K, Cristobal-Perez E, Harvey N, Quesada M . Isolation and characterization of microsatellite loci in Astroniumgraveolens (Anacardiaceae) and cross amplification in related species. Mol Biol Rep. 2020; 47(5):4003-4007. DOI: 10.1007/s11033-020-05397-4. View

18.

Moraes M, Kubota T, Rossini B, Marino C, Freitas M, Moraes M . Long-distance pollen and seed dispersal and inbreeding depression in (Fabaceae: Caesalpinioideae) in the Brazilian savannah. Ecol Evol. 2018; 8(16):7800-7816. PMC: 6144967. DOI: 10.1002/ece3.4253. View

19.

Hagler J, Mueller S, Teuber L, Van Deynze A, Martin J . A method for distinctly marking honey bees, Apis mellifera, originating from multiple apiary locations. J Insect Sci. 2012; 11:143. PMC: 3281414. DOI: 10.1673/031.011.14301. View