Quantity, organization, and distribution of chloroplast microsatellites in all species of Eucalyptus with available plastome sequence

Mateus Chagas Andrade,Matheus Perek,Michele Moro,Fernanda Bortolanza Pereira,Evandro Vagner Tambarussi

doi:10.1590/1984-70332018v18n1a13

Abstract

Abstract In this study, we quantify and document the distribution and organization of cpSSRs in the chloroplast genome of 31 Eucalyptus species. Our sample included all previously sequenced plastomes of Eucalyptus species available from the NCBI online database. We processed the complete cpDNA sequences and identified mono-, di-, tri-, tetra-, penta-, and hexanucleotide cpSSRs, with the majority of cpSSRs classified as mononucleotide. After genome microsatellite selection, we evaluated the microsatellites for coding and non-coding regions and cpSSRs were predominantly identified in non-coding regions of cpDNA for all nucleotide types. Penta- and hexanucleotide cpSSRs were the least frequent types of microsatellites. We also developed and virtually amplified 60 primers pairs that can be used in studies of Eucalyptus species. Thus, these cpSSR regions can be used in studies assessing the ecology, breeding, and conservation of the genus.

Highlights

Eucalyptus L’Hér. is the most dominant genus in Australian flora and with approximately 700 species, it is the largest genus in the Myrtaceae family (Smith et al 2003)
This study is based on complete plastid genome sequences available from the National Center for Biotechnology Information (NCBI; https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?opt=plastid&taxid=2759)
The complete cpDNA sequences were collected from NCBI and processed using the FastPCR 6.5.40.0 software (Kalendar et al 2016) to identify the microsatellite regions as mono, di, tri, tetra, penta, or hexanucleotide

Summary

Introduction

Eucalyptus L’Hér. is the most dominant genus in Australian flora and with approximately 700 species, it is the largest genus in the Myrtaceae family (Smith et al 2003). Because of its extensive use in forestry, plant ecologists, breeders and geneticists have significant interest in establishing methods for fast and robust Eucalyptus identification or species distinction. The use of markerassisted approaches in Eucalyptus breeding programs is common (Mahajan and Gupta 2012, Fuchs et al 2015). These approaches are powerful tools for phylogenetic and population research (Doorduin et al 2011) and can be used to assist ecologists and breeders in their analyses (Steane et al 1998, Freeman et al 2001, McKinnon et al 2001, McKinnon et al 2010, Melotto-Passarin et al 2011)

Objectives

Methods

Results