Transcriptome sequencing and microsatellite marker discovery in Ailanthus altissima (Mill.) Swingle (Simaroubaceae)

• Published in: Molecular biology reports Vol. 48; no. 3; pp. 2007 - 2023
• Main Authors: Saina, Josphat K., Li, Zhi-Zhong, Mekbib, Yeshitila, Gichira, Andrew W., Liao, Yi-Ying
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-03-2021; Springer Nature B.V
• Subjects: Ailanthus - genetics; Ailanthus altissima; Alleles; Animal Anatomy; Animal Biochemistry; Biomedical and Life Sciences; Chloroplasts; Chloroplasts - genetics; Databases, Genetic; Diversity indices; Expressed Sequence Tags; Gene Expression Regulation, Plant; Gene flow; Gene Ontology; Gene transfer; Genetic diversity; Genetic Loci; Genetic markers; Genetic resources; Genetics, Population; Genomes; Haplotypes - genetics; Heterozygosity; Histology; Indigenous species; Industrial applications; Life Sciences; Microsatellite Repeats - genetics; Microsatellites; Molecular biology; Molecular Sequence Annotation; Morphology; Nucleotide sequence; Original Article; Phylogeny; Polymorphism, Genetic; Population; Population genetics; Population structure; Sequence Analysis, RNA; Simple sequence repeats; Transcriptome - genetics; Transcriptomes; Next-generation; Genetic diversity; EST-SSR markers; Chloroplast microsatellites; Ailanthus altissima
• ISSN: 0301-4851; 1573-4978
• DOI: 10.1007/s11033-020-05402-w

Ailanthus altissima
Swingle, is a tree species native to East Asia and has a great potential in decorative, bioenergy and industrial applications in many countries. To date, despite its commercial importance, the genomic and genetic resources available for this species are still insufficient. In this study, we characterized the transcriptome of
A. altissima
and developed thirteen EST-SSRs (expressed sequence tag-simple sequence repeats) based on Illumina paired-end RNA sequencing (RNA-seq). Besides, we developed ten polymorphic chloroplast microsatellite (cpSSR) markers using the available chloroplast genome of
A. altissima
. The transcriptome data produced 87,797 unigenes, of which 64,891 (73.91%) unigenes were successfully annotated in at least one protein database. For cpSSR markers the number of detected alleles (N) per marker varied from three at cpSSR12 to twelve at cpSSR8, the unbiased haploid diversity indices (uh) varied from 0.111 to 0.485, and haploid diversity indices (h) ranged from 0.101 to 0.444 with an average unbiased haploid diversity index (uh) of 0.274. Overall, a total of 65 different cpSSR alleles were identified at the ten loci among 165 individuals of
A. altissima
. The allele number per locus for EST-SSRs varied from 2.143 to 9.357, and the values of observed and expected heterozygosity ranged from 0.312 to 1.000 and 0.505 to 0.826, respectively. The molecular markers developed in this study will facilitate future genetic diversity, population structure, long distance-gene transfer and pollen-based gene flow analyses of
A. altissima
populations from its known distribution ranges in China focusing on planted and natural forest stands.