De novo assembly and characterization of transcriptome and microsatellite marker development for Taro (Colocasia esculenta (L.) Schott.)

Abstract

Taro (Colocasia esculenta. (L.) Schott) is a genus of perennial plants that is widely distributed in the tropics or subtropics of Asia, Africa and America, which is the fourteenth most consumed vegetable of the world. However, molecular genetic research of Colocasia has been hindered by the insufficient genomic and transcriptome information. Here, the transcriptome of taro variety ‘Jingjiang Xiangsha’ from Jiangsu, China, was sequenced using the Illumina HiSeqTM 2000 platform in 2015. A total of 58,263,364 reads were generated, and assembly resolved into 65,878 unigenes with a N50 length of 1,357 bp. A total of 40,375 unigene sequences were successfully annotated based on searches against six public databases. Among the annotated unigenes, 14,753 were identified by gene Ontologyterms, 16,643 were classified to Clusters of Orthologous Groups categories, and 25,401 were mapped to 127 pathways in the Kyoto Encyclopedia of genes and genomes database. Also, 11,363 potential microsatellite loci were identified in 5,671 unigenes, and 150 primer pairs were randomly selected and amplified in 18 accessions of C. esculenta. A total of 100 primer pairs showed polymorphisms in repeat length. The number of alleles per locus ranged from 2 to 8. Across the 100 microsatellite loci, the polymorphism information content values ranged from 0.042 to 0.778. The transcriptomic data and microsatellite markers will play important roles in future functional gene analyses and genetic map construction of taro.   Key words: Colocasia, genetic diversity, microsatellite markers, transcriptome.