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Background   Amorphophallus  is a genus of perennial plants widely distributed in the tropics or subtropics of West Africa and South Asia. Its corms contain a high level of water-soluble glucomannan; therefore, it has long been used as a medicinal herb and food source. Genetic studies of  Amorphophallus  have been hindered by a lack of genetic markers. A large number of molecular markers are required for genetic diversity study and improving disease resistance in  Amorphophallus . Here, we report large scale of transcriptome sequencing of two species:  Amorphophallus konjac  and  Amorphophallus bulbifer  using deep sequencing technology, and microsatellite (SSR) markers were identified based on these transcriptome sequences.    Results  cDNAs of  A. konjac  and  A. bulbifer  were sequenced using Illumina HiSeq™ 2000 sequencing technology. A total of 135,822 non-redundant unigenes were assembled from about 9.66 gigabases, and 19,596 SSRs were identified in 16,027 non-redundant unigenes. Di-nucleotide SSRs were the most abundant motif (61.6%), followed by tri- (30.3%), tetra- (5.6%), penta- (1.5%), and hexa-nucleotides (1%) repeats. The top di- and tri-nucleotide repeat motifs included AG/CT (45.2%) and AGG/CCT (7.1%), respectively. A total of 10,754 primer pairs were designed for marker development. Of these, 320 primers were synthesized and used for validation of amplification and assessment of polymorphisms in 25 individual plants. The total of 275 primer pairs yielded PCR amplification products, of which 205 were polymorphic. The number of alleles ranged from 2 to 14 and the polymorphism information content valued ranged from 0.10 to 0.90. Genetic diversity analysis was done using 177 highly polymorphic SSR markers. A phenogram based on Jaccard’s similarity coefficients was constructed, which showed a distinct cluster of 25  Amorphophallus  individuals.    Conclusion  A total of 10,754 SSR markers have been identified in  Amorphophallus  using transcriptome sequencing. One hundred and seventy-seven polymorphic markers were successfully validated in 25 individuals. The large number of genetic markers developed in the present study should contribute greatly to research into genetic diversity and germplasm characterization in  Amorphophallus .

Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae)