Constructing Eleusine Transcriptome References for Determination African Finger Millet (Eleusine coracana) Parentage.

Eleusine coracana, also known as finger millet, is an allotetraploid minor crop primarily grown in East Africa and India. Controversy exists regarding the identity of its diploid parental species, especially the paternal genome donor. Genetic resources for finger millet are minimal compared to major crops, limiting research to resolve the parentage and origin evolutionary questions. In this study, we developed transcriptomes for 7 Eleusine species from fully developed seedlings using Illumina technology and three de novo assemblers (Trinity, Velvet, and SOAPdenovo2) with a redundancy-reducing EvidentialGene pipeline. Using the constructed transcriptomes previously assembled together with E. indica plastid and mitochondria genome to acquire plastid and mitochondria genes from each Eleusine species. Through mapping E. coracana reads to the chloroplast and mitochondria genes of all Eleusine species, fewer variants were detected between E. coracana and E. indica compare to all other species. Phylogenetic analysis further confirmed E. indica as the maternal parent. E. coracana reads filtered for only chloroplast and mitochondria genes were mapped to E.indica transcriptome and the unmapped reads were extracted and assembled. Other five Eleusine species’ transcriptome reads were mapped to the unmapped unique CDS set (E.coracana Synthetic B transcriptome), however, no mapped percentage exceeded 54.5%. By comparison, the reads of E. indica mapping to the E.coracana Synthetic A transcriptome is 72.9%. Variants and phylogenetic analyses found that no Eleusine species close to the E.coracana Synthetic B transcriptome branch. Evidence suggests E. indica as the A genome donor and the B genome donor is extinct or is another unidentified species.