Transcriptome Analysis Reveals Unique Relationships Among<i>Eleusine</i>Species and Heritage of<i>Eleusine coracana</i>

Abstract

Relationships in the genus <i>Eleusine</i> were obtained through transcriptome analysis. <i>Eleusine coracana</i> (<i>E. coracana</i> ssp. <i>coracana</i>), also known as finger millet, is an allotetraploid minor crop primarily grown in East Africa and India. Domesticated <i>E. coracana</i> evolved from wild <i>E. africana</i> (<i>E. coracana</i> ssp. <i>africana</i>) with the maternal genome donor largely supported to be <i>E. indica</i>; however, the paternal genome donor remains elusive. We developed transcriptomes for six <i>Eleusine</i> species from fully developed seedlings using Illumina technology and three <i>de novo</i> assemblers (Trinity, Velvet, and SOAPdenovo2) with the redundancy-reducing EvidentialGene pipeline. Mapping <i>E. coracana</i> reads to the chloroplast genes of all <i>Eleusine</i> species detected fewer variants between <i>E. coracana</i> and <i>E. indica</i> compared to all other species. Phylogenetic analysis further supports <i>E. indica</i> as the maternal parent of <i>E. coracana</i> and <i>E. africana</i>, in addition to a close relationship between <i>E. indica</i> and <i>E. tristachya</i>, and between <i>E. floccifolia</i> and <i>E. multiflora</i>, and <i>E. intermedia</i> as a separate group. A close relationship between <i>E. floccifolia</i> and <i>E. multiflora</i> was unexpected considering they are reported to have distinct nuclear genomes, BB and CC, respectively. Further, it was expected that <i>E. intermedia</i> and <i>E. floccifolia</i> would have a closer relationship considering they have similar nuclear genomes, AB and BB, respectively. A rethinking of the labeling of ancestral genomes of <i>E. floccifolia</i>, <i>E. multiflora</i>, and <i>E. intermedia</i> is maybe needed based on this data.