Abstract
BackgroundFinger millet (Eleusine coracana 2n = 4x = 36) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India. Its genome has been sequenced multiple times, but A and B subgenomes could not be separated because no published genome for E. indica existed. The classification of A and B subgenomes is important for understanding the evolution of this crop and provide a means to improve current and future breeding programs.ResultsWe produced subgenome calls for 704 syntenic blocks and inferred A or B subgenomic identity for 59,377 genes 81% of the annotated genes. Phylogenetic analysis of a super matrix containing 455 genes shows high support for A and B divergence within the Eleusine genus. Synonymous substitution rates between A and B genes support A and B calls. The repetitive content on highly supported B contigs is higher than that on similar A contigs. Analysis of syntenic singletons showed evidence of biased fractionation showed a pattern of A genome dominance, with 61% A, 37% B and 1% unassigned, and was further supported by the pattern of loss observed among cyto-nuclear interacting genes.ConclusionThe evidence of individual gene calls within each syntenic block, provides a powerful tool for inference for subgenome classification. Our results show the utility of a draft genome in resolving A and B subgenomes calls, primarily it allows for the proper polarization of A and B syntenic blocks. There have been multiple calls for the use of phylogenetic inference in subgenome classification, our use of synteny is a practical application in a system that has only one parental genome available.
Highlights
Finger millet (Eleusine coracana 2n = 4x = 36) is a hardy, nutraceutical, climate change tolerant, orphan crop that is consumed throughout eastern Africa and India
It has been hypothesized that the original allopolyploidy was the point of origin of the wild species E. africana that underwent domestication to form the crop species E. coracana, and evidence in support of this hypothesis is largely based on the phylogenetic analysis of small sets of single copy nuclear genes [8, 11, 12], ITS and plastid markers [9, 13, 14], or cytogenetic methods [10]
We demonstrate evidence and examples of subgenome bias occurring within Eleusine coracana
Summary
Eleusine coracana (finger millet) is an important smallseed cereal crop in its native Africa and South Asia [1, 2]. It has been classified as a nutraceutical [3, 4] and has a panoply of uses from beer brewing to feed for livestock [5]. Hall et al BMC Genomics (2021) 22:175 donor [8, 9], based on the strength plastid phylogenetic analysis, some have suggested that E. coracana is the result of multiple hybridization events, between the B genome donor, E. indica and E. tristachya [11, 12]. It has yet to be tested on a genomic scale
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