Physical and functional relationships of rpa1a sugarcane hom(e)ologous BACs compared to sorghum. The rpa1a genes are represented by white arrows and other genes by black arrows. LTR retrotransposons are represented by blue boxes, DNA transposons by brown boxes and Harbinger transposons by black vertical lines. Only contiguous TE sequences greater than 3,000 bp are shown. A. A physical and phylogenetic analysis of the genomic region of the rpa1a gene from 12 BACs and S. bicolor. The neighbor-joining tree was inferred with using the highest ranked substitution model (Tajima-Nei) and 1000 bootstrap replications . The Arabic numberals are bootstrap values, roman numerals indicate the three phylogenetic groups identified. Colinear genes and TEs are connected by shaded areas. B. Mapping of sRNA and mRNA libraries against one BAC from each phylogenetic group (I, II and III) and SHCRBa_035_B09 and SHCRBa_196_O13. Both sRNA and mRNA mappings are to scale. Dotted ovals indicate sRNA and mRNA peaks discussed in the text. Y axis show the mRNA and sRNA mapping density, that correspond to the proportion of mRNA or sRNA mapping in each base, normalized by the BAC size.