Fig. 1: Reconstructed haplotypes in the SLR of P. deltoides chromosome XIX.

a Genetic map and physical positions of the SLR (red bar) and the telomere. SSR makers are shown on the top and the numbers of observed recombination events are shown under the chromosome diagram, with zero in both the genetic and physical maps at the telomere end of the chromosome. The FERR gene is located at the right end of chromosome XIX, the end most distant from the telomere of this telocentric chromosome. b SLR-X and SLR-Y haplotypes reconstructed from genome sequences of our sequenced male (see main text). The yellow bars at the left indicate the X and Y telomeres, and physical distances (kb) from the telomere end are shown under each bar. The dashed lines represent deleted sequences, whereas the loops on SLR-Y represent the two Y-specific hemizygous sequence (YHS) described in the text. The gray portion on SLR-X indicates a region described in the text, where divergence between SLR-X and SLR-Y is higher than elsewhere in the SLR. c The Y-specific region rebuilt from 13 PCR amplified fragments (fragment names are shown above the arrows). Red asterisks indicate the fragments are further amplified with natural stands of P. deltoides. d Agarose gel electrophoresis profile for fragment F_657 in females and males. Similar results were obtained in two independent experiments. M molecular marker, B blank control. Source data underlying d are provided as a Source Data file.