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Fig. 2 | BMC Biology

Fig. 2

From: Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution

Fig. 2

Completeness of the chromosome-scale (PGA2) assembly. For each of the 16 chromosomes, the top panel indicates the density of genes (blue) and putative centromeric repeats (red). Red tick marks on the left-hand side indicate the y-axis scale for the centromeric repeats, and blue tick marks on the right-hand side indicate the scale for gene density. Gene density values are scaled relative to centromeric repeat values such that the first blue and red ticks are 0 while subsequent blue ticks represent the value of the corresponding sequential red tick (i.e., the second blue tick for Chr1 has a value of 5.0e-08). Gray asterisks in plots for Chr1, Chr5, Chr6, and Chr10 represent the approximate positions of mapped single nucleotide polymorphisms (SNPs) from contigs 343, 177, 833, and 747, respectively, which were not assembled into the pseudomolecules. Red boxes in the middle panel represent 1-Mb bins containing regions categorized as being telomeric. In the bottom panel, the genetic position of mapped markers is plotted as a function of physical distance

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