PMC

Comparative physical map of O. nivara with rice chromosome 1. SyMap screenshots showing the completed physical map of O. nivara chromosome 1 aligned to the O. sativa chromosome 1 pseudomolecule. (A) Whole-chromosome view of the O. nivara pseudomolecule aligned to the O. sativa chromosome 1 pseudomolecule, showing overgo marker alignments only. (B) Whole-chromosome view of the O. nivara pseudomolecule aligned to the O. sativa chromosome 1 pseudomolecule, showing both overgo marker and BAC end sequence (BES) alignments. (C) Zoomed-in view of the overgo and BES alignments between O. nivara contig 1 and the O. sativa chromosome 1 pseudomolecule. (D) More detailed view of (C) showing the actual clones comprising O. nivara contig 1 and their BESs. In this view, the alignments of individual BES can be seen, as well as individual clones that were detected by overgo markers, and the alignments of those markers to the O. sativa chromosome 1 pseudomolecule. In (A-C), BAC contigs are represented by numbered blocks which are stacked vertically to form the O. nivara pseudomolecule shown on the left of each alignment, while the O. sativa pseudomolecule is shown in brown on the right of each alignment. The red 'X' on the O. sativa pseudomolecule represents the centromere. Overgo marker names are listed in red text to the left of each alignment, while coordinates along the O. sativa pseudomolecule are listed in blue text to the right of each alignment. Green lines stretching from the O. nivara pseudomolecule to the O. sativa pseudomolecule in each alignment show where clones from the O. nivara contig align to the O. sativa chromosome, while purple lines show where O. nivara clones' BESs align to the O. sativa pseudomolecule. In (D), blue vertical lines on the left half of the figure represent O. nivara BAC clones. Circles on the ends of the clones represent BESs. Open circles are BESs that did not match sequences from O. sativa, while closed circles are BESs that matched O. sativa sequences. Purple lines stretching from a BES on the left to the pseudomolecule on the right show where the BES to which the line is attached aligns to the pseudomolecule. In the case of overgo markers, a marker will often hit more than one BAC clone. Green lines stretch from the middle of all clones hit by that marker to a red "marker join dot." The green line stretching from the marker join dot to the pseudomolecule shows where the marker sequence is located on the pseudomolecule, thereby showing where the O. nivara clones hit by the marker align to the O. sativa pseudomolecule.

Alignment of O. officinalis contig to region of rice chromosome 1 showing putative inversion. Alignment of an O. officinalis contig to rice chromosome 1. Overgos confirm the placement of clones in the contig such that a putative genomic inversion of the region stretching from approximately 21.94 MB to 23.40 MB on the rice pseudomolecule is apparent. The brown bar on the right side of the figure represents a portion of the O. sativa chromosome 1 pseudomolecule, and the coordinates along the pseudomolecule are listed in blue on the righthand side of the pseudomolecule. Blue vertical lines on the left half of the figure represent O. officinalis BAC clones. Circles on the ends of the clones represent BAC end sequences (BES). Open circles are BESs that did not match sequences from O. sativa, while closed circles are BESs that matched O. sativa sequences. Purple lines stretching from a BES on the left to the pseudomolecule on the right show where the BES to which the line is attached aligns to the pseudomolecule. Red text on the left side of the figure shows the names of overgo markers with hits to clones in the O. officinalis BAC contig shown. In the case of overgo markers, a marker will often hit more than one BAC clone. Green lines stretch from the middle of all clones hit by that marker to a red "marker join dot." The green line stretching from the marker join dot to the pseudomolecule shows where the marker sequence is located on the pseudomolecule, thereby showing where the O. officinalis clones hit by the marker align to the O. sativa pseudomolecule.

Alignment of O. officinalis contig to rice chromosome 1. A detailed view of the alignment of an O. officinalis BAC contig to the O. sativa chromosome 1 pseudomolecule using BAC end sequences (BES) and overgo markers. The hybridizations of overgos 4jp1069094 and 4jp1110186 in particular to O. officinalis BAC clones drove the merger of two initially separated contigs to form the O. officinalis contig shown here. The brown bar on the right side of the figure represents a portion of the O. sativa chromosome 1 pseudomolecule, and the coordinates along the pseudomolecule are listed in blue on the righthand side of the pseudomolecule. Blue vertical lines on the left half of the figure represent O. officinalis BAC clones. Circles on the ends of the clones represent BESs. Open circles are BESs that did not match sequences from O. sativa, while closed circles are BESs that matched O. sativa sequences. Purple lines stretching from a BES on the left to the pseudomolecule on the right show where the BES to which the line is attached aligns to the pseudomolecule. Red text on the left side of the figure shows the names of overgo markers with hits to clones in the O. officinalis BAC contig shown. In the case of overgo markers, a marker will often hit more than one BAC clone. Green lines stretch from the middle of all clones hit by that marker to a red "marker join dot." The green line stretching from the marker join dot to the pseudomolecule shows where the marker sequence is located on the pseudomolecule, thereby showing where the O. officinalis clones hit by the marker align to the O. sativa pseudomolecule.

(A) Dot plot of the pilot BAC pseudochromosome (PI A11) as aligned to the corresponding NI A11 draft pseudomolecule. (B) Dot plot of the pilot BAC pseudochromosome (PI A11) as aligned to the corresponding BI A01 draft pseudomolecule. (C) Dot plot of the pilot BAC pseudochromosome (PI D11) as aligned to the corresponding NI D11 draft pseudomolecule. (D) Dot plot of the pilot BAC pseudochromosome (PI D11) as aligned to the corresponding BI D07 draft pseudomolecule.

Nipponbare transcripts covered by Kasalath pseudomolecule sequences. The horizontal axis represents the sequence coverage (×100%) of each gene annotated on Nipponbare pseudomolecules.

Order of markers in the four linkage maps compared to the final pseudomolecule generated through consensus map derivation using the AllMaps software with Unequal Weights2 parameters through whole-genome run

Note: 3B pseudomolecule is from short (left) to long (right) arm in base pair (bp).

The y-axis represents the number of genes with a certain length. Genes range in size from 0.1 kb to 39.2 kb.

In silico restriction maps of pseudomolecules (Zm1S_supercontig and Zm9L_supercontig) were found to align () to optical contigs (OMcontig_15 and 23). This allowed the identification of common and discordant regions. SwaI restriction sites are depicted by vertical lines. Regions of the optical contig and the pseudomolecule that align are teal colored, and the aligned regions are pointed to with black connecting lines.

Rate of uniquely mapped NGS reads from 50 rice accessions by using Nipponbare, Kasalath, and 93-11 pseudomolecule sequences as references. Arabic numerals under the horizontal axis represent different accessions of cultivated and wild rice (see Supplementary Table S2 for details).

Single-nucleotide polymorphism (SNP) density and distribution across the genome of the peanut. (A) The distribution of the number of SNPs on each chromosomal pseudomolecule. (B) SNP density on each chromosomal pseudomolecule. The horizontal axis shows the length of the pseudomolecule; the number of SNPs per 20-kb window is shown as color index.

Overview of 35L-10PP pooled BAC 454 assembly. Read coverage in each scaffold is indicated in red. Arrows indicate points of BAC overlap. Black numbers are uncorrected pseudomolecule positions. Blue lines indicate genetic marker (in purple) positions in the pseudomolecule.

Distribution of the four most frequent motifs along 3B pseudomolecule (in base pairs). Distribution is estimated along chromosome 3B pseudomolecule (774 Mb) using a sliding window of 10 Mb and a step of 1 Mb.

Heat maps for % sequence alignments and average scores. Colour coded moving windows/100 functionally annotated, expressed TIGR rice loci (MWs/FAexpTRL) for each rice pseudomolecule (1–12). For each pseudomolecule: column 1–6 = MWs for % significant MegaBLAST alignments between Os_CD and test databases Lp_MF, Zm_MF, Zm_TA, Hv_TA, Gm_TA and At_TA respectively; column 7 = position of MWs containing rice centromere (dark vertical bar); column 8–13 = MWs for average score of significant MegaBLAST alignments between Os_CD and test databases Lp_MF, Zm_MF, Zm_TA, Hv_TA, Gm_TA and At_TA, respectively [see Additional file Table 3 for colour code quantification]. Pseudomolecule representations are aligned along the centromeres.

Genomic similarity between genomes of Vch-N1252 and Vch-Q4233. Graphical representation of a pair-wise alignment between Vch-N1252 and a pseudomolecule of Vch-N1252 with identified SNPs of Vch-Q4233 incorporated. The pseudomolecule was generated from an output from snippy version 4.6.0 (https://github.com/tseemann/snippy). The image was generated using snipit (https://github.com/aineniamh/snipit). Default settings were used for both programs.

Positions of (a) 23 single-nucleotide polymorphisms on two genetic linkage maps and on the 7H pseudomolecule of the RGT Planet genome sequence assembly [] and (b) 11 single-nucleotide polymorphisms in a candidate region of that pseudomolecule.

Comparative map of the potato genetic map (BP: integrated map of BCT, PD and PCC1), the potato genome (DM) and the tomato genome (TM). The potato genetic map was scaled to the size of the corresponding DM pseudomolecule setting the last COS marker of each linkage group equal to the size of the pseudomolecule. Likewise, the tomato genetic map was scaled using the pseudomolecule size of the corresponding tomato physical map. Lines are drawn between corresponding COSII markers. A generic tree is drawn to the left hand grouping visually the two potato maps versus the tomato map. Linkage groups and pseudomolecules are drawn sequentially from left to right as indicated by the numbers.

NIAB2015 chromosome 3A compared to four other genetic maps (a, b) CM2014 (c, d) SynOp (e) 9KCONS (f) IWGSC2 pseudomolecule. (a, c, e) cM‐cM genetic map comparison, NIAB2015 on x‐axis. (b, d) direct comparison between chromosome diagrams, NIAB2015 on left (f) comparison of NIAB2015 (cM, x‐axis) to IWGSC2 pseudomolecule (base pairs).

Pseudomolecule construction of Satsuma by aligning the scaffolds to the three genetic maps. Chr 1 to 9 represents constructed pseudomolecules by merging three genetic maps of Satsuma offsprings. Numbers in parenthesis indicate the length of constructed pseudomolecule. Central round rectangle is a schematic diagram of the merged pseudomolecule. P1 (green), P2 (orange), and P3 (blue) of each side correspond to the genetic maps of population 1 (161 SSR, 512 SNP, 957 cM), population 2 (349 SSR, 476 SNP, 1,017 cM), and population 3 (278 SSR, 919 cM), respectively. Each line denotes a DNA marker that was mapped to the scaffold and applied for scaffold assembly.

Chromosome length per haplotype compared to PN40024_12X.v4 genome. Chromosome length per haplotype in Mbp for each pseudomolecule built (Merlot-Root-Hap-CF; Merlot-Leaf-Hap-CF; Merlot-Root-Hap-MG; Merlot-Leaf-Hap-MG) against PN40024.v4.