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Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum.

Hass-Jacobus BL, Futrell-Griggs M, Abernathy B, Westerman R, Goicoechea JL, Stein J, Klein P, Hurwitz B, Zhou B, Rakhshan F, Sanyal A, Gill N, Lin JY, Walling JG, Luo MZ, Ammiraju JS, Kudrna D, Kim HR, Ware D, Wing RA, San Miguel P, Jackson SA - BMC Genomics (2006)

Bottom Line: When rice overgos were aligned to available S. bicolor sequence, 29% of the overgos aligned with three or fewer mismatches; of these, 41% gave positive hybridization signals.Overgo hybridization patterns supported colinearity of loci in regions of sorghum chromosome 3 and rice chromosome 1 and suggested that a possible genomic inversion occurred in this syntenic region in one of the two genomes after the divergence of S. bicolor and O. sativa.The results of this study emphasize the importance of identifying conserved sequences in the reference sequence when designing overgo probes in order for those probes to hybridize successfully in distantly related species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA. barbara.jacobus@alumni.purdue.edu

ABSTRACT

Background: With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies. The genus Oryza includes 23 species that shared a common ancestor 8-10 million years ago making this an ideal model for investigations into the processes underlying domestication, as many of the Oryza species are still undergoing domestication. This study integrates high-throughput, hybridization-based markers with BAC end sequence and fingerprint data to construct physical maps of rice chromosome 1 orthologues in two wild Oryza species. Similar studies were undertaken in Sorghum bicolor, a species which diverged from cultivated rice 40-50 million years ago.

Results: Overgo markers, in conjunction with fingerprint and BAC end sequence data, were used to build sequence-ready BAC contigs for two wild Oryza species. The markers drove contig merges to construct physical maps syntenic to rice chromosome 1 in the wild species and provided evidence for at least one rearrangement on chromosome 1 of the O. sativa versus Oryza officinalis comparative map. When rice overgos were aligned to available S. bicolor sequence, 29% of the overgos aligned with three or fewer mismatches; of these, 41% gave positive hybridization signals. Overgo hybridization patterns supported colinearity of loci in regions of sorghum chromosome 3 and rice chromosome 1 and suggested that a possible genomic inversion occurred in this syntenic region in one of the two genomes after the divergence of S. bicolor and O. sativa.

Conclusion: The results of this study emphasize the importance of identifying conserved sequences in the reference sequence when designing overgo probes in order for those probes to hybridize successfully in distantly related species. As interspecific markers, overgos can be used successfully to construct physical maps in species which diverged less than 8 million years ago, and can be used in a more limited fashion to examine colinearity among species which diverged as much as 40 million years ago. Additionally, overgos are able to provide evidence of genomic rearrangements in comparative physical mapping studies.

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Related in: MedlinePlus

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.
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Figure 4: 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.

Mentions: Clone data from the overgo probe hybridizations, in conjunction with clone fingerprint data, was used to construct physical maps of the rice chromosome 1 orthologues in O. nivara and O. officinalis. The O. nivara physical map of chromosome 1 is shown in Figure 4. While in most cases it is not possible to ascertain whether overgo markers were solely responsible for contig builds or merges in the physical map, we have determined that at least 89 of the overgo markers shown in Figure 4 confirmed the in silico alignment of the BES to the corresponding pseudomolecule of O. sativa chromosome 1, providing robustness to the physical map. Close inspection of the physical maps also revealed areas where overgos aided in the assembly of contigs, especially by bringing together clones in areas of low coverage. Three examples of these areas are shown in Figure 5.


Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum.

Hass-Jacobus BL, Futrell-Griggs M, Abernathy B, Westerman R, Goicoechea JL, Stein J, Klein P, Hurwitz B, Zhou B, Rakhshan F, Sanyal A, Gill N, Lin JY, Walling JG, Luo MZ, Ammiraju JS, Kudrna D, Kim HR, Ware D, Wing RA, San Miguel P, Jackson SA - BMC Genomics (2006)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1590032&req=5

Figure 4: 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.
Mentions: Clone data from the overgo probe hybridizations, in conjunction with clone fingerprint data, was used to construct physical maps of the rice chromosome 1 orthologues in O. nivara and O. officinalis. The O. nivara physical map of chromosome 1 is shown in Figure 4. While in most cases it is not possible to ascertain whether overgo markers were solely responsible for contig builds or merges in the physical map, we have determined that at least 89 of the overgo markers shown in Figure 4 confirmed the in silico alignment of the BES to the corresponding pseudomolecule of O. sativa chromosome 1, providing robustness to the physical map. Close inspection of the physical maps also revealed areas where overgos aided in the assembly of contigs, especially by bringing together clones in areas of low coverage. Three examples of these areas are shown in Figure 5.

Bottom Line: When rice overgos were aligned to available S. bicolor sequence, 29% of the overgos aligned with three or fewer mismatches; of these, 41% gave positive hybridization signals.Overgo hybridization patterns supported colinearity of loci in regions of sorghum chromosome 3 and rice chromosome 1 and suggested that a possible genomic inversion occurred in this syntenic region in one of the two genomes after the divergence of S. bicolor and O. sativa.The results of this study emphasize the importance of identifying conserved sequences in the reference sequence when designing overgo probes in order for those probes to hybridize successfully in distantly related species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA. barbara.jacobus@alumni.purdue.edu

ABSTRACT

Background: With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies. The genus Oryza includes 23 species that shared a common ancestor 8-10 million years ago making this an ideal model for investigations into the processes underlying domestication, as many of the Oryza species are still undergoing domestication. This study integrates high-throughput, hybridization-based markers with BAC end sequence and fingerprint data to construct physical maps of rice chromosome 1 orthologues in two wild Oryza species. Similar studies were undertaken in Sorghum bicolor, a species which diverged from cultivated rice 40-50 million years ago.

Results: Overgo markers, in conjunction with fingerprint and BAC end sequence data, were used to build sequence-ready BAC contigs for two wild Oryza species. The markers drove contig merges to construct physical maps syntenic to rice chromosome 1 in the wild species and provided evidence for at least one rearrangement on chromosome 1 of the O. sativa versus Oryza officinalis comparative map. When rice overgos were aligned to available S. bicolor sequence, 29% of the overgos aligned with three or fewer mismatches; of these, 41% gave positive hybridization signals. Overgo hybridization patterns supported colinearity of loci in regions of sorghum chromosome 3 and rice chromosome 1 and suggested that a possible genomic inversion occurred in this syntenic region in one of the two genomes after the divergence of S. bicolor and O. sativa.

Conclusion: The results of this study emphasize the importance of identifying conserved sequences in the reference sequence when designing overgo probes in order for those probes to hybridize successfully in distantly related species. As interspecific markers, overgos can be used successfully to construct physical maps in species which diverged less than 8 million years ago, and can be used in a more limited fashion to examine colinearity among species which diverged as much as 40 million years ago. Additionally, overgos are able to provide evidence of genomic rearrangements in comparative physical mapping studies.

Show MeSH
Related in: MedlinePlus