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Whitelist Us! Here's how to disable adblocking on our site. Click on the icon for your Adblocker in your browser. We constructed a new cow-human synteny map that expands upon previous maps. We also identified for the first time a portion of the B. Seven years after the first whole-genome assembly of the human genome [ 1 ], sequencing and assembly of mammalian genomes has become almost routine. However, despite the continuing progress on sequencing technology, the assembly problem is far from solved. Assemblies of large genomes contain numerous errors, and many years of work can be dedicated to correcting errors and improving an assembly [ 2 ].

Technical progress in computational assembly methods offers the potential to make many of these improvements far faster and more efficiently than would be possible by laboratory methods. Having an accurate assembly of the genome of an important species provides an invaluable substrate for future research. For example, studies of genetic diversity need a good reference genome in order to catalog differences in new strains or lineages.

Expression analyses that sequence RNA from various tissues rely on the genome to map out gene models and to discover such features as alternative splicing. Creating a more complete, accurate reference genome avoids much wasted effort that might result from attempts to use erroneous polymorphisms or other errors.

As that study pointed out, an improved assembly "greatly improves the precision of biological analyses To assemble the genome of the domestic cow, Bos taurus , we have augmented the latest assembly software with additional post-processing algorithms that utilize paired-end sequence information, mapping data, and synteny with the human genome to detect errors, correct inverted segments, and fill gaps in the sequence.

The resulting assembly provides a very high-quality resource for annotation and ongoing studies in the genetics of the domestic cow as well as comparative mammalian genomics. Our assembly of the B. The remaining Mbp are contained in unplaced contiguous sequences contigs. Figure 1 shows the amount of sequence placed in each of the 29 autosomes and chromosome X. As the figure shows, length is inversely correlated with chromosome number, with a few exceptions, including chromosomes 11, 20, and Chromosome Chr lengths in base pairs based on amount of sequence in the B.

We evaluated our assembly University of Maryland assembly of B. Each of the assemblies contains both 'placed' sequence, for which the location on the chromosomes is known, and 'unplaced' sequence. As we describe below, all sequence on BtX in our assembly is homologous to the human X chromosome HsX. Independently generated mapping data provide another measure of the quality of the assembly.

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We aligned all of the 17, markers of which 17, are unique in their composite map Cmap to both assemblies. Of the Cmap markers, 14, align to the UMD2 assembly's chromosomes, versus 13, markers 6. One likely reason for the larger size and greater genome coverage of our assembly is the BAC-based assembly strategy employed by the Atlas assembler used to build BCM4 [ 5 ]. That strategy involved breaking the genome into BAC-sized pieces, assembling those pieces using BAC reads and whole-genome shotgun WGS reads, and then merging the results.

This strategy fails to incorporate reads that fall outside the regions covered by BACs. We directly aligned the two assemblies against each other in order to detect any major disagreements. Figure 3 illustrates two relatively large inversions, spanning 4 and 2. In both of these cases, as in all other large discrepancies, the Cmap data support the UMD2 assembly. Alignment plots for all 30 chromosomes are provided online in Additional data file 2.

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We conducted a comparison between the two assemblies for differences in the number of apparent segmental duplications, focusing on the types of duplications that might confound assembly. If these regions were incorrectly collapsed duplications in UMD2, then coverage by WGS reads should be higher approximately twice the genome-wide level and mate pairs flanking the regions would show inconsistencies [ 6 ].

However, after analyzing regions that are single-copy in UMD2 and duplicated in BCM4, we found no substantial discrepancies in either mate pairs or coverage, indicating that the regions are most likely single-copy. It is possible that BCM4 failed to merge overlapping BACs from different haplotypes , which would give the appearance of segmental duplications; further analysis will be necessary to resolve this question. Another indicator of assembly completeness, and also of its potential for annotation, is the extent to which known gene sequences can be mapped onto it.

We aligned 8, independently validated full-length cow mRNA sequences to the two assemblies, using spliced alignment mapping tools see Materials and methods. Figure 4a and Table S1 in Additional data file 1 show the number of sequences that had more than a fraction f of their bases contained in each genome for a range of f values. Together, the two assemblies contain all but 28 of the mRNA sequences, as well as paralogs of 25 of the remaining 28 genes. More significant differences between the two genomes become apparent when the aligned fraction of the gene is considered.

We also directly compared the distributions of gene coverage between the two assemblies, shown in Figure 4b.

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Overall, UMD2 has a more complete representation of the genes while containing nearly every gene in BCM4, and therefore provides a more comprehensive resource for gene annotation. Assembly comparison by gene mapping. Negative values indicate that BCM4 has more genes at a given level, while positive values indicate that UMD2 has more.

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Some of these might be valid haplotype differences, in which the two assemblies are both correct, while others might be errors. We focused our analysis on a subset of positions where the underlying read data indicated that the position was highly likely to be homozygous, because a large majority or all reads agreed with one another. We also required that each SND was flanked by bp exact matches in both assemblies see Materials and methods , which reduced the set of SNDs to , We then looked for cases where no more than one read confirmed one assembly, and all other reads at least three confirmed the other assembly.

Another way to look at fine-grain accuracy is to compare the assembly to independently generated sequences. We compared both assemblies to six finished BACS, from a different cow than the source of the whole-genome project. Although some of these mismatches are likely due to true polymorphisms, the excess discrepancies in BCM4 are likely to represent erroneous base calls, indicating a higher error rate in BCM4.

Because two-thirds of the data came from a female cow, and the male DNA was based on a BAC library Materials and methods , only a very limited amount of the assembly can be assigned to the Y chromosome. It is worth noting here that the BCM4 assembly does not assign any sequence to the Y chromosome. We aligned all unplaced contigs to the human Y chromosome in an effort to identify B. When contigs in the same scaffolds were included, the total increased to 94 contigs, covering , bp. These contigs include a portion of the male sex determination gene SRY [ 7 ].

Because few of these contigs are currently ordered with respect to one another, further work will be required to construct a better picture of the Y chromosome's structure. Although humans are closer to mice than to cows, cows and humans have sufficient DNA sequence similarity to enable us to map the human genome almost entirely onto cow.

Previous efforts based on mapping data showed that human and cow have approximately homologous blocks of DNA [ 8 ]. We used flexible criteria see Materials and methods to align all cow chromosomes to all human chromosomes, creating a new, high-resolution synteny map of human and cow. A region was considered a homologous synteny block HSB if the human-cow alignment extended for at least Kbp and if it was not interrupted by an inversion or by an HSB on another chromosome. A modified Oxford grid, shown in Table 3 , shows the numbers of syntenic blocks shared between all human and cow chromosomes.

Our new, more-detailed map largely agrees with previously identified blocks, with a number of important differences. In a few cases, our map has fewer HSBs between a pair of chromosomes, but in many more cases, we detected new synteny blocks that had been missed previously; most of these were inversions or interruptions in larger blocks. Overall, our map increases the total number of HSBs to These were created from evolutionary breakpoints minus 23 human chromosomes that have appeared since the divergence of human and cow.

Figure 5 , which shows the alignment of BtX and HsX, reveals that five large blocks cover most of the two chromosomes, with one additional, much smaller block of Kbp spanning the region from approximately Not visible on this scale, though, are seven additional inversions, bringing the total number of HSBs for the X chromosome to Aligment of B. Most of the two chromosomes is shared in the five large blocks evident in the figure.

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