Strategies for the systematic sequencing of complex genomes

Green, Eric D.

doi:10.1038/35084503

Cited by 163 publications

(99 citation statements)

References 90 publications

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“…An approach recommended for the systematic sequencing of complex genomes is a strategy in which both the clone-by-clone approach and the wholegenome shotgun sequencing (WGS) methods are combined (Green 2001). For this WGS approach to work efficiently, high-quality physical maps are essential, especially for the larger genomes, which includes wheat (Meyers et al 2004).…”

Section: Discussionmentioning

confidence: 99%

High-Resolution Radiation Hybrid Map of Wheat Chromosome 1D

Kalavacharla

Hossain

et al. 2006

Genetics

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Physical mapping methods that do not rely on meiotic recombination are necessary for complex polyploid genomes such as wheat (Triticum aestivum L.). This need is due to the uneven distribution of recombination and significant variation in genetic to physical distance ratios. One method that has proven valuable in a number of nonplant and plant systems is radiation hybrid (RH) mapping. This work presents, for the first time, a high-resolution radiation hybrid map of wheat chromosome 1D (D genome) in a tetraploid durum wheat (T. turgidum L., AB genomes) background. An RH panel of 87 lines was used to map 378 molecular markers, which detected 2312 chromosome breaks. The total map distance ranged from $3,341 cR 35,000 for five major linkage groups to 11,773 cR 35,000 for a comprehensive map. The mapping resolution was estimated to be $199 kb/break and provided the starting point for BAC contig alignment. To date, this is the highest resolution that has been obtained by plant RH mapping and serves as a first step for the development of RH resources in wheat.

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Section: Discussionmentioning

confidence: 99%

High-Resolution Radiation Hybrid Map of Wheat Chromosome 1D

Kalavacharla

Hossain

et al. 2006

Genetics

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“…BAC clones containing genomic regions encompassing the chimpanzee, baboon, and rat Siglec gene clusters were isolated and mapped from BACPAC Resource libraries (www.chori.org͞ bacpac) by using an established universal probe hybridization strategy (15,17) and were subjected to standard shotgun sequencing (18,19) by the National Institutes of Health Intramural Sequencing Center (www.nisc.nih.gov) to an advanced draft stage (see individual GenBank entries and Supporting Text, which is published as supporting information on the PNAS web site, for details and methods for assembly of sequence sets, pairwise sequence alignment, and gene prediction͞annotation).…”

Section: Methodsmentioning

confidence: 99%

Large-scale sequencing of the CD33-related Siglec gene cluster in five mammalian species reveals rapid evolution by multiple mechanisms

Angata

Margulies

Green

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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153

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Siglecs are a recently discovered family of animal lectins that belong to the Ig superfamily and recognize sialic acids (Sias). CD33-related Siglecs (CD33rSiglecs) are a subgroup with as-yetunknown functions, characterized by sequence homology, expression on innate immune cells, conserved cytosolic tyrosine-based signaling motifs, and a clustered localization of their genes. To better understand the biology and evolution of CD33rSiglecs, we sequenced and compared the CD33rSiglec gene cluster from multiple mammalian species. Within the sequenced region, the segments containing CD33rSiglec genes showed a lower degree of sequence conservation. In contrast to the adjacent conserved kallikrein-like genes, the CD33rSiglec genes showed extensive species differences, including expansions of gene subsets; gene deletions, including one human-specific loss of a novel functional primate Siglec (Siglec-13); exon shuffling, generating hybrid genes; accelerated accumulation of nonsynonymous substitutions in the Sia-recognition domain; and multiple instances of mutations of an arginine residue essential for Sia recognition in otherwise intact Siglecs. Nonsynonymous differences between human and chimpanzee orthologs showed uneven distribution between the two ␤ sheets of the Sia-recognition domain, suggesting biased mutation accumulation. These data indicate that CD33rSiglec genes are undergoing rapid evolution via multiple genetic mechanisms, possibly due to an evolutionary ''arms race'' between hosts and pathogens involving Sia recognition. These studies, which reflect one of the most complete comparative sequence analyses of a rapidly evolving gene cluster, provide a clearer picture of the ortholog status of CD33rSiglecs among primates and rodents and also facilitate rational recommendations regarding their nomenclature.

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“…2), which is within 60 kb of STS3. Large length mutations that differentiate haplotypes can cause substantial problems for shotgun sequence-assembly programs such as  (N. Putnam, personal communication) and  (Green, 2001). Currently more than one-third of the 8.1X Populus genome shotgun assembly database occurs in scaffolds smaller than one megabase (Populus Genome Sequencing Consortium, unpublished), and much of this misassembly is probably caused by hemizygosity in the sequenced tree.…”

Section: Disease-resistance Candidate Genesmentioning

confidence: 99%

Genetic and physical mapping of Melampsora rust resistance genes in Populus and characterization of linkage disequilibrium and flanking genomic sequence

et al. 2004

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Summary• In an attempt to elucidate the molecular mechanisms of Melampsora rust resistance in Populus trichocarpa , we have mapped two resistance loci, MXC3 and MER , and intensively characterized the flanking genomic sequence for the MXC3 locus and the level of linkage disequilibrium (LD) in natural populations.• We used an interspecific backcross pedigree and a genetic map that was highly saturated with AFLP and SSR markers, and assembled shotgun-sequence data in the region containing markers linked to MXC3 .• The two loci were mapped to different linkage groups. Linkage disequilibrium for MXC3 was confined to two closely linked regions spanning 34 and 16 kb, respectively. The MXC3 region also contained six disease-resistance candidate genes.• The MER and MXC3 loci are clearly distinct, and may have different mechanisms of resistance, as different classes of putative resistance genes were present near each locus. The suppressed recombination previously observed in the MXC3 region was possibly caused by extensive hemizygous rearrangements confined to the original parent tree. The relatively low observed LD may facilitate association studies using candidate genes for rust resistance, but will probably inhibit marker-aided selection.

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Strategies for the systematic sequencing of complex genomes

Cited by 163 publications

References 90 publications

High-Resolution Radiation Hybrid Map of Wheat Chromosome 1D

High-Resolution Radiation Hybrid Map of Wheat Chromosome 1D

Large-scale sequencing of the CD33-related Siglec gene cluster in five mammalian species reveals rapid evolution by multiple mechanisms

Genetic and physical mapping of Melampsora rust resistance genes in Populus and characterization of linkage disequilibrium and flanking genomic sequence

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