Reference-guided assembly of four diverse
            <i>Arabidopsis thaliana</i>
            genomes

Schneeberger, Korbinian; Ossowski, Stephan; Ott, Felix; Klein, Juliane D.; Wang, Xi; Lanz, Christa; Smith, Lisa M.; Cao, Jun; Fitz, Joffrey; Warthmann, Norman; Henz, Stefan R.; Huson, Daniel H.; Weigel, Detlef

doi:10.1073/pnas.1107739108

Cited by 232 publications

(243 citation statements)

References 43 publications

(40 reference statements)

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“…Only markers (i) identified by all three softwares (deletions only by Shore), (ii) observed in >80% of 75 (=7 + 31 × 2 + 2 × 3) sequenced F 2 genomes in corresponding heterozygous regions, and (iii) concordant with the 461,070 identified previously (18), were considered to be adequate. This set comprises 373,614 SNPs and 41,743 1-to 3-bp Ler deletions, a total of 415,357 markers, representing on average 1 every 289 bp.…”

Section: Resultsmentioning

confidence: 99%

Great majority of recombination events in Arabidopsis are gene conversion events

Yang

Yuan

Wang

et al. 2012

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

105

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The evolutionary importance of meiosis may not solely be associated with allelic shuffling caused by crossing-over but also have to do with its more immediate effects such as gene conversion. Although estimates of the crossing-over rate are often well resolved, the gene conversion rate is much less clear. In Arabidopsis, for example, nextgeneration sequencing approaches suggest that the two rates are about the same, which contrasts with indirect measures, these suggesting an excess of gene conversion. Here, we provide analysis of this problem by sequencing 40 F 2 Arabidopsis plants and their parents. Small gene conversion tracts, with biased gene conversion content, represent over 90% (probably nearer 99%) of all recombination events. The rate of alteration of protein sequence caused by gene conversion is over 600 times that caused by mutation. Finally, our analysis reveals recombination hot spots and unexpectedly high recombination rates near centromeres. This may be responsible for the previously unexplained pattern of high genetic diversity near Arabidopsis centromeres.W hen considering the population genetic impact of recombination, classical theories predominantly concentrate on the impact of allelic shuffling, mediated by crossing-over, and the effect this has on linkage disequilibrium and, in turn, the effect the fate of one allele has on its genomic neighbors (1). However, when programmed double-strand breaks (DSBs) are introduced into chromosomes to initiate meiotic recombination, both crossover (CO) and noncrossover (non-CO) recombination events can occur.

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Section: Resultsmentioning

confidence: 99%

Great majority of recombination events in Arabidopsis are gene conversion events

Yang

Yuan

Wang

et al. 2012

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

105

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“…Numerous genomic polymorphisms have been reported between two Arabidopsis ecotypes (geographic variants), Columbia (Col, TAIR10 assembly; ref. 35) and Landsberg erecta (Ler), including copy number variants (CNVs), large deletions, insertions, and inversions (31,(36)(37)(38). These SVs significantly influence genotyping, particularly SNP calling.…”

Section: Resultsmentioning

confidence: 99%

Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping

Chen

Copenhaver

et al. 2014

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

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DNA polymorphisms are important markers in genetic analyses and are increasingly detected by using genome resequencing. However, the presence of repetitive sequences and structural variants can lead to false positives in the identification of polymorphic alleles. Here, we describe an analysis strategy that minimizes false positives in allelic detection and present analyses of recently published resequencing data from Arabidopsis meiotic products and individual humans. Our analysis enables the accurate detection of sequencing errors, small insertions and deletions (indels), and structural variants, including large reciprocal indels and copy number variants, from comparisons between the resequenced and reference genomes. We offer an alternative interpretation of the sequencing data of meiotic products, including the number and type of recombination events, to illustrate the potential for mistakes in single-nucleotide polymorphism calling. Using these examples, we propose that the detection of DNA polymorphisms using resequencing data needs to account for nonallelic homologous sequences. Fig. 1 A and B). They can have phenotypic consequences and also serve as molecular markers for genetic analyses, facilitating linkage and association studies of genetic diseases, and other traits in humans (4-6), animals, plants, (7)(8)(9)(10) and other organisms. Using DNA polymorphisms for modern genetic applications requires low-error, high-throughput analytical strategies. Here, we illustrate the use of short-read nextgeneration sequencing (NGS) data to detect DNA polymorphisms in the context of whole-genome analysis of meiotic products.There are many methods for detecting SNPs (11-14) and structural variants (SVs) (15-25), including NGS, which can capture nearly all DNA polymorphisms (26-28). This approach has been widely used to analyze markers in crop species such as rice (29), genes associated with diseases (6, 26), and meiotic recombination in yeast and plants (30,31). However, accurate identification of DNA polymorphisms can be challenging, in part because short-read sequencing data have limited information for inferring chromosomal context.Genomes usually contain repetitive sequences that can differ in copy number between individuals (26-28, 31); therefore, resequencing analyses must account for chromosomal context to avoid mistaking highly similar paralogous sequences for polymorphisms. Here, we use recently published datasets to describe several DNA sequence features that can be mistaken as allelic (32, 33) and describe a strategy for differentiating between repetitive sequences and polymorphic alleles. We illustrate the effectiveness of these analyses by examining the reported polymorphisms from the published datasets.Meiotic recombination is initiated by DNA double-strand breaks (DSBs) catalyzed by the topoisomerase-like SPORULATION 11 (SPO11). DSBs are repaired as either crossovers (COs) between chromosomes (Fig. 1C), or noncrossovers (NCOs). Both COs and NCOs can be accompanied by gene conversion (GC) events, whic...

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“…Characterization of domestication-associated genes and their genetic variation relies on high-quality genome sequences of both the cultivated species and its immediate progenitor 44,45 . Hence, we further sequenced the O. rufipogon accession W1943 with 100-fold genome coverage and carried out de novo genome assembly.…”

Section: Identification Of Domestication-associated Variantsmentioning

confidence: 99%

A map of rice genome variation reveals the origin of cultivated rice

Huang

Kurata

Wei

et al. 2012

Nature

1,388

109

1,518

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Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.Cultivated rice (Oryza sativa L.), which is grown worldwide and is one of the most important cereals for human nutrition, is considered to have been domesticated from wild rice (Oryza rufipogon) thousands of years ago 1-4 . The differences between O. sativa and O. rufipogon are reflected in a wide range of morphological and physiological traits [5][6][7][8][9] . Despite the fact that rice is a major cereal and a model system for plant biology, the evolutionary origins and domestication processes of cultivated rice have long been debated. The puzzles about rice domestication include: (1) where the geographic origin of cultivated rice was, (2) which types of O. rufipogon served as its direct wild progenitor, and (3) whether the two subspecies of cultivated rice, indica and japonica, are derived from a single or multiple domestications.A wide range of genetic and archaeological studies have been carried out to examine the phylogenetic relationships of rice, and investigate the demographic history of rice domestication [10][11][12][13][14][15][16][17][18][19] . Molecular phylogenetic analyses indicated that indica and japonica originated independently 3,10,20 . However, the well-characterized domestication genes in rice were found to be fixed in both subspecies with the same alleles, thus supporting a single domestication origin [6][7][8][9]16 . Recently, a demographic analysis of single-nucleotide polymorphisms (SNPs) detected from 630 gene fragments suggested a single domestication origin of rice 17 . Meanwhile, population genetics analyses of genome-wide data of cultivated and wild rice have tended to suggest that indica and japonica genomes generally appear to be of independent origin 1...

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Reference-guided assembly of four diverse Arabidopsis thaliana genomes

Cited by 232 publications

References 43 publications

Great majority of recombination events in Arabidopsis are gene conversion events

Great majority of recombination events in Arabidopsis are gene conversion events

Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping

A map of rice genome variation reveals the origin of cultivated rice

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