Requirements for a Deductive Query Language in a Genome-Mapping Database

A genome map of cultivated alfalfa was constructed using segregating restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNAs (RAPDs) in a diploid backcross population generated from noninbred parents. Among the 153 loci scored in 87 progeny, four segregation ratios were observed for codominant and dominant markers: 1:1, 1:2:1, 1:1:1:1, and 3:1. Deviations from expected Mendelian ratios (p < 0.05) were observed for 34% of the loci studied. A genome map was assembled from two separate linkage maps, each constructed from a subset of the segregation data. One linkage map was constructed from 46 RFLP and 40 RAPD markers segregating 1:1 from the F1 parent of the backcross and the other linkage map was constructed from 33 RFLP and 28 RAPD markers segregating 1:1 from the recurrent parent. Sixteen loci with alleles segregating 1:1 from both parents were used as locus bridges to align individual linkage groups between the two maps. The combined use of RFLPs and RAPDs was an effective method for developing an alfalfa genome map.Key words: genome mapping, RAPD, RFLP, locus bridges.

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Customized optical mapping by CRISPR–Cas9 mediated DNA labeling with multiple sgRNAs

Nucleic Acids Research ◽

10.1093/nar/gkaa1088 ◽

2020 ◽

Author(s):

Heba Z Abid ◽

Eleanor Young ◽

Jennifer McCaffrey ◽

Kaitlin Raseley ◽

Dharma Varapula ◽

...

Keyword(s):

Genome Mapping ◽

Repetitive Sequences ◽

Genomic Region ◽

Sequence Motif ◽

Whole Genome ◽

Long Distance ◽

Dna Labeling ◽

Guide Rnas ◽

Multiple Loci ◽

A Genome

Abstract Whole-genome mapping technologies have been developed as a complementary tool to provide scaffolds for genome assembly and structural variation analysis (1,2). We recently introduced a novel DNA labeling strategy based on a CRISPR–Cas9 genome editing system, which can target any 20bp sequences. The labeling strategy is specifically useful in targeting repetitive sequences, and sequences not accessible to other labeling methods. In this report, we present customized mapping strategies that extend the applications of CRISPR–Cas9 DNA labeling. We first design a CRISPR–Cas9 labeling strategy to interrogate and differentiate the single allele differences in NGG protospacer adjacent motifs (PAM sequence). Combined with sequence motif labeling, we can pinpoint the single-base differences in highly conserved sequences. In the second strategy, we design mapping patterns across a genome by selecting sets of specific single-guide RNAs (sgRNAs) for labeling multiple loci of a genomic region or a whole genome. By developing and optimizing a single tube synthesis of multiple sgRNAs, we demonstrate the utility of CRISPR–Cas9 mapping with 162 sgRNAs targeting the 2Mb Haemophilus influenzae chromosome. These CRISPR–Cas9 mapping approaches could be particularly useful for applications in defining long-distance haplotypes and pinpointing the breakpoints in large structural variants in complex genomes and microbial mixtures.

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Genome Mapping in Citrullus Populations Segregating for Fusarium Wilt Resistance

HortScience ◽

10.21273/hortsci.33.3.499f ◽

1998 ◽

Vol 33 (3) ◽

pp. 499f-500

Author(s):

Leigh K. Hawkins ◽

Fenny Dane ◽

Billy Rhodes

Keyword(s):

Molecular Markers ◽

Fusarium Wilt ◽

Genome Mapping ◽

Citrullus Lanatus ◽

Random Amplified Polymorphic Dna ◽

Plant Introduction ◽

Wilt Resistance ◽

A Genome ◽

Race 2 ◽

Fusarium Wilt Resistance

Fusarium wilt, caused by the soilborne fungus Fusarium oxysporum f.sp.niveum(FON), is one of the most economically important diseases of watermelon (Citrullus lanatus) worldwide. FON has been divided into three races (races 0, 1, and 2) determined by differential pathogenicity assays. Most commercial cultivars are resistant to races 0 and 1; whereas none are resistant to race 2. Few morphological and isozyme variations are seen in the cultivated watermelon, but molecular markers, such as random amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs), have been shown to generate several polymorphisms. Segregating populations, derived from a cross between watermelon cultivar New Hampshire Midget, susceptible to all three races of FON and the resistant C. lanatus plant introduction PI 296341, were used to detect molecular markers linked to Fusarium wilt resistance. In a preliminary experiment, more than 180 10-mer primers were screened against the parents and the F1. Informative RAPD primers were identified and used in conjunction with AFLP and SSR markers to generate a genome map.

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Development of Microsatellites: A Powerful Genetic Marker

The Agriculturists ◽

10.3329/agric.v13i1.26559 ◽

2016 ◽

Vol 13 (1) ◽

pp. 152-172 ◽

Cited By ~ 3

Author(s):

M Moniruzzaman ◽

R Khatun ◽

Zahira Yaakob ◽

M S Khan ◽

A A Mintoo

Keyword(s):

Tandem Repeats ◽

Genomic Library ◽

De Novo ◽

Genome Mapping ◽

Variable Number ◽

Genomic Libraries ◽

Microsatellite Isolation ◽

Major Disadvantage ◽

A Genome ◽

Variable Number Tandem Repeats

The tandem repeats, conserved short segments of DNA, which are found in all prokaryotic and eukaryotic genomes, are called microsatellites. It is also known as variable number tandem repeats (VNTRs), simple sequence repeats (SSRs) and short tandem repeats (STRs). Microsatellites present in both coding and non-coding regions of a genome. The high polymorphism of microsatellites makes them powerful genetic markers for genome mapping of many organisms. It is also suitable for ancient and forensic DNA studies for population genetics and conservation of biological resources. The major disadvantage of microsatellites is that for the first time they need to be isolated de novo from most species being examined. The task of microsatellite isolation is quite cumbersome involving in terms of effort and time, because it traditionally involves screening of genomic libraries. Cross-species amplification, Mining microsatellites from nucleotide sequenced data and Genomic library- based method are general methods of microsatellite isolation. Cross-species method may not effective for all species, Data mining is not applicable if there is no or limited data of DNA sequence. Genomic library based method is the best choice. Traditional protocol, primer extension protocol, selective hybridization, and Fast Isolation by AFLP of Sequences containing repeats (FIASCO) are the protocols of microsatellite development based on genomic library. FIASCO is the best protocol ever developed.The Agriculturists 2015; 13(1) 152-172

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Segmental allotetraploidy and allelic interactions in buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.) as revealed by genome mapping

Genome ◽

10.1139/g03-005 ◽

2003 ◽

Vol 46 (2) ◽

pp. 304-313 ◽

Cited By ~ 30

Author(s):

R W Jessup ◽

B L Burson ◽

G Burow ◽

Y -W Wang ◽

C Chang ◽

...

Keyword(s):

Restriction Fragment ◽

Fragment Length ◽

Genome Mapping ◽

Linkage Groups ◽

Cenchrus Ciliaris ◽

Preferential Pairing ◽

Pennisetum Ciliare ◽

Length Polymorphisms ◽

A Genome ◽

Restriction Fragment Length

Linkage analyses increasingly complement cytological and traditional plant breeding techniques by providing valuable information regarding genome organization and transmission genetics of complex polyploid species. This study reports a genome map of buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.). Maternal and paternal maps were constructed with restriction fragment length polymorphisms (RFLPs) segregating in 87 F1 progeny from an intraspecific cross between two heterozygous genotypes. A survey of 862 heterologous cDNAs and gDNAs from across the Poaceae, as well as 443 buffelgrass cDNAs, yielded 100 and 360 polymorphic probes, respectively. The maternal map included 322 RFLPs, 47 linkage groups, and 3464 cM, whereas the paternal map contained 245 RFLPs, 42 linkage groups, and 2757 cM. Approximately 70 to 80% of the buffelgrass genome was covered, and the average marker spacing was 10.8 and 11.3 cM on the respective maps. Preferential pairing was indicated between many linkage groups, which supports cytological reports that buffelgrass is a segmental allotetraploid. More preferential pairing (disomy) was found in the maternal than paternal parent across linkage groups (55 vs. 38%) and loci (48 vs. 15%). Comparison of interval lengths in 15 allelic bridges indicated significantly less meiotic recombination in paternal gametes. Allelic interactions were detected in four regions of the maternal map and were absent in the paternal map.Key words: linkage map, segmental allopolyploidy, restriction fragment length polymorphism, Poaceae, chromosome pairing.

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FGMP: assessing fungal genome completeness and gene content

10.1101/049619 ◽

2016 ◽

Cited By ~ 1

Author(s):

Ousmane H. Cissé ◽

Jason E. Stajich

Keyword(s):

Genome Mapping ◽

Genomic Data ◽

Model Systems ◽

Fungal Genome ◽

Model Organisms ◽

Computational Framework ◽

A Genome ◽

Dna Elements ◽

High Throughput Dna Sequencing ◽

Genome Assemblies

AbstractBackgroundInexpensive high-throughput DNA sequencing has democratized access to genetic information for most organisms so that research utilizing a genome or transcriptome of an organism is not limited to model systems. However, the quality of the assemblies of sampled genomes can vary greatly which hampers utility for comparisons and meaningful interpretation. The uncertainty of the completeness of a given genome sequence can limit feasibility of asserting patterns of high rates of gene loss reported in many lineages.ResultsWe propose a computational framework and sequence resource for assessing completeness of fungal genomes called FGMP (Fungal Genome Mapping Project). Our approach is based on evolutionary conserved sets of proteins and DNA elements and is applicable to various types of genomic data. We present a comparison of FGMP and state-of-the-art methods for genome completeness assessment utilizing 246 genome assemblies of fungi. We discuss genome assembly improvements/degradations in 57 cases where assemblies have been updated, as recorded by NCBI assembly archive.ConclusionFGMP is an accurate tool for quantifying level of completion from fungal genomic data. It is particularly useful for non-model organisms without reference genomes and can be used directly on unassembled reads, which can help reducing genome sequencing costs.

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A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics

10.1101/2021.02.17.431678 ◽

2021 ◽

Author(s):

Nikolay Alabi ◽

Yihan Wu ◽

Oliver Bossdorf ◽

Loren H. Rieseberg ◽

Robert I. Colautti

Keyword(s):

Western Europe ◽

De Novo ◽

Genome Mapping ◽

Draft Genome ◽

Alliaria Petiolata ◽

Ecological Knowledge ◽

Garlic Mustard ◽

Draft Genome Assembly ◽

A Genome ◽

Invasion Genetics

AbstractThe emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ~70× coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121Mb; L50 = 2) with 99.7% of the 1.1Gb genome mapping to contigs of at least 50Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe Almost, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite a genome-wide average of < 2% heterozygosity. The continuity and gene space quality of our draft genome assembly will enable genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation efforts.

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Genome-Wide Characterization of B-BOX Gene Family and Their Responses to Light Quality and Cold Stress in Tomato

10.21203/rs.3.rs-64408/v1 ◽

2020 ◽

Author(s):

Xin Bu ◽

Xiujie Wang ◽

Jiarong Yan ◽

Ying Zhang ◽

Shunyuan Zhou ◽

...

Keyword(s):

Gene Family ◽

Low Temperatures ◽

Light Quality ◽

Genome Mapping ◽

Regulatory Elements ◽

Protein Motif ◽

Genome Wide ◽

A Genome ◽

Duplication Events ◽

High Conservation

Abstract Background: Perceiving incoming environmental information is critical for optimizing plant growth and development. Multiple B-box proteins (BBXs) play essential roles in light-dependent developmental processes in plants. However, whether BBXs function as a signal integrator between light and temperature in tomato plants remains elusive.Results: In this study, 31 SlBBX genes were identified from the newly released tomato (Solanum lycopersicum) genome sequences, and were clustered into five subgroups with phylogenetic analysis. Gene structure and protein motif analyses showed relatively high conservation of closely clustered SlBBX genes within each subgroup; however, genome mapping analysis indicated the uneven distribution of the SlBBX genes on tomato chromosomes. Synteny analysis indicated that segmental duplication events happened in the expansion of the SlBBX genes in tomato. Promoter cis-regulatory elements prediction indicated that SlBBX genes were highly responsive to light, hormones, and stress conditions. Furthermore, the transcript analysis revealed that various SlBBX genes differed significantly in expression after exposure to different light quality and low temperatures, while 61.3% of SlBBX genes were responsive to both light and low temperatures. Conclusions: Our study presented a genome-wide survey of SlBBX gene family in tomato, and emphasized their functions in perceiving light quality and low temperature, which may improve the current understanding of SlBBX gene functions in integrating light and temperature signals for plant adaptation to adverse environments.

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Genome Report: A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab339 ◽

2021 ◽

Author(s):

Nikolay Alabi ◽

Yihan Wu ◽

Oliver Bossdorf ◽

Loren H Rieseberg ◽

Robert I Colautti

Keyword(s):

De Novo Assembly ◽

De Novo ◽

Genome Mapping ◽

Draft Genome ◽

Alliaria Petiolata ◽

Conservation Strategies ◽

Ecological Knowledge ◽

Garlic Mustard ◽

A Genome ◽

Invasion Genetics

Abstract The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC3-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ∼70 × coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7% of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite < 2% genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.

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Experiences with Resource Provisioning for Scientific Workflows Using Corral

Scientific Programming ◽

10.1155/2010/208568 ◽

2010 ◽

Vol 18 (2) ◽

pp. 77-92 ◽

Cited By ~ 7

Author(s):

Gideon Juve ◽

Ewa Deelman ◽

Karan Vahi ◽

Gaurang Mehta

Keyword(s):

Large Scale ◽

Genome Mapping ◽

Resource Provisioning ◽

Distributed Resources ◽

Local Cluster ◽

Loosely Coupled ◽

Large Numbers ◽

A Genome ◽

Order Of Magnitude ◽

Level Scheduling

The development of grid and workflow technologies has enabled complex, loosely coupled scientific applications to be executed on distributed resources. Many of these applications consist of large numbers of short-duration tasks whose runtimes are heavily influenced by delays in the execution environment. Such applications often perform poorly on the grid because of the large scheduling overheads commonly found in grids. In this paper we present a provisioning system based on multi-level scheduling that improves workflow runtime by reducing scheduling overheads. The system reserves resources for the exclusive use of the application, and gives applications control over scheduling policies. We describe our experiences with the system when running a suite of real workflow-based applications including in astronomy, earthquake science, and genomics. Provisioning resources with Corral ahead of the workflow execution, reduced the runtime of the astronomy application by up to 78% (45% on average) and of a genome mapping application by an order of magnitude when compared to traditional methods. We also show how provisioning can benefit applications both on a small local cluster as well as a large-scale campus resource.

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