ArticleGenome research2000
A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing.
Article in Genome research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
63 citing papers in PubMed, 149 citations in OpenAlex.
- Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era.Plants (Basel, Switzerland) · 2020Review
- An Improved Recombineering Toolset for Plants.The Plant cell · 2020Article
- Article
- Construction of a high-coverage bacterial artificial chromosome library and comprehensive genetic linkage map of yellowtail Seriola quinqueradiata.BMC research notes · 2014Article
- Expression of endogenous para-retroviral genes and molecular analysis of the integration events in its plant host Dahlia variabilis.Virus genes · 2014Article
- Generation of physical map contig-specific sequences.Frontiers in genetics · 2014Review
- Bacilliform DNA-containing plant viruses in the tropics: commonalities within a genetically diverse group.Molecular plant pathology · 2013Review
- Construction and characterization of a BAC library from the Coffea arabica genotype Timor Hybrid CIFC 832/2.Genetica · 2013Article
- BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.).BMC genomics · 2011Article
- Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.).BMC plant biology · 2011Article
- ps-2, the gene responsible for functional sterility in tomato, due to non-dehiscent anthers, is the result of a mutation in a novel polygalacturonase gene.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- A BAC library of Beta vulgaris L. for the targeted isolation of centromeric DNA and molecular cytogenetics of Beta species.Genetica · 2009Article
- Tomato phenylalanine ammonia-lyase gene family, highly redundant but strongly underutilized.The Journal of biological chemistry · 2008Article
- Comprehensive resources for tomato functional genomics based on the miniature model tomato micro-tom.Current genomics · 2008Article
- Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato.BMC plant biology · 2008Article
- Construction of a BAC library and mapping BAC clones to the linkage map of Barramundi, Lates calcarifer.BMC genomics · 2008Article
- Novel bacterial artificial chromosome vector pUvBBAC for use in studies of the functional genomics of Listeria spp.Applied and environmental microbiology · 2008Article
- FISH mapping and molecular organization of the major repetitive sequences of tomato.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2008Article
- End-sequencing and characterization of silkworm (Bombyx mori) bacterial artificial chromosome libraries.BMC genomics · 2007Article
- Development of a physical map of the soybean pathogen Fusarium virguliforme based on synteny with Fusarium graminearum genomic DNA.BMC genomics · 2007Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently a new strategy using BAC end sequences as sequence-tagged connectors (STCs) was proposed for whole-genome sequencing projects. In this study, we present the construction and detailed characterization of a 15.0 haploid genome equivalent BAC library for the cultivated tomato, Lycopersicon esculentum cv. Heinz 1706. The library contains 129,024 clones with an average insert size of 117.5 kb and a chloroplast content of 1.11%. BAC end sequences from 1490 ends were generated and analyzed as a preliminary evaluation for using this library to develop an STC framework to sequence the tomato genome. A total of 1205 BAC end sequences (80.9%) were obtained, with an average length of 360 high-quality bases, and were searched against the GenBank database. Using a cutoff expectation value of <10(-6), and combining the results from BLASTN, BLASTX, and TBLASTX searches, 24.3% of the BAC end sequences were similar to known sequences, of which almost half (48.7%) share sequence similarities to retrotransposons and 7% to known genes. Some of the transposable element sequences were the first reported in tomato, such as sequences similar to maize transposon Activator (Ac) ORF and tobacco pararetrovirus-like sequences. Interestingly, there were no BAC end sequences similar to the highly repeated TGRI and TGRII elements. However, the majority (70.3%) of STCs did not share significant sequence similarities to any sequences in GenBank at either the DNA or predicted protein levels, indicating that a large portion of the tomato genome is still unknown. Our data demonstrate that this BAC library is suitable for developing an STC database to sequence the tomato genome. The advantages of developing an STC framework for whole-genome sequencing of tomato are discussed.
Indexed as
Identifiers
10645957PMC310507W2130660293What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.