The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
Sequence and Comparative Analysis of the Maize NB Mitochondrial Genome
Open accessAbstract
The NB mitochondrial genome found in most fertile varieties of commercial maize (Zea mays subsp. mays) was sequenced. The 569,630-bp genome maps as a circle containing 58 identified genes encoding 33 known proteins, 3 ribosomal RNAs, and 21 tRNAs that recognize 14 amino acids. Among the 22 group II introns identified, 7 are trans-spliced. There are 121 open reading frames (ORFs) of at least 300 bp, only 3 of which exist in the mitochondrial genome of rice (Oryza sativa). In total, the identified mitochondrial genes, pseudogenes, ORFs, and cis-spliced introns extend over 127,555 bp (22.39%) of the genome. Integrated plastid DNA accounts for an additional 25,281 bp (4.44%) of the mitochondrial DNA, and phylogenetic analyses raise the possibility that copy correction with DNA from the plastid is an ongoing process. Although the genome contains six pairs of large repeats that cover 17.35% of the genome, small repeats (20–500 bp) account for only 5.59%, and transposable element sequences are extremely rare. MultiPip alignments show that maize mitochondrial DNA has little sequence similarity with other plant mitochondrial genomes, including that of rice, outside of the known functional genes. After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly three-fourths of the maize NB mitochondrial genome is still of unknown origin and function.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
Self-citationThe Pfam Protein Families Database
Bateman, A. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.276 · Cited by 14,000
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
Lowe, T. M., & Eddy, S. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.5.955 · Cited by 10,905
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment
Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,967
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
Consed: A Graphical Tool for Sequence Finishing
Gordon, D., Abajian, C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.195 · Cited by 3,302
Artemis: sequence visualization and annotation
Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M.-A., & Barrell, B. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.10.944 · Cited by 3,078
The COG database: new developments in phylogenetic classification of proteins from complete genomes
Tatusov, R. L. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.22 · Cited by 1,895
The staden sequence analysis package
Staden, R. (1996) · Molecular Biotechnology · doi:10.1007/bf02900361 · Cited by 1,263
PipMaker—A Web Server for Aligning Two Genomic DNA Sequences
Schwartz, S., Zhang, Z., Frazer, K. A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R., & Miller, W. (2000) · Genome Research · doi:10.1101/gr.10.4.577 · Cited by 1,174
The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides
Unseld, M., Marienfeld, J. R., Brandt, P., & Brennicke, A. (1997) · Nature Genetics · doi:10.1038/ng0197-57 · Cited by 991
The Pfam Protein Families Database
Bateman, A. G., Birney, E., Cerruti, L., Durbin, R. M., Etwiller, L., Eddy, S. R., Griffiths‐Jones, S., Howe, K., Marshall, M. S., & Sonnhammer, E. L. L. (2002) · PubMed Central · Cited by 764
Mitochondrial genomes: anything goes
Burger, G., Gray, M. W., & Franz Lang, B. (2003) · Trends in Genetics · doi:10.1016/j.tig.2003.10.012 · Cited by 629
Maier, R. M., Neckermann, K., Igloi, G. L., & Kössel, H. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0460 · Cited by 626
An ancestral mitochondrial DNA resembling a eubacterial genome in miniature
Lang, B. F., Burger, G., O'Kelly, C. J., Cedergren, R., Golding, G. B., Lemieux, C., Sankoff, D., Turmel, M., & Gray, M. W. (1997) · Nature · doi:10.1038/387493a0 · Cited by 620
Notsu, Y., Masood, S., Nishikawa, T., Kubo, N., Akiduki, G., Nakazono, M., Hirai, A., & Kadowaki, K. (2002) · Molecular Genetics and Genomics · doi:10.1007/s00438-002-0767-1 · Cited by 600
Oda, K., Yamato, K., Ohta, E., Nakamura, Y., Takemura, M., Nozato, N., Akashi, K., Kanegae, T., Ogura, Y., Kohchi, T., et al. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90708-r · Cited by 591
NUMTs in Sequenced Eukaryotic Genomes
Richly, E. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh110 · Cited by 523
The Chlamydomonas reinhardtii Plastid Chromosome
Maul, J. E., Lilly, J. W., Cui, L., dePamphilis, C. W., Miller, W., Harris, E. H., & Stern, D. B. (2002) · The Plant Cell · doi:10.1105/tpc.006155 · Cited by 426
Mitochondrial and chloroplast genomes of maize have a 12-kilobase DNA sequence in common
Stern, D. B., & Lonsdale, D. (1982) · Nature · doi:10.1038/299698a0 · Cited by 413
Evolutionary dynamics of grass genomes
Gaut, B. S. (2002) · New Phytologist · doi:10.1046/j.1469-8137.2002.00352.x · Cited by 403
Koch, M., Haubold, B., & Mitchell‐Olds, T. (2001) · American Journal of Botany · doi:10.2307/2657117 · Cited by 395
Bogsch, E. G., Sargent, F., Stanley, N. R., Berks, B. C., Robinson, C., & Palmer, T. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.29.18003 · Cited by 374
Palmer, J. D., Adams, K. L., Cho, Y., Parkinson, C. L., Qiu, Y.-L., & Song, K. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.13.6960 · Cited by 363
The physical map and organisatlon of the mitochondrial genome from the fertile cytoplasm of maize
Lonsdale, D., Hodge, T. P., & Fauron, C. M. ‐. (1984) · Nucleic Acids Research · doi:10.1093/nar/12.24.9249 · Cited by 323
Self-citationContrasting modes and tempos of genome evolution in land plant organelles
Palmer, J. D. (1990) · Trends in Genetics · doi:10.1016/0168-9525(90)90125-p · Cited by 260
MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences
Schwartz, S. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg579 · Cited by 236
Gene transfer from organelles to the nucleus: Frequent and in big chunks
Martin, W. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1633606100 · Cited by 219
Enrichment of Gene-Coding Sequences in Maize by Genome Filtration
Whitelaw, C. A., Barbazuk, W. B., Pertea, G., Chan, A. P., Cheung, F., Lee, Y., Zheng, L., van Heeringen, S., Karamycheva, S., Bennetzen, J. L., et al. (2003) · Science · doi:10.1126/science.1090047 · Cited by 208
Self-citationReaching for the ring: the study of mitochondrial genome structure
Bendich, A. J. (1993) · Current Genetics · doi:10.1007/bf00336777 · Cited by 203
The mystery of the rings: structure and replication of mitochondrial genomes from higher plants
Backert, S., Lynn Nielsen, B., & Börner, T. (1997) · Trends in Plant Science · doi:10.1016/s1360-1385(97)01148-5 · Cited by 174
Miropeats: graphical DNA sequence comparisons
Parsons, J. D. (1995) · Computer applications in the biosciences · doi:10.1093/bioinformatics/11.6.615 · Cited by 141
Tu, Z. J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.98.4.1699 · Cited by 130
The mitochondrial genome of Arabidopsis is composed of both native and immigrant information
Marienfeld, J. R., Unseld, M., & Brennicke, A. (1999) · Trends in Plant Science · doi:10.1016/s1360-1385(99)01502-2 · Cited by 129
Adams, K. L., Rosenblueth, M., Qiu, Y., & Palmer, J. D. (2001) · Genetics · doi:10.1093/genetics/158.3.1289 · Cited by 115
Wahleithner, J. A., Macfarlane, J. L., & Wolstenholme, D. R. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.2.548 · Cited by 93
Grasses as a Single Genetic System. Reassessment 2001
Freeling, M. (2001) · PLANT PHYSIOLOGY · doi:10.1104/pp.125.3.1191 · Cited by 90
Weber‐Lotfi, F., Dietrich, A., Weil, J. H., & Maréchal‐Drouard, L. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.17.5027 · Cited by 89
Striking differences in mitochondrial tRNA import between different plant species
Kumar, R., Small, I., Maréchal‐Drouard, L., et al. (1996) · Molecular and General Genetics MGG · doi:10.1007/bf02173005 · Cited by 76
A Magnetic Attraction to High-Throughput Genomics
Hawkins, T. L., McKernan, K. J., Jacotot, L., et al. (1997) · Science · doi:10.1126/science.276.5320.1887 · Cited by 57
Sangaré, A., Weil, J. H., Grienenberger, J. M., Fauron, C. M. ‐., & Lonsdale, D. (1990) · Molecular and General Genetics MGG · doi:10.1007/bf00265058 · Cited by 47
Self-citationThe BamHI, XhoI, SmaI restriction enzyme maps of the normal maize mitochondrial genome genotype B37
Fauron, C. M. ‐., & Havlik, M. H. (1988) · Nucleic Acids Research · doi:10.1093/nar/16.21.10395 · Cited by 31
Self-citationPlant mitochondrial rps2 genes code for proteins with a C-terminal extension that is processed
Perrotta, G., Grienenberger, J. M., & Gualberto, J. M. (2002) · Plant Molecular Biology · doi:10.1023/a:1019878212696 · Cited by 27
Cited by
Alverson, A. J., Wei, X., Rice, D. W., Stern, D. B., Barry, K., & Palmer, J. D. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq029 · Cited by 631
DNA Transfer from Organelles to the Nucleus: The Idiosyncratic Genetics of Endosymbiosis
Kleine, T., Maier, U. G., & Leister, D. (2009) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.043008.092119 · Cited by 391
Why Do We Still Have a Maternally Inherited Mitochondrial DNA? Insights from Evolutionary Medicine
Wallace, D. C. (2007) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.76.081205.150955 · Cited by 363
Richardson, A. O., Rice, D. W., Young, G. J., Alverson, A. J., & Palmer, J. D. (2013) · BMC Biology · doi:10.1186/1741-7007-11-29 · Cited by 344
Cytoplasmic male sterility (CMS) in hybrid breeding in field crops
Bohra, A., Jha, U. C., Adhimoolam, P., Bisht, D., & Singh, N. P. (2016) · Plant Cell Reports · doi:10.1007/s00299-016-1949-3 · Cited by 323
Metadata
- Authors
- Clifton, S. W., Minx, P., Fauron, C. M.-R., Gibson, M., Allen, J. O., Sun, H., Thompson, M., Barbazuk, W. B., Kanuganti, S., Tayloe, C., Meyer, L., Wilson, R. K., & Newton, K. J.
- Venue
- Plant Physiology
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-11-01
- Volume
- 136
- Issue
- 3
- Pages
- 3486-3503
- ISSN
- 0032-0889 (ISSN-L)
- 1532-2548
- OpenAlex
- W2155015138
- Cited by
- 353
- References
- 45
- FWCI
- 16.49
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
