Analysis of genomic sequences from peanut (Arachis hypogaea)

Electronic Journal of Biotechnology

Volumn 8, Issue 3, 2005, Pages 226-237

  Jayashree, B ^a   Ferguson, Morag ^b   Ilut, Dan ^c   Doyle, Jeff ^c   Crouch, Jonathan H ^a  

^a INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

^b International Centre for Tropical Agriculture   (Kenya)

^c Department of Molecular Biology and Genetics   (United States)

Author keywords

Arachis hypogaea; Codon usage; Gene based markers; Peanut; SSR markers

Indexed keywords

BIOMARKERS; CROPS; GENES;

ARACHIS HYPOGEA; CODON USAGE; GENE-BASED MARKERS; SSR MARKERS;

GENETIC ENGINEERING;

ARABIDOPSIS; ARTICLE; BARREL MEDIC; CODON USAGE; DATA BASE; GENE CLUSTER; GENE SEQUENCE; GENOME; LEGUME; LOTUS; LOTUS JAPONICUS; MEDICAGO; MICROSATELLITE MARKER; NONHUMAN; NUCLEOTIDE SEQUENCE; PEANUT; SEQUENCE ANALYSIS; SOYBEAN; TAXONOMY;

FARM CROPS; GENES; GENETIC ENGINEERING; MARKERS; PEANUTS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; ARACHIS HYPOGAEA; GLYCINE MAX; LOTUS CORNICULATUS VAR. JAPONICUS; MEDICAGO; MEDICAGO TRUNCATULA;

EID: 29144493116     PISSN: 07173458     EISSN: 07173458     Source Type: Journal    
DOI: 10.2225/vol8-issue3-fulltext-3     Document Type: Article

References (33)

1. ALTSCHUL, S.F.; MADDEN, T.L.; SCHÄFFER, A.A.; ZHANG, J.; ZHANG, Z.; MILLER, W. and LIPMAN, D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 1997, vol. 25, no. 17, p. 3389-3402.
2. BENNETZEN, J.L. Comparative sequence analysis of plant nuclear genomes. Plant Cell, 2000, vol.12, no. 7, p.1021-1030.
3. BIANCHI-HALL, C.; KEYS, R. and STALKER H. Use of protein profiles to characterize peanut cultivars. Peanut Science, 1994, vol. 21, no. 2, p.152-159.
4. BUROW, M.D.; SIMPSON, C.E.; STARR, J.L. and PATERSON, A.H. Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.): Broadening the gene pool of a monophyletic polyploid species. Genetics, 2001, vol. 159, no. 2, p. 823-837.
5. CARDLE, L.; RAMSAY, L.; MILBOURNE, D.; MACAULAY, M.; MARSHALL, D. and WAUGH, R. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics, 2001, vol. 156, no.2, p. 847-854.
6. DOYLE, J.J. and LUCKOW, A.M. The rest of the Iceberg. Legume diversity and evolution in a phylogenetic context. Plant Physiology, 2003, vol. 131, no. 3, p. 900-910.
7. DEVOS, K.M.; BEALES, J.; NAGAMURA, Y. and SASAKI, T. Arabidopsis-Rice: will colinearity allow gene prediction across the eudicot-monocot divide? Genome Research, 1999, vol. 9, no. 9, p. 825-829.
8. ECKARDT, N.A. Everything in its place: Conservation of gene order among distantly related plant species. Plant Cell, 2001, vol. 13, no. 4, p. 723-725.
9. FERGUSON, M.E.; BUROW, M.D.; SCHULZE, S.R.; BRAMEL, P.J.; PATERSON, A.H.; KRESOVICH, S. and MITCHELL, S. Microsatellite identification and characterization in peanut (A. hypogaea L.). Theoretical and Applied Genetics, 2004, vol. 108, no. 6, p.1064-1070.
10. GOLDMAN, N. and YANG, Z.H. A codon based model of nucleotide substitution for protein coding DNA sequences. Molecular Biology and Evolution, 1994, vol. 11, no. 5, p. 725-736.
11. GRANT, D.; CREGAN, P. and SHOEMAKER, R. C. Genome organization in dicots: Genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proceedings of the National Academy of Sciences, USA, 2002, vol. 97, no. 8, p. 4168-4173.
12. GRANTHAM, R.; GAUTIER, C.; GUOY, M.; JACOBZONE, M. and MERCIER, R. Codon catalogue usage is a genome strategy for genome expressivity. Nucleic Acids Research, 1981, vol. 9, no. 1, p. r43-r75.
13. GRIESHAMMER, U. and WYNNE, J.C. Isozyme variability in mature seeds of U.S. peanut cultivars and collections. Peanut Science, 1990, vol. 17, no. 2, p. 72-75.
14. HALWARD, T; STALKER, H.T. and KOCHERT, G. Development of an RFLP linkage map in peanut species. Theoretical and Applied Genetics, 1993, vol. 87, no. 3, p. 379-384.
15. HALWARD, T.; STALKER, T.; LARUE, E. and KOCHERT, G. Use of single-primer DNA amplifications in genetic studies of peanut (Arachis hypogaea L.). Plant Molecular Biology, 1992, vol. 18, no. 2, p. 315-325.
16. HALWARD, T.M.; STALKER, H.T.; LARUE, E.A. and KOCHERT. G. Genetic variation detectable with molecular markers among unadapted germ-plasm resources of cultivated peanut and related wild species. Genome, 1991, vol. 34, no. 6, p. 1013-1020.
17. HESLOP-HARRISON, J.S. Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell, 2000, vol.12, no. 5, p. 617-636.
18. HUANG, X. and MADAN, A. CAP3: A DNA Sequence Assembly Program. Genome Research, 1999, vol. 9, no. 9, p. 868-877.
19. KOCHERT, G.; HALWARD, T.; BRANCH, W.D. and SIMPSON, C.E. RFLP variability in peanut (Arachis hypogaea L.) cultivars and wild species. Theoretical and Applied Genetics, 1991, vol. 81, no. 5, p. 565-570.
20. KOCHERT, G.; STALKER, H. T.; GIMENES, M.; GALGARO, L.; LOPES, C. R.; and MOORE K. RFLP and cytological evidence on the origin and evolution of allotetraploid domesticated peanut, Arachis hypogaea (Leguminosae). American Journal of Botany, 1996, vol. 83, no. 10, p. 1282-1291.
21. KOLKER, E.; MAKAROVA, K.S.; SHABALINA. S.; PICONE, A.F.; PURVINE, S.; HOLZMAN, T.; CHERNY, T.; ARMBRUSTER, D.; MUNSON, R.S. Jr; KOLESOV, G.; FRISHMAN, D. and GALPERIN, M.Y. Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Research, 2004, vol. 32, no. 8, p. 2353-2361.
22. LACKS. G. and STALKER, H. Isozyme analyses of Arachis species and interspecific hybrids. Peanut Science, 1993, vol. 20, p. 76-81.
23. LANHAM, P.; FORSTER, B.; MCNICOL, P.; MOSS, J. and POWELL, W. Seed storage protein variation in Arachis species. Genome, 1994, vol. 37, no. 3, p. 487-496.
24. LONG, M.Y. and GILLESPIE, J.H. Codon usage divergence of homologous vertebrate genes and codon usage clock. Journal of Molecular Evolution, 1991, vol. 32, p. 6-15.
25. NAKAMURA, Y.; GOJOBORI, T. and IKEMURA, T. Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Research, 2000, vol. 28, no. 1, p. 292.
26. NESTI, C.; POLI, G.; CHICCA, M.; AMBROSINO, P. and SCAPOLI, C. and BARRAI, I. Phylogeny inferred from codon usage pattern in 31 organisms. Computer Applications for the Biosciences, 1995, vol. 11, no. 2, p. 167-171.
27. PATERSON, A.H.; BOWERS, J.E.; BUROW, M.D.; DRAYE, X.; ELSIK, C.G.; JIANG, C.-X.; KATSAR, C.S.; LAN, T.-H.; LIN, Y.-R.; MING, R. and WRIGHT, R.J. Comparative genomics of plant chromosomes. Plant Cell, 2000, vol. 12, no. 9, p. 1523-1540.
28. PAIK-RO, O.G.; SMITH, R.L. and KNAUFT, D.A. Restriction fragment length polymorphism evaluation of six peanut species within the Arachis section. Theoretical and Applied Genetics, 1992, vol. 84, no. 1-2, p. 201-208.
29. QUACKENBUSH, J.; CHO, J.; LEE, D.; LIANG, F.; HOLT, I.; KARAMYCHEVA, S.; PARVIZI, B.; PERTEA, G.; SULTANA, R. and WHITE, J. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Research, 2001, vol. 29, no. 1, p. 159-164.
30. QUACKENBUSH, J.; LIANG, F.; HOLT, I.; PERTEA, G. and UPTON, J. The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Research, 2000, vol. 28 no.1, p. 141-145.
31. SAVOY, C. Peanut (Arachis hypogaea L.). Seed protein characterization and genotype sample classification using polyacrylamide gel electrophoresis. Biochemistry Biophysics Research Communication, 1976, vol. 68, no. 3, p. 886-893.
32. TOMBS, M.P. Variant forms of Arachis. Nature, 1963, vol. 200, p. 1321-1322.
33. ZHU, H.; KIM, D-J.; BAEK, J-M.; CHOI, H-K.; ELLIS, L.C.; KUESTER, H.; MCCOMBIE, W.R.; PENG, H-M. and COOK, D.R. Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization. Plant Physiology, 2003, vol. 131, no. 3, p. 1018-1026.