Erratum to Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia Burkei (Madieae, Asteraceae) (American Journal of Botany, (2014) 101, 4, (722-729), 10.3732/ajb.1400049);Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae)

American Journal of Botany

Volumn 101, Issue 4, 2014, Pages 722-729

  Walker, Joseph F ^a   Zanis, Michael J ^b   Emery, Nancy C ^c  

^a PURDUE UNIVERSITY   (United States)

^b SEATTLE UNIVERSITY   (United States)

^c PURDUE UNIVERSITY   (United States)

Author keywords

Asteraceae; Intramolecular recombination; Inversion; Lasthenia burkei; Madieae; Phylogenetics; Plastome; Whole chloroplast genome

Indexed keywords

ANGIOSPERM; CHLOROPLAST; COMPARATIVE STUDY; EVOLUTIONARY BIOLOGY; GENOME; MOLECULAR ANALYSIS; POPULATION GENETICS; RNA;

ASTERACEAE; CHLOROPLAST GENOME; CHROMOSOME INVERSION; COMPARATIVE STUDY; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY;

ASTERACEAE; CHROMOSOME INVERSION; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, CHLOROPLAST; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84898730398     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.1500990     Document Type: Erratum

References (37)

1. BALDWIN, B. G., AND J. PANERO. 2007. Tribe Madieae (Compositae). In J. W. Kadereit and C. Jeffrey [eds.], The families and genera of vascular plants, Vol. VIII, Flowering plants. Eudicots-Asterales, 492-507, Springer, New York, New York, USA.
2. BREMER, K. 1994. Asteraceae: Cladistics and classification. Timber Press, Portland, Oregon, USA.
3. BROWN, J. M., AND A. R. LEMMON. 2007. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Systematic Biology 56: 643-655 Website http://www.ncbi.nlm.nih. gov/pubmed/17661232 [Accessed January 11, 2014].
4. BRUDNO, M., C. B. DO, G. M. COOPER, M. F. KIM, E. DAVYDOV, NISC COMPARATIVE SEQUENCING PROGRAM, ERIC D. GREEN, ET AL. 2003a. LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA Outline of Algorithms. Genome Research 13: 721-731.
5. BRUDNO, M., S. MALDE, A. POLIAKOV, C. B. DO, O. COURONNE, I. DUBCHAK, AND S. BATZOGLOU. 2003b. Glocal alignment: finding rearrangements during alignment. Bioinformatics (Oxford, England) 19 (Suppl. 1): i54-i62.
6. CASTOE, T., T. DOAN, AND C. PARKINSON. 2004. Data partitions and complex models in Bayesian analysis: The phylogeny of gymnophthalmid lizards. Systematic Biology 53: 448-469 Website http://sysbio. oxfordjournals.org/cgi/doi/10.1080/10635150490445797 [Accessed 10 January, 2014].
7. CHAN, R., B. G. BALDWIN, AND R. ORNDUFF. 2001. Goldfields revisited: A molecular phylogenetic perspective on the evolution of Lasthenia (Compositae: Heliantheae Sensu Lato). International Journal of Plant Sciences 162: 1347-1360.
8. CONANT, G. C., AND K. H. WOLFE. 2008. GenomeVx: Simple web-based creation of editable circular chromosome maps. Bioinformatics (Oxford, England) 24: 861-862.
9. DOORDUIN, L., B. GRAVENDEEL, Y. LAMMERS, Y. ARIYUREK, T. C. A. WOENG, AND K. VRIELING. 2011. The complete chloroplast genome of 17 individuals of pest species Jacobaea vulgaris: SNPs, microsatellites and barcoding markers for population and phylogenetic studies. DNA Research 18: 93-105.
10. DOYLE, J. J., J. I. DAVIS, R. J. SORENG, D. GARVIN, AND M. J. ANDERSON. 1992. Chloroplast DNA inversions and the origin of the grass family (Poaceae). Plant Biology 89: 7722-7726.
11. EMERY, N., E. FORRESTEL, G. JUI, AND M. PARK. 2012. Niche evolution across spatial scales: Climate and habitat specialization in California Lasthenia (Asteraceae). Ecology 93: S151-S166.
12. Frazer, K. A., L. Pachter, A. Poliakov, E. M. Rubin, AND I. Dubchak. 2004. VISTA: Computational tools for comparative genomics. Nucleic Acids Research 32 (Suppl. 2.): W273-W279.
13. FULLERTON, S. M., A. B. CARVALHO, AND A. G. CLARK. 2001. Letter to the editor: Local rates of recombination are positively correlated with GC content in the human genome. Molecular Biology and Evolution 18: 1139-1142.
14. HIRATSUKA, J., H. SHIMADA, R. WHITTIER, T. ISHIBASHI, M. SAKAMOTO, M. MORI, C. KONDO, ET AL. 1989. The complete sequence of the rice (Oryza satira) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Molecular & General Genetics 217: 185-194.
15. JANSEN, R. K., Z. CAI. L. A. RAUBESON, H. DANIELL, C. W. DEPAMPHILIS, J. LEEBENS-MACK, K. F. MÜLLER, ET AL. 2007. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceedings of the National Academy of Sciences, USA 104: 19369-19374.
16. JANSEN, R. K., AND J. D. PALMER. 1987a. A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae). Proceedings of the National Academy of Sciences, USA 84: 5818-5822.
17. JANSEN, R. K., AND J. D. PALMER. 1987b. Chloroplast DNA from lettuce and Barnadesia (Asteraceae): Structure, gene localization, and characterization of a large inversion. Current Genetics 11: 553-564. Available at website http://link.springer.com/10.1007/BF00384619.
18. KEELER-WOLF, T., D. ELAM, S. F LINT, AND L. P LANNER. 1998. California vernal pool assessment preliminary report. Department of Fish and Game, State of California, Sacramento, California, USA.
19. KELCHNER, S. 2000. The evolution of non-coding chloroplast DNA and its application in plant systematics. Annals of the Missouri Botanical Garden 87: 482-498. Website http://www.jstor.org/stable/10.2307/2666142 [Accessed 5 December, 2013].
20. LARKIN, M. A., G. BLACKSHIELDS, N. P. BROWN, R. CHENNA, P. A. MCGETTIGAN, H. MCWILLIAM, F. VALENTIN, ET AL. 2007. Clustal W and Clustal X version 2.0. Bioinformatics (Oxford, England) 23: 2947-2948.
21. LIBRADO, P., AND J. ROZAS. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics (Oxford, England) 25: 1451-1452 Website http://www.ncbi.nlm.nih.gov/ pubmed/19346325 [Accessed 6 August, 2013].
22. LIU, C., L. SHI, Y. ZHU, H. CHEN, J. ZHANG, X. LIN, AND X. GUAN. 2012. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics 13: 715.
23. LIU, Y., N. HUO, L. DONG, Y. WANG, S. Z HANG, H.A. YOUNG, AND X. FENG. 2013. Complete chloroplast genome sequences of Mongolia medicine Artemisia frigida and phylogenetic relationships with other plants. PLoS One 8: e57533.
24. MADDISON, W., AND D. MADDISON. 2011. Mesquite: A modular system for evolutionary analysis. Version 2.75. Website http://mesquiteproject.org.
25. NIE, X., S. LV, Y. ZHANG, X. DU, L. WANG, S. S. BIRADAR, X. T AN, E T AL. 2 012. Complete chloroplast genome sequence of a major invasive species, Crofton weed (Ageratina adenophora). PLoS One 7: e36869 Website http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3350484 &tool=pmcentrez&rendertype=abstract [Accessed 4 October, 2013].
26. ORNDUFF, R. 1966. A biosystematic survey of the Goldfield genus Lasthenia (Compositae: Helenieae). University of California Publi cations in Botany 40, University of California Press, Berkeley, Cali fornia, USA.
27. PANERO, J., AND V. FUNK. 2002. Toward a phylogenetic subfamilial classification for the Compositae (Asteraceae). Proceedings of the Biological Society of Washington 115: 909-922.
28. RAJAKARUNA, N. 2004. The edaphic factor in the origin of plant species. International Geology Review 46: 471-478.
29. SHAW, J., AND E. LICKEY. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The tortoise and the hare III. American Journal of Botany 94: 275-288.
30. SHAW, J., E. B. LICKEY, J. T. BECK, S. B. FARMER, W. LIU, M. JEREMY, S. C. KUNSIRI, ET AL. 2005. The tortoise and the hare II: Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92: 142-166.
31. SIMPSON, J. T., K. W ONG, S. D. JACKMAN, J. E. SCHEIN, S. J. M. JONES, AND I. BIROL. 2009. ABySS: A parallel assembler for short read sequence data. Genome Research 19: 1117-1123.
32. SMITH, N. G. C., M. T. WEBSTER, AND H. ELLEGREN. 2002. Deterministic mutation rate variation in the human genome. Genome Research 12: 1350-1356. Website http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid=186654&tool=pmcentrez&rendertype=abstract [Accessed 16 September, 2013].
33. STAMATAKIS, A., P. HOOVER, AND J. ROUGEMONT. 2008. A rapid bootstrap algorithm for the RAxML Web servers. Systematic Biology 57: 758-771.
34. TIMME, R., AND J. KUEHL. 2007. A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: Identification of divergent regions and categorization of shared repeats. American Journal of Botany 94: 302-312.
35. WOLFE, K. H., W. H. LI, AND P. M. SHARP. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences, USA 84: 9054-9058 Website http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid=299690&tool=pmcentrez&rendertype=abstract.
36. WYMAN, S. K., R. K. J ANSEN, AND J. L. BOORE. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics (Oxford, England) 20: 3252-3255.
37. ZERBINO, D. R., AND E. BIRNEY. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829 Website http://www.pubmedcentral.nih.gov/articlerender. fcgi?artid=2336801&tool=pmcentrez&rendertype=abstract [Accessed 20 January, 2014].