Alverson:Publications

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(New page: {{Alverson}})
(20 intermediate revisions not shown.)
Line 1: Line 1:
{{Alverson}}
{{Alverson}}
 +
 +
 +
==Angiosperm organelle genomes==
 +
 +
#Tuteja, R., R.K. Saxena, J. Davila, T. Shah, W. Chen, Y.L. Xiao, G. Fan, K.B. Saxena, <strong>A.J. Alverson</strong>, C. Spillane, C. Town, S. Mackenzie, and R. Kumar. 2013. Cytoplasmic male sterility associated chimeric ORFs identified by mitochondrial genome sequencing of four ''Cajanus'' genotypes. DNA Research ''in press''. [http://dx.doi.org/10.1093/dnares/dst025 doi: 10.1093/dnares/dst025]
 +
# Richardson, A. O., D. W. Rice, G. J. Young, <strong>A. J. Alverson</strong>, and J. D. Palmer. 2013. The "fossilized" mitochondrial genome of ''Liriodendron tulipifera'': Ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate. BMC Biology. 11:29. [http://dx.doi.org/10.1186/1741-7007-11-29 doi: 10.1186/1741-7007-11-29]
 +
# Zheng, Y-H., <strong>A. J. Alverson</strong>, Q-F. Wang, and J. D. Palmer. 2013. A multi-locus chloroplast phylogeny of ''Cucurbita'': Evolution of domesticated and wild species. Journal of Systematics and Evolution 51(3), 326-334. [http://dx.doi.org/10.1111/jse.12006 doi: 10.1111/jse.12006]
 +
# Sloan, D. B., <strong>A. J. Alverson</strong>, M. Wu, J. D. Palmer, and D. R. Taylor. Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence within the angiosperm genus ''Silene''. 2012. Genome Biology and Evolution 4, 294-306. [http://dx.doi.org/10.1093/gbe/evs006 doi: 10.1093/gbe/evs006]
 +
# Sloan, D. B., <strong>A. J. Alverson</strong>, J. P. Chuckalovcak, M. Wu, D. E. McCauley, J. D. Palmer, and D. R. Taylor. 2012. Rapid evolution of enormous, multichromosomal genomes in flowering plants. PLoS Biology 10(1): e1001241 [http://dx.doi.org/10.1371/journal.pbio.1001241 doi: 10.1371/journal.pbio.1001241] [http://f1000.com/13755957 F1000]
 +
# Mower, J. P., D. B. Sloan, and <strong>A. J. Alverson</strong>. 2012. Plant mitochondrial genome diversity: The genomics revolution. pp. 123–144 in Wendel, J. F., J. Greilhuber, J. Dolezel, and I. J. Leitch (eds). Plant Genomes, their Residents, and their Evolutionary Dynamics. Springer Verlag.
 +
# <strong>Alverson, A. J.</strong>, D. W. Rice, S. Dickinson, Barry, K., and J. D. Palmer. 2011. Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber (''Cucumis sativus''). The Plant Cell 23, 2499-2513. [http://dx.doi.org/10.1105/tpc.111.087189 doi: 10.1105/tpc.111.087189]  [http://dx.doi.org/10.1105/tpc.111.230711 Featured article]
 +
# <strong>Alverson, A. J.</strong>, S. Zhuo, D. W. Rice, D. B. Sloan, and J. D. Palmer. 2011. The mitochondrial genome of the legume ''Vigna radiata'' and the analysis of recombination across short mitochondrial repeats. PLoS ONE 6(1): e16404.
 +
# <strong>Alverson, A. J.</strong>, X. X. Wei, D. W. Rice, D. B. Stern, K. Barry, and J. D. Palmer. 2010. Insights into the evolution of mitochondrial genome size from complete sequences of ''Citrullus lanatus'' and ''Cucurbita pepo'' (Cucurbitaceae). Molecular Biology and Evolution 27, 1436-1448. [http://dx.doi.org/10.1093/molbev/msq029 doi: 10.1093/molbev/msq029]
 +
# Sloan, D. B., A. H. MacQueen, <strong>A. J. Alverson</strong>, J. D. Palmer, and D. R. Taylor. 2010. Extensive loss of RNA editing sites in rapidly evolving ''Silene'' mitochondrial genomes: selection vs. retroprocessing as the driving force. Genetics 185, 1369-1380. [http://dx.doi.org/10.1534/genetics.110.118000 doi: 10.1534/genetics.110.118000]
 +
# Sloan, D. B., <strong>A. J. Alverson</strong>, H. Storchova, J. D. Palmer, and D. R. Taylor. 2010. Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm ''Silene latifolia''. BMC Evolutionary Biology 10, 274. [http://dx.doi.org/10.1186/1471-2148-10-274 doi: 10.1186/1471-2148-10-274]
 +
# Sanchez-Puerta, M. V., Y. Cho, J. P. Mower, <strong>A. J. Alverson</strong>, and J. D. Palmer. 2008. Frequent, phylogenetically local horizontal transfer of the cox1 group I intron in flowering plant mitochondria. Molecular Biology and Evolution 25, 1762-1777. [http://dx.doi.org/10.1093/molbev/msn129 doi: 10.1093/molbev/msn129]
 +
# Jansen, R. K., C. Kaittanis, C. Saski, S. B. Lee, J. Tomkins, <strong>A. J. Alverson</strong>, and H. Daniell. 2006. Phylogenetic analyses of ''Vitis'' (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evolutionary Biology 6. [http://dx.doi.org/10.1186/1471-2148-6-32 doi: 10.1186/1471-2148-6-32]
 +
# Jansen, R. K., L. A. Raubeson, J. L. Boore, C. W. DePamphilis, T. W. Chumley, R. C. Haberle, S. K. Wyman, <strong>A. J. Alverson</strong>, R. Peery, S. J. Herman, H. M. Fourcade, J. V. Kuehl, J. R. McNeal, J. Leebens-Mack, and L. Cui. 2005. Methods for obtaining and analyzing whole chloroplast genome sequences. In Molecular Evolution: Producing the Biochemical Data, Part B, pp. 348-384. [http://dx.doi.org/10.1016/S0076-6879(05)95020-9 doi: 10.1016/S0076-6879(05)95020-9]
 +
 +
 +
==Diatoms==
 +
# <strong>Alverson, A. J.</strong>, B. Beszteri, M. L. Julius, and E. C. Theriot. 2011. The model marine diatom ''Thalassiosira pseudonana'' likely descended from a freshwater ancestor in the genus ''Cyclotella''. BMC Evolutionary Biology 11, 125. [http://dx.doi.org/10.1186/1471-2148-11-125 doi: 10.1186/1471-2148-11-125]
 +
# Theriot, E. C., J. J. Cannone, R. R. Gutell, and <strong>A. J. Alverson</strong> 2009. The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny. European Journal of Phycology 44, 277-290. [http://dx.doi.org/10.1080/09670260902749159 doi: 10.1080/09670260902749159]
 +
# <strong>Alverson, A. J.</strong> 2008. Molecular systematics and the diatom species. Protist 159, 339-353. [http://dx.doi.org/10.1016/j.protis.2008.04.001 doi: 10.1016/j.protis.2008.04.001]
 +
# <strong>Alverson, A. J.</strong>, R. K. Jansen, and E. C. Theriot. 2009. Reply to Medlin and Kaczmarska (2008). Molecular Phylogenetics and Evolution 50: 409–410.
 +
# <strong>Alverson, A. J.</strong>, R. K. Jansen, and E. C. Theriot. 2007. Bridging the Rubicon: Phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms. Molecular Phylogenetics and Evolution 45, 193-210. [http://dx.doi.org/10.1016/j.ympev.2007.03.024 doi: 10.1016/j.ympev.2007.03.024]
 +
# <strong>Alverson, A. J.</strong> 2007. Strong purifying selection in the silicon transporters of marine and freshwater diatoms. Limnology and Oceanography 52, 1420-1429. [http://dx.doi.org/10.4319/lo.2007.52.4.1420 doi: 10.4319/lo.2007.52.4.1420]
 +
# <strong>Alverson, A. J.</strong>, S-H. Kang, and E. C. Theriot. 2006. Cell wall morphology and systematic importance of ''Thalassiosira ritscheri'' (Hustedt) Hasle, with a description of ''Shionodiscus'' gen. nov. Diatom Research 21, 251-262. [http://dx.doi.org/10.1080/0269249X.2006.9705667 doi: 10.1080/0269249X.2006.9705667]
 +
# Thamatrakoln, K., <strong>A. J. Alverson</strong>, and M. Hildebrand. 2006. Comparative sequence analysis of diatom silicon transporters: Toward a mechanistic model of silicon transport. Journal of Phycology 42, 822-834. [http://dx.doi.org/10.1111/j.1529-8817.2006.00233.x doi: 10.1111/j.1529-8817.2006.00233.x]
 +
# <strong>Alverson, A. J.</strong>, J. J. Cannone, R. R. Gutell, and E. C. Theriot. 2006. The evolution of elongate shape in diatoms. Journal of Phycology 42, 655-668. [http://dx.doi.org/10.1111/j.1529-8817.2006.00228.x doi: 10.1111/j.1529-8817.2006.00228.x]
 +
# <strong>Alverson, A. J.</strong>, and L. Kolnick. 2005. Intragenomic nucleotide polymorphism among small subunit (18S) rDNA paralogs in the diatom genus ''Skeletonema'' (Bacillariophyta). Journal of Phycology 41, 1248-1257. [http://dx.doi.org/10.1111/j.1529-8817.2005.00136.x doi: 10.1111/j.1529-8817.2005.00136.x]
 +
# <strong>Alverson, A. J.</strong>, and E. C. Theriot. 2005. Comments on recent progress toward reconstructing the diatom phylogeny. Journal of Nanoscience and Nanotechnology 5, 57-62. [http://dx.doi.org/10.1166/jnn.2005.007 doi: 10.1166/jnn.2005.007]
 +
# <strong>Alverson, A. J.</strong>, K. M. Manoylov, and R. J. Stevenson. 2003. Laboratory sources of error for community attributes from counting algae. Journal of Applied Phycology 15: 357–369.
 +
# <strong>Alverson, A. J.</strong> and G. W. Courtney. 2002. Temporal patterns of diatom ingestion by larval net-winged midges (Diptera: Blephariceridae: ''Blepharicera''). Freshwater Biology 47: 2087–2097.
 +
# <strong>Alverson, A. J.</strong>, M. R. Luttenton, and G. W. Courtney. 2001. Niche overlap of sympatric ''Blepharicera'' larvae (Diptera: Blephariceridae) from the southern Appalachian Mountains.  Journal of the North American Benthological Society 20: 564–581.

Revision as of 09:58, 24 July 2013

The Alverson Lab

Home        Research        Publications        People        Links        Contact       



Angiosperm organelle genomes

  1. Tuteja, R., R.K. Saxena, J. Davila, T. Shah, W. Chen, Y.L. Xiao, G. Fan, K.B. Saxena, A.J. Alverson, C. Spillane, C. Town, S. Mackenzie, and R. Kumar. 2013. Cytoplasmic male sterility associated chimeric ORFs identified by mitochondrial genome sequencing of four Cajanus genotypes. DNA Research in press. doi: 10.1093/dnares/dst025
  2. Richardson, A. O., D. W. Rice, G. J. Young, A. J. Alverson, and J. D. Palmer. 2013. The "fossilized" mitochondrial genome of Liriodendron tulipifera: Ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate. BMC Biology. 11:29. doi: 10.1186/1741-7007-11-29
  3. Zheng, Y-H., A. J. Alverson, Q-F. Wang, and J. D. Palmer. 2013. A multi-locus chloroplast phylogeny of Cucurbita: Evolution of domesticated and wild species. Journal of Systematics and Evolution 51(3), 326-334. doi: 10.1111/jse.12006
  4. Sloan, D. B., A. J. Alverson, M. Wu, J. D. Palmer, and D. R. Taylor. Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence within the angiosperm genus Silene. 2012. Genome Biology and Evolution 4, 294-306. doi: 10.1093/gbe/evs006
  5. Sloan, D. B., A. J. Alverson, J. P. Chuckalovcak, M. Wu, D. E. McCauley, J. D. Palmer, and D. R. Taylor. 2012. Rapid evolution of enormous, multichromosomal genomes in flowering plants. PLoS Biology 10(1): e1001241 doi: 10.1371/journal.pbio.1001241 F1000
  6. Mower, J. P., D. B. Sloan, and A. J. Alverson. 2012. Plant mitochondrial genome diversity: The genomics revolution. pp. 123–144 in Wendel, J. F., J. Greilhuber, J. Dolezel, and I. J. Leitch (eds). Plant Genomes, their Residents, and their Evolutionary Dynamics. Springer Verlag.
  7. Alverson, A. J., D. W. Rice, S. Dickinson, Barry, K., and J. D. Palmer. 2011. Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber (Cucumis sativus). The Plant Cell 23, 2499-2513. doi: 10.1105/tpc.111.087189 Featured article
  8. Alverson, A. J., S. Zhuo, D. W. Rice, D. B. Sloan, and J. D. Palmer. 2011. The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats. PLoS ONE 6(1): e16404.
  9. Alverson, A. J., X. X. Wei, D. W. Rice, D. B. Stern, K. Barry, and J. D. Palmer. 2010. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Molecular Biology and Evolution 27, 1436-1448. doi: 10.1093/molbev/msq029
  10. Sloan, D. B., A. H. MacQueen, A. J. Alverson, J. D. Palmer, and D. R. Taylor. 2010. Extensive loss of RNA editing sites in rapidly evolving Silene mitochondrial genomes: selection vs. retroprocessing as the driving force. Genetics 185, 1369-1380. doi: 10.1534/genetics.110.118000
  11. Sloan, D. B., A. J. Alverson, H. Storchova, J. D. Palmer, and D. R. Taylor. 2010. Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia. BMC Evolutionary Biology 10, 274. doi: 10.1186/1471-2148-10-274
  12. Sanchez-Puerta, M. V., Y. Cho, J. P. Mower, A. J. Alverson, and J. D. Palmer. 2008. Frequent, phylogenetically local horizontal transfer of the cox1 group I intron in flowering plant mitochondria. Molecular Biology and Evolution 25, 1762-1777. doi: 10.1093/molbev/msn129
  13. Jansen, R. K., C. Kaittanis, C. Saski, S. B. Lee, J. Tomkins, A. J. Alverson, and H. Daniell. 2006. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evolutionary Biology 6. doi: 10.1186/1471-2148-6-32
  14. Jansen, R. K., L. A. Raubeson, J. L. Boore, C. W. DePamphilis, T. W. Chumley, R. C. Haberle, S. K. Wyman, A. J. Alverson, R. Peery, S. J. Herman, H. M. Fourcade, J. V. Kuehl, J. R. McNeal, J. Leebens-Mack, and L. Cui. 2005. Methods for obtaining and analyzing whole chloroplast genome sequences. In Molecular Evolution: Producing the Biochemical Data, Part B, pp. 348-384. doi: 10.1016/S0076-6879(05)95020-9


Diatoms

  1. Alverson, A. J., B. Beszteri, M. L. Julius, and E. C. Theriot. 2011. The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella. BMC Evolutionary Biology 11, 125. doi: 10.1186/1471-2148-11-125
  2. Theriot, E. C., J. J. Cannone, R. R. Gutell, and A. J. Alverson 2009. The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny. European Journal of Phycology 44, 277-290. doi: 10.1080/09670260902749159
  3. Alverson, A. J. 2008. Molecular systematics and the diatom species. Protist 159, 339-353. doi: 10.1016/j.protis.2008.04.001
  4. Alverson, A. J., R. K. Jansen, and E. C. Theriot. 2009. Reply to Medlin and Kaczmarska (2008). Molecular Phylogenetics and Evolution 50: 409–410.
  5. Alverson, A. J., R. K. Jansen, and E. C. Theriot. 2007. Bridging the Rubicon: Phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms. Molecular Phylogenetics and Evolution 45, 193-210. doi: 10.1016/j.ympev.2007.03.024
  6. Alverson, A. J. 2007. Strong purifying selection in the silicon transporters of marine and freshwater diatoms. Limnology and Oceanography 52, 1420-1429. doi: 10.4319/lo.2007.52.4.1420
  7. Alverson, A. J., S-H. Kang, and E. C. Theriot. 2006. Cell wall morphology and systematic importance of Thalassiosira ritscheri (Hustedt) Hasle, with a description of Shionodiscus gen. nov. Diatom Research 21, 251-262. doi: 10.1080/0269249X.2006.9705667
  8. Thamatrakoln, K., A. J. Alverson, and M. Hildebrand. 2006. Comparative sequence analysis of diatom silicon transporters: Toward a mechanistic model of silicon transport. Journal of Phycology 42, 822-834. doi: 10.1111/j.1529-8817.2006.00233.x
  9. Alverson, A. J., J. J. Cannone, R. R. Gutell, and E. C. Theriot. 2006. The evolution of elongate shape in diatoms. Journal of Phycology 42, 655-668. doi: 10.1111/j.1529-8817.2006.00228.x
  10. Alverson, A. J., and L. Kolnick. 2005. Intragenomic nucleotide polymorphism among small subunit (18S) rDNA paralogs in the diatom genus Skeletonema (Bacillariophyta). Journal of Phycology 41, 1248-1257. doi: 10.1111/j.1529-8817.2005.00136.x
  11. Alverson, A. J., and E. C. Theriot. 2005. Comments on recent progress toward reconstructing the diatom phylogeny. Journal of Nanoscience and Nanotechnology 5, 57-62. doi: 10.1166/jnn.2005.007
  12. Alverson, A. J., K. M. Manoylov, and R. J. Stevenson. 2003. Laboratory sources of error for community attributes from counting algae. Journal of Applied Phycology 15: 357–369.
  13. Alverson, A. J. and G. W. Courtney. 2002. Temporal patterns of diatom ingestion by larval net-winged midges (Diptera: Blephariceridae: Blepharicera). Freshwater Biology 47: 2087–2097.
  14. Alverson, A. J., M. R. Luttenton, and G. W. Courtney. 2001. Niche overlap of sympatric Blepharicera larvae (Diptera: Blephariceridae) from the southern Appalachian Mountains. Journal of the North American Benthological Society 20: 564–581.

Personal tools