Faculty Openings

Dr. Victor A. Albert

Empire Innovation Professor
637 Hochstetter Hall
phone: (716) 645-4983


The Amborella Genome Project: An Evolutionary Reference for Plant Biology  

Research Summary

Victor Albert’s research employs genomic, developmental, and genetic approaches to understanding problems in plant evolutionary biology. Areas of current interest include:

- Sequencing and characterization of the avocado and Amborella genomes, Amborella being the sister species to all other flowering plants, and avocado lying near the base of angiosperm phylogeny; use these and other genomes in an attempt to uncover reproductive regulatory mechanisms common to the “ancestral angiosperm”

- Genomics of the coffee plant; seeking evidence for factors underlying the massive diversification of its parent lineage in fruit types and secondary compound chemistries, and working toward better knowledge of traits important for developing agricultural systems

- Reconstruction of whole-genome duplication history as it relates to the diversification of flowering plants, also the ancestral gene order for all angiosperms

- The genetic basis for “adaptive” radiations of plant forms, for example in the bladderwort/butterwort lineage of carnivorous plants; this includes complete genome sequencing of the humped bladderwort, Utricularia gibba

- Evo-devo research on the evolution of reproductive development in flowering plants; topics include B-function MADS box genes and CYCLOIDEA-like genes; the former help specify petal identity, whereas the latter participate in the control of organ symmetry


Selected Publications (see also Prof. Albert's Google Scholar page)

• Carretero-Paulet L, Librado P, Chang TH, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA. High Gene Family Turnover Rates and Gene Space Adaptation in the Compact Genome of the Carnivorous Plant Utricularia gibba. Molecular Biology and Evolution. 2015 May;32(5):1284-95.

• Carretero-Paulet L, Chang TH, Librado P, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA. Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba. Genome Biology and Evolution. 2015 Jan 9;7(2):444-56.

• Albert VA, Carretero-Paulet L. A genome to unveil the mysteries of orchids. Nature Genetics. 2015 Jan;47(1):3-4.

• Albert VA, Chang TH. Evolution of a hot genome. Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5069-70.

• Juntheikki-Palovaara I, Tähtiharju S, Lan T, Broholm SK, Rijpkema AS, Ruonala R, Kale L, Albert VA, Teeri TH, Elomaa P. Functional diversification of duplicated CYC2 clade genes in regulation of inflorescence development in Gerbera hybrida (Asteraceae). Plant Journal. 2014 Sep;79(5):783-96.

• Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V,Joët T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Muñoz, A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science. 2014 Sep 5;345(6201):1181-4.

•Amborella Genome Project. The Amborella genome and the evolution of flowering plants. Science. 2013 Dec 20;342(6165):1241089.

• Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB. Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science. 2013 Dec 20;342(6165):1516-7.

• Ibarra-Laclette, E, Lyons, E, Hernandez-Guzman, G, Perez-Torres, CA, Carretero-Paulet, L, Chang, T-H, Lan, T, Welch, AJ, Juarez, MJ, Simpson, J, Fernandez-Cortes, A, Arteaga-Vazquez, M, Gongora-Castillo, E, Acevedo-Hernandez, G, Schuster, SC, Himmelbauer, H, Minoche, AE, Xu, S, Lynch, M, Oropeza-Aburto, A, Cervantes-Perez, SA, de Jesus Ortega-Estrada, M, Cervantes-Luevano, JI, Michael, TP, Mockler, T, Bryant, D, Herrera-Estrella, A, Albert, VA, Herrera-Estrella, L. 2013. Architecture and evolution of a minute plant genome. Nature. 2013 Jun 6;498(7452):94-8.

• Hofer KA, Ruonala R, Albert VA. The double-corolla phenotype in the Hawaiian lobelioid genus Clermontia involves ectopic expression of PISTILLATA B-function MADS box gene homologs. Evodevo. 2012 Nov 1;3(1):26

• Tähtiharju S, Rijpkema AS, Vetterli A, Albert VA, Teeri TH, Elomaa P. Evolution and diversification of the CYC/TB1 gene family in Asteraceae--a comparative study in Gerbera (Mutisieae) and sunflower (Heliantheae). Mol Biol Evol. 2012 Apr;29(4):1155-66.

• Ibarra-Laclette E, Albert VA, Pérez-Torres CA, Zamudio-Hernández F, Ortega-Estrada Mde J, Herrera-Estrella A, Herrera-Estrella L. Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome. BMC Plant Biol. 2011 Jun 3;11:101.

• Zuccolo A, Bowers JE, Estill JC, Xiong Z, Luo M, Sebastian A, Goicoechea JL, Collura K, Yu Y, Jiao Y, Duarte J, Tang H, Ayyampalayam S, Rounsley S, Kudrna D,  Paterson AH, Pires JC, Chanderbali A, Soltis DE, Chamala S, Barbazuk B, Soltis PS, Albert VA, Ma H, Mandoli D, Banks J, Carlson JE, Tomkins J, dePamphilis CW, Wing RA, Leebens-Mack J. A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biol. 2011;12(5):R48.

• Ruokolainen S, Ng YP, Albert VA, Elomaa P, Teeri TH. Over-expression of the Gerbera hybrida At-SOC1-like1 gene Gh-SOC1 leads to floral organ identity deterioration. Ann Bot. 2011 Jun;107(9):1491-9.

• Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science. 2011 May 20;332(6032):960-3.

• Chanderbali AS, Yoo MJ, Zahn LM, Brockington SF, Wall PK, Gitzendanner MA, Albert VA, Leebens-Mack J, Altman NS, Ma H, dePamphilis CW, Soltis DE, Soltis PS. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. Proc Natl Acad  Sci U S A. 2010 Dec 28;107(52):22570-5.

• Muñoz A, Zheng C, Zhu Q, Albert VA, Rounsley S, Sankoff D. Scaffold filling, contig fusion and comparative gene order inference. BMC Bioinformatics. 2010 Jun  4;11:304.

• Albert VA, Jobson RW, Michael TP, Taylor DJ. The carnivorous bladderwort (Utricularia, Lentibulariaceae): a system inflates. J Exp Bot. 2010;61(1):5-9.

• Broholm SK, Pöllänen E, Ruokolainen S, Tähtiharju S, Kotilainen M, Albert VA,  Elomaa P, Teeri TH. Functional characterization of B class MADS-box transcription factors in Gerbera hybrida. J Exp Bot. 2010;61(1):75-85.

• Sankoff D, Zheng C, Wall PK, dePamphilis C, Leebens-Mack J, Albert VA. Towards improved reconstruction of ancestral gene order in angiosperm phylogeny. J Comput Biol. 2009 Oct 5;16(10):1353-1367.

• Zheng C, Kerr Wall P, Leebens-Mack J, de Pamphilis C, Albert VA, Sankoff D. Gene loss under neighborhood selection following whole genome duplication and the reconstruction of the ancestral Populus genome. J Bioinform Comput Biol. 2009 Jun;7(3):499-520.

• Chanderbali AS, Albert VA, Leebens-Mack J, Altman NS, Soltis DE, Soltis PS. Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae). Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8929-34.

• Nieminen K, Immanen J, Laxell M, Kauppinen L, Tarkowski P, Dolezal K, Tahtiharju S, Elo A, Decourteix M, Ljung K, Bhalerao R, Keinonen K, Albert VA, Helariutta Y. Cytokinin signaling regulates cambial development in poplar. Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):20032-7.

• Broholm, SK, Tahtiharju S, Laitinen RAE, Albert VA, Teeri TH, Elomaa P. A TCP domain transcription factor controls flower type specification along the radial axis of the Gerbera (Asteraceae) inflorescence. Proc Natl Acad Sci U S A 2008 Jul;105(26):9117-9122.

• Soltis DE, Albert VA, Leebens-Mack J, Palmer JD, Wing RA, Depamphilis CW, Ma H, Carlson JE, Altman N, Kim S, Wall PK, Zuccolo A, Soltis PS. The Amborella genome: an evolutionary reference for plant biology. Genome Biol. 2008 Mar 10;9(3):402

• Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA, Ma H, dePamphilis CW. Widespread genome duplications throughout the history of flowering plants. Genome Res. 2006 Jun;16(6):738-49.

• Albert VA, Soltis DE, Carlson JE, Farmerie WG, Wall PK, Ilut DC, Solow TM, Mueller LA, Landherr LL, Hu Y, Buzgo M, Kim S, Yoo MJ, Frohlich MW, Perl-Treves R, Schlarbaum SE, Bliss BJ, Zhang X, Tanksley SD, Oppenheimer DG, Soltis PS, Ma H, DePamphilis CW, Leebens-Mack JH. Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol. 2005 Mar 30;5:5.

• Jobson RW, Nielsen R, Laakkonen L, Wikström M, Albert VA. Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation. Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):18064-8.

• Uimari A, Kotilainen M, Elomaa P, Yu D, Albert VA, Teeri TH. Integration of reproductive meristem fates by a SEPALLATA-like MADS-box gene. Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15817-22.

• Albert VA, Williams SE, Chase MW. Carnivorous plants: phylogeny and structural evolution. Science. 1992 Sep 11;257(5076):1491-5.


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