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Items: 1 to 50 of 87

1.

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory.

Fukushima K, Fang X, Alvarez-Ponce D, Cai H, Carretero-Paulet L, Chen C, Chang TH, Farr KM, Fujita T, Hiwatashi Y, Hoshi Y, Imai T, Kasahara M, Librado P, Mao L, Mori H, Nishiyama T, Nozawa M, Pálfalvi G, Pollard ST, Rozas J, Sánchez-Gracia A, Sankoff D, Shibata TF, Shigenobu S, Sumikawa N, Uzawa T, Xie M, Zheng C, Pollock DD, Albert VA, Li S, Hasebe M.

Nat Ecol Evol. 2017 Feb 6;1(3):59. doi: 10.1038/s41559-016-0059.

PMID:
28812732
2.

Dissecting functions of SEPALLATA-like MADS box genes in patterning of the pseudanthial inflorescence of Gerbera hybrida.

Zhang T, Zhao Y, Juntheikki I, Mouhu K, Broholm SK, Rijpkema AS, Kins L, Lan T, Albert VA, Teeri TH, Elomaa P.

New Phytol. 2017 Nov;216(3):939-954. doi: 10.1111/nph.14707. Epub 2017 Jul 25.

PMID:
28742220
3.

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome.

Lan T, Renner T, Ibarra-Laclette E, Farr KM, Chang TH, Cervantes-Pérez SA, Zheng C, Sankoff D, Tang H, Purbojati RW, Putra A, Drautz-Moses DI, Schuster SC, Herrera-Estrella L, Albert VA.

Proc Natl Acad Sci U S A. 2017 May 30;114(22):E4435-E4441. doi: 10.1073/pnas.1702072114. Epub 2017 May 15. Erratum in: Proc Natl Acad Sci U S A. 2017 Jun 19;:.

4.

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.

Salojärvi J, Smolander OP, Nieminen K, Rajaraman S, Safronov O, Safdari P, Lamminmäki A, Immanen J, Lan T, Tanskanen J, Rastas P, Amiryousefi A, Jayaprakash B, Kammonen JI, Hagqvist R, Eswaran G, Ahonen VH, Serra JA, Asiegbu FO, de Dios Barajas-Lopez J, Blande D, Blokhina O, Blomster T, Broholm S, Brosché M, Cui F, Dardick C, Ehonen SE, Elomaa P, Escamez S, Fagerstedt KV, Fujii H, Gauthier A, Gollan PJ, Halimaa P, Heino PI, Himanen K, Hollender C, Kangasjärvi S, Kauppinen L, Kelleher CT, Kontunen-Soppela S, Koskinen JP, Kovalchuk A, Kärenlampi SO, Kärkönen AK, Lim KJ, Leppälä J, Macpherson L, Mikola J, Mouhu K, Mähönen AP, Niinemets Ü, Oksanen E, Overmyer K, Palva ET, Pazouki L, Pennanen V, Puhakainen T, Poczai P, Possen BJHM, Punkkinen M, Rahikainen MM, Rousi M, Ruonala R, van der Schoot C, Shapiguzov A, Sierla M, Sipilä TP, Sutela S, Teeri TH, Tervahauta AI, Vaattovaara A, Vahala J, Vetchinnikova L, Welling A, Wrzaczek M, Xu E, Paulin LG, Schulman AH, Lascoux M, Albert VA, Auvinen P, Helariutta Y, Kangasjärvi J.

Nat Genet. 2017 Jun;49(6):904-912. doi: 10.1038/ng.3862. Epub 2017 May 8.

PMID:
28481341
5.

Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content.

Hamon P, Grover CE, Davis AP, Rakotomalala JJ, Raharimalala NE, Albert VA, Sreenath HL, Stoffelen P, Mitchell SE, Couturon E, Hamon S, de Kochko A, Crouzillat D, Rigoreau M, Sumirat U, Akaffou S, Guyot R.

Mol Phylogenet Evol. 2017 Apr;109:351-361. doi: 10.1016/j.ympev.2017.02.009. Epub 2017 Feb 16.

PMID:
28212875
6.

Functional characterization and expression of GASCL1 and GASCL2, two anther-specific chalcone synthase like enzymes from Gerbera hybrida.

Kontturi J, Osama R, Deng X, Bashandy H, Albert VA, Teeri TH.

Phytochemistry. 2017 Feb;134:38-45. doi: 10.1016/j.phytochem.2016.11.002. Epub 2016 Nov 21.

PMID:
27884449
7.

Studying Evolutionary Dynamics of Gene Families Encoding SUMO-Activating Enzymes with SeaView and ProtTest.

Carretero-Paulet L, Albert VA.

Methods Mol Biol. 2016;1450:273-84. doi: 10.1007/978-1-4939-3759-2_22.

PMID:
27424762
8.

Sequence Search and Comparative Genomic Analysis of SUMO-Activating Enzymes Using CoGe.

Carretero-Paulet L, Albert VA.

Methods Mol Biol. 2016;1450:261-72. doi: 10.1007/978-1-4939-3759-2_21.

PMID:
27424761
9.

Evolutionary Co-Option of Floral Meristem Identity Genes for Patterning of the Flower-Like Asteraceae Inflorescence.

Zhao Y, Zhang T, Broholm SK, Tähtiharju S, Mouhu K, Albert VA, Teeri TH, Elomaa P.

Plant Physiol. 2016 Sep;172(1):284-96. doi: 10.1104/pp.16.00779. Epub 2016 Jul 5. Erratum in: Plant Physiol. 2016 Dec;172(4):2530-2531.

10.

Evolution of RLSB, a nuclear-encoded S1 domain RNA binding protein associated with post-transcriptional regulation of plastid-encoded rbcL mRNA in vascular plants.

Yerramsetty P, Stata M, Siford R, Sage TL, Sage RF, Wong GK, Albert VA, Berry JO.

BMC Evol Biol. 2016 Jun 29;16(1):141. doi: 10.1186/s12862-016-0713-1.

11.

Syntenic block overlap multiplicities with a panel of reference genomes provide a signature of ancient polyploidization events.

Zheng C, Santos Muñoz D, Albert VA, Sankoff D.

BMC Genomics. 2015;16 Suppl 10:S8. doi: 10.1186/1471-2164-16-S10-S8. Epub 2015 Oct 2.

12.

De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis.

Ibarra-Laclette E, Zamudio-Hernández F, Pérez-Torres CA, Albert VA, Ramírez-Chávez E, Molina-Torres J, Fernández-Cortes A, Calderón-Vázquez C, Olivares-Romero JL, Herrera-Estrella A, Herrera-Estrella L.

BMC Genomics. 2015 Sep 2;16:657. doi: 10.1186/s12864-015-1821-9.

13.

Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids.

Ibarra-Laclette E, Méndez-Bravo A, Pérez-Torres CA, Albert VA, Mockaitis K, Kilaru A, López-Gómez R, Cervantes-Luevano JI, Herrera-Estrella L.

BMC Genomics. 2015 Aug 13;16:599. doi: 10.1186/s12864-015-1775-y.

14.

The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family.

Lin CS, Chen JJ, Huang YT, Chan MT, Daniell H, Chang WJ, Hsu CT, Liao DC, Wu FH, Lin SY, Liao CF, Deyholos MK, Wong GK, Albert VA, Chou ML, Chen CY, Shih MC.

Sci Rep. 2015 Mar 12;5:9040. doi: 10.1038/srep09040.

15.

High Gene Family Turnover Rates and Gene Space Adaptation in the Compact Genome of the Carnivorous Plant Utricularia gibba.

Carretero-Paulet L, Librado P, Chang TH, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA.

Mol Biol Evol. 2015 May;32(5):1284-95. doi: 10.1093/molbev/msv020. Epub 2015 Jan 31.

PMID:
25637935
16.

Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba.

Carretero-Paulet L, Chang TH, Librado P, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA.

Genome Biol Evol. 2015 Jan 9;7(2):444-56. doi: 10.1093/gbe/evu288.

17.

A genome to unveil the mysteries of orchids.

Albert VA, Carretero-Paulet L.

Nat Genet. 2015 Jan;47(1):3-4. doi: 10.1038/ng.3179.

PMID:
25547596
18.

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.

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.

Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274. Epub 2014 Sep 4.

19.

Functional diversification of duplicated CYC2 clade genes in regulation of inflorescence development in Gerbera hybrida (Asteraceae).

Juntheikki-Palovaara I, Tähtiharju S, Lan T, Broholm SK, Rijpkema AS, Ruonala R, Kale L, Albert VA, Teeri TH, Elomaa P.

Plant J. 2014 Sep;79(5):783-96. doi: 10.1111/tpj.12583. Epub 2014 Jul 15.

20.

Evolution of a hot genome.

Albert VA, Chang TH.

Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5069-70. doi: 10.1073/pnas.1402378111. Epub 2014 Mar 27. No abstract available.

21.

The dynamics of functional classes of plant genes in rediploidized ancient polyploids.

Chen EC, Buen Abad Najar C, Zheng C, Brandts A, Lyons E, Tang H, Carretero-Paulet L, Albert VA, Sankoff D.

BMC Bioinformatics. 2013;14 Suppl 15:S19. doi: 10.1186/1471-2105-14-S15-S19. Epub 2013 Oct 15.

22.

Ancient eudicot hexaploidy meets ancestral eurosid gene order.

Zheng C, Chen E, Albert VA, Lyons E, Sankoff D.

BMC Genomics. 2013;14 Suppl 7:S3. doi: 10.1186/1471-2164-14-S7-S3. Epub 2013 Nov 5.

23.

Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.

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.

Science. 2013 Dec 20;342(6165):1516-7. doi: 10.1126/science.1241130.

PMID:
24357320
24.

Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica.

Immanen J, Nieminen K, Duchens Silva H, Rodríguez Rojas F, Meisel LA, Silva H, Albert VA, Hvidsten TR, Helariutta Y.

BMC Genomics. 2013 Dec 16;14:885. doi: 10.1186/1471-2164-14-885.

25.

Functional diversification of duplicated chalcone synthase genes in anthocyanin biosynthesis of Gerbera hybrida.

Deng X, Bashandy H, Ainasoja M, Kontturi J, Pietiäinen M, Laitinen RA, Albert VA, Valkonen JP, Elomaa P, Teeri TH.

New Phytol. 2014 Mar;201(4):1469-83. doi: 10.1111/nph.12610. Epub 2013 Nov 25.

26.

The Fragaria vesca homolog of suppressor of overexpression of constans1 represses flowering and promotes vegetative growth.

Mouhu K, Kurokura T, Koskela EA, Albert VA, Elomaa P, Hytönen T.

Plant Cell. 2013 Sep;25(9):3296-310. doi: 10.1105/tpc.113.115055. Epub 2013 Sep 13.

27.

Evolutionary diversification and characterization of the eubacterial gene family encoding DXR type II, an alternative isoprenoid biosynthetic enzyme.

Carretero-Paulet L, Lipska A, Pérez-Gil J, Sangari FJ, Albert VA, Rodríguez-Concepción M.

BMC Evol Biol. 2013 Sep 3;13:180. doi: 10.1186/1471-2148-13-180.

28.

Molecular evolutionary mechanisms driving functional diversification of the HSP90A family of heat shock proteins in eukaryotes.

Carretero-Paulet L, Albert VA, Fares MA.

Mol Biol Evol. 2013 Sep;30(9):2035-43. doi: 10.1093/molbev/mst113. Epub 2013 Jun 27.

PMID:
23813917
29.

Architecture and evolution of a minute plant genome.

Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L, Chang TH, Lan T, Welch AJ, Juárez MJ, Simpson J, Fernández-Cortés A, Arteaga-Vázquez M, Góngora-Castillo E, Acevedo-Hernández G, Schuster SC, Himmelbauer H, Minoche AE, Xu S, Lynch M, Oropeza-Aburto A, Cervantes-Pérez SA, de Jesús Ortega-Estrada M, Cervantes-Luevano JI, Michael TP, Mockler T, Bryant D, Herrera-Estrella A, Albert VA, Herrera-Estrella L.

Nature. 2013 Jun 6;498(7452):94-8. doi: 10.1038/nature12132. Epub 2013 May 12.

30.

The unique pseudanthium of Actinodium (Myrtaceae) - morphological reinvestigation and possible regulation by CYCLOIDEA-like genes.

Claßen-Bockhoff R, Ruonala R, Bull-Hereñu K, Marchant N, Albert VA.

Evodevo. 2013 Mar 1;4(1):8. doi: 10.1186/2041-9139-4-8.

31.
32.

Evolution and diversification of the CYC/TB1 gene family in Asteraceae--a comparative study in Gerbera (Mutisieae) and sunflower (Heliantheae).

Tähtiharju S, Rijpkema AS, Vetterli A, Albert VA, Teeri TH, Elomaa P.

Mol Biol Evol. 2012 Apr;29(4):1155-66. doi: 10.1093/molbev/msr283. Epub 2011 Nov 18.

PMID:
22101417
33.

Is GC bias in the nuclear genome of the carnivorous plant Utricularia driven by ROS-based mutation and biased gene conversion?

Ibarra-Laclette E, Albert VA, Herrera-Estrella A, Herrera-Estrella L.

Plant Signal Behav. 2011 Nov;6(11):1631-4. doi: 10.4161/psb.6.11.17657. Epub 2011 Nov 1.

34.

Dynamic distribution patterns of ribosomal DNA and chromosomal evolution in Paphiopedilum, a lady's slipper orchid.

Lan T, Albert VA.

BMC Plant Biol. 2011 Sep 12;11:126. doi: 10.1186/1471-2229-11-126.

35.

Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome.

Ibarra-Laclette E, Albert VA, Pérez-Torres CA, Zamudio-Hernández F, Ortega-Estrada Mde J, Herrera-Estrella A, Herrera-Estrella L.

BMC Plant Biol. 2011 Jun 3;11:101. doi: 10.1186/1471-2229-11-101.

36.

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.

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.

Genome Biol. 2011;12(5):R48. doi: 10.1186/gb-2011-12-5-r48. Epub 2011 May 27.

37.

Over-expression of the Gerbera hybrida At-SOC1-like1 gene Gh-SOC1 leads to floral organ identity deterioration.

Ruokolainen S, Ng YP, Albert VA, Elomaa P, Teeri TH.

Ann Bot. 2011 Jun;107(9):1491-9. doi: 10.1093/aob/mcr112. Epub 2011 May 13.

38.

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.

Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV.

Science. 2011 May 20;332(6032):960-3. doi: 10.1126/science.1203810. Epub 2011 May 5.

39.

Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower.

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.

Proc Natl Acad Sci U S A. 2010 Dec 28;107(52):22570-5. doi: 10.1073/pnas.1013395108. Epub 2010 Dec 13.

40.

Large scale interaction analysis predicts that the Gerbera hybrida floral E function is provided both by general and specialized proteins.

Ruokolainen S, Ng YP, Albert VA, Elomaa P, Teeri TH.

BMC Plant Biol. 2010 Jun 25;10:129. doi: 10.1186/1471-2229-10-129.

41.

Characterization of SQUAMOSA-like genes in Gerbera hybrida, including one involved in reproductive transition.

Ruokolainen S, Ng YP, Broholm SK, Albert VA, Elomaa P, Teeri TH.

BMC Plant Biol. 2010 Jun 25;10:128. doi: 10.1186/1471-2229-10-128.

42.

Scaffold filling, contig fusion and comparative gene order inference.

Muñoz A, Zheng C, Zhu Q, Albert VA, Rounsley S, Sankoff D.

BMC Bioinformatics. 2010 Jun 4;11:304. doi: 10.1186/1471-2105-11-304.

43.

The carnivorous bladderwort (Utricularia, Lentibulariaceae): a system inflates.

Albert VA, Jobson RW, Michael TP, Taylor DJ.

J Exp Bot. 2010;61(1):5-9. doi: 10.1093/jxb/erp349.

PMID:
20007200
44.

Towards improved reconstruction of ancestral gene order in angiosperm phylogeny.

Sankoff D, Zheng C, Wall PK, dePamphilis C, Leebens-Mack J, Albert VA.

J Comput Biol. 2009 Oct;16(10):1353-67. doi: 10.1089/cmb.2009.0103.

PMID:
19803735
45.

Functional characterization of B class MADS-box transcription factors in Gerbera hybrida.

Broholm SK, Pöllänen E, Ruokolainen S, Tähtiharju S, Kotilainen M, Albert VA, Elomaa P, Teeri TH.

J Exp Bot. 2010;61(1):75-85. doi: 10.1093/jxb/erp279.

46.

Gene loss under neighborhood selection following whole genome duplication and the reconstruction of the ancestral Populus genome.

Zheng C, Kerr Wall P, Leebens-Mack J, DE Pamphilis C, Albert VA, Sankoff D.

J Bioinform Comput Biol. 2009 Jun;7(3):499-520.

PMID:
19507287
47.

Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae).

Chanderbali AS, Albert VA, Leebens-Mack J, Altman NS, Soltis DE, Soltis PS.

Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8929-34. doi: 10.1073/pnas.0811476106. Epub 2009 May 18.

48.

Polyploidy and angiosperm diversification.

Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, Depamphilis CW, Wall PK, Soltis PS.

Am J Bot. 2009 Jan;96(1):336-48. doi: 10.3732/ajb.0800079.

49.

Cytokinin signaling regulates cambial development in poplar.

Nieminen K, Immanen J, Laxell M, Kauppinen L, Tarkowski P, Dolezal K, Tähtiharju S, Elo A, Decourteix M, Ljung K, Bhalerao R, Keinonen K, Albert VA, Helariutta Y.

Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):20032-7. doi: 10.1073/pnas.0805617106. Epub 2008 Dec 8.

50.

A TCP domain transcription factor controls flower type specification along the radial axis of the Gerbera (Asteraceae) inflorescence.

Broholm SK, Tähtiharju S, Laitinen RA, Albert VA, Teeri TH, Elomaa P.

Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):9117-22. doi: 10.1073/pnas.0801359105. Epub 2008 Jun 23.

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