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Data supporting the nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae).

Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH.

Data Brief. 2016 Mar 2;7:532-6. doi: 10.1016/j.dib.2016.02.063. eCollection 2016 Jun.


A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales.

McKain MR, Tang H, McNeal JR, Ayyampalayam S, Davis JI, dePamphilis CW, Givnish TJ, Pires JC, Stevenson DW, Leebens-Mack JH.

Genome Biol Evol. 2016 Mar 17. pii: evw060. [Epub ahead of print]


Identification of genes differentially expressed during early interactions between the stem rot fungus (Sclerotium rolfsii) and peanut (Arachis hypogaea) cultivars with increasing disease resistance levels.

Jogi A, Kerry JW, Brenneman TB, Leebens-Mack JH, Gold SE.

Microbiol Res. 2016 Mar;184:1-12. doi: 10.1016/j.micres.2015.11.003. Epub 2015 Dec 17.


Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae).

Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH.

Mol Phylogenet Evol. 2016 Apr;97:32-42. doi: 10.1016/j.ympev.2015.12.015. Epub 2015 Dec 31.


Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.

Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH, dePamphilis CW.

PLoS One. 2016 Jan 5;11(1):e0146062. doi: 10.1371/journal.pone.0146062. eCollection 2016.


The pineapple genome and the evolution of CAM photosynthesis.

Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo HB, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen LY, Shirley N, Lin YR, Liu LY, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith JA, Cushman JC, Paull RE, Yu Q.

Nat Genet. 2015 Dec;47(12):1435-42. doi: 10.1038/ng.3435. Epub 2015 Nov 2.


Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots.

Barrett CF, Baker WJ, Comer JR, Conran JG, Lahmeyer SC, Leebens-Mack JH, Li J, Lim GS, Mayfield-Jones DR, Perez L, Medina J, Pires JC, Santos C, Wm Stevenson D, Zomlefer WB, Davis JI.

New Phytol. 2016 Jan;209(2):855-70. doi: 10.1111/nph.13617. Epub 2015 Sep 9.


Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next-generation sequencing.

Comer JR, Zomlefer WB, Barrett CF, Davis JI, Stevenson DW, Heyduk K, Leebens-Mack JH.

Am J Bot. 2015 Jun;102(6):888-99. doi: 10.3732/ajb.1500057. Epub 2015 May 29.


Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells.

Augustin MM, Ruzicka DR, Shukla AK, Augustin JM, Starks CM, O'Neil-Johnson M, McKain MR, Evans BS, Barrett MD, Smithson A, Wong GK, Deyholos MK, Edger PP, Pires JC, Leebens-Mack JH, Mann DA, Kutchan TM.

Plant J. 2015 Jun;82(6):991-1003. doi: 10.1111/tpj.12871.


Bayesian phylogeny of sucrose transporters: ancient origins, differential expansion and convergent evolution in monocots and dicots.

Peng D, Gu X, Xue LJ, Leebens-Mack JH, Tsai CJ.

Front Plant Sci. 2014 Nov 12;5:615. doi: 10.3389/fpls.2014.00615. eCollection 2014.


Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor.

Floyd SK, Ryan JG, Conway SJ, Brenner E, Burris KP, Burris JN, Chen T, Edger PP, Graham SW, Leebens-Mack JH, Pires JC, Rothfels CJ, Sigel EM, Stevenson DW, Neal Stewart C Jr, Wong GK, Bowman JL.

Mol Phylogenet Evol. 2014 Dec;81:159-73. doi: 10.1016/j.ympev.2014.06.017. Epub 2014 Sep 27.


Phylogenetics and diversification of morning glories (tribe Ipomoeeae, Convolvulaceae) based on whole plastome sequences.

Eserman LA, Tiley GP, Jarret RL, Leebens-Mack JH, Miller RE.

Am J Bot. 2014 Jan;101(1):92-103. doi: 10.3732/ajb.1300207. Epub 2013 Dec 26.


The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage.

Bagal UR, Leebens-Mack JH, Lorenz WW, Dean JF.

BMC Genomics. 2012 Jun 11;13 Suppl 3:S1. doi: 10.1186/1471-2164-13-S3-S1.


Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies.

Zahn LM, Ma X, Altman NS, Zhang Q, Wall PK, Tian D, Gibas CJ, Gharaibeh R, Leebens-Mack JH, Depamphilis CW, Ma H.

Genome Biol. 2010;11(10):R101. doi: 10.1186/gb-2010-11-10-r101. Epub 2010 Oct 15.


Positive selection and expression divergence following gene duplication in the sunflower CYCLOIDEA gene family.

Chapman MA, Leebens-Mack JH, Burke JM.

Mol Biol Evol. 2008 Jul;25(7):1260-73. doi: 10.1093/molbev/msn001. Epub 2008 Apr 3.


An expressed sequence tag (EST) library from developing fruits of an Hawaiian endemic mint (Stenogyne rugosa, Lamiaceae): characterization and microsatellite markers.

Lindqvist C, Scheen AC, Yoo MJ, Grey P, Oppenheimer DG, Leebens-Mack JH, Soltis DE, Soltis PS, Albert VA.

BMC Plant Biol. 2006 Aug 23;6:16.


Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis.

Gilbert MT, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, Carlson JE, Leebens-Mack JH, Schuster SC.

Nucleic Acids Res. 2007;35(1):1-10. Epub 2006 Aug 18.


EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot.

Carlson JE, Leebens-Mack JH, Wall PK, Zahn LM, Mueller LA, Landherr LL, Hu Y, Ilut DC, Arrington JM, Choirean S, Becker A, Field D, Tanksley SD, Ma H, dePamphilis CW.

Plant Mol Biol. 2006 Oct;62(3):351-69. Epub 2006 Aug 17.


Using partial genomic fosmid libraries for sequencing complete organellar genomes.

McNeal JR, Leebens-Mack JH, Arumuganathan K, Kuehl JV, Boore JL, DePamphilis CW.

Biotechniques. 2006 Jul;41(1):69-73.


Widespread genome duplications throughout the history of flowering plants.

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.

Genome Res. 2006 Jun;16(6):738-49. Epub 2006 May 15.

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