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Items: 1 to 50 of 118

1.

Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement.

Wu S, Lau KH, Cao Q, Hamilton JP, Sun H, Zhou C, Eserman L, Gemenet DC, Olukolu BA, Wang H, Crisovan E, Godden GT, Jiao C, Wang X, Kitavi M, Manrique-Carpintero N, Vaillancourt B, Wiegert-Rininger K, Yang X, Bao K, Schaff J, Kreuze J, Gruneberg W, Khan A, Ghislain M, Ma D, Jiang J, Mwanga ROM, Leebens-Mack J, Coin LJM, Yencho GC, Buell CR, Fei Z.

Nat Commun. 2018 Nov 2;9(1):4580. doi: 10.1038/s41467-018-06983-8.

2.

Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots.

Givnish TJ, Zuluaga A, Spalink D, Soto Gomez M, Lam VKY, Saarela JM, Sass C, Iles WJD, de Sousa DJL, Leebens-Mack J, Chris Pires J, Zomlefer WB, Gandolfo MA, Davis JI, Stevenson DW, dePamphilis C, Specht CD, Graham SW, Barrett CF, Ané C.

Am J Bot. 2018 Oct 24. doi: 10.1002/ajb2.1178. [Epub ahead of print]

PMID:
30368769
3.

Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots.

Kakrana A, Mathioni SM, Huang K, Hammond R, Vandivier L, Patel P, Arikit S, Shevchenko O, Harkess AE, Kingham B, Gregory BD, Leebens-Mack JH, Meyers BC.

Genome Res. 2018 Sep;28(9):1333-1344. doi: 10.1101/gr.228163.117. Epub 2018 Jul 12.

PMID:
30002159
4.

Parallel evolution of storage roots in morning glories (Convolvulaceae).

Eserman LA, Jarret RL, Leebens-Mack JH.

BMC Plant Biol. 2018 May 29;18(1):95. doi: 10.1186/s12870-018-1307-4.

5.

Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism.

Heyduk K, Ray JN, Ayyampalayam S, Leebens-Mack J.

Am J Bot. 2018 Mar;105(3):587-601. doi: 10.1002/ajb2.1017. Epub 2018 Feb 20.

PMID:
29746718
6.

Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae).

Unruh SA, McKain MR, Lee YI, Yukawa T, McCormick MK, Shefferson RP, Smithson A, Leebens-Mack JH, Pires JC.

Am J Bot. 2018 Apr;105(4):631-640. doi: 10.1002/ajb2.1047. Epub 2018 Apr 2. Erratum in: Am J Bot. 2018 May;105(5):957.

PMID:
29608785
7.

Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses.

Edger PP, Hall JC, Harkess A, Tang M, Coombs J, Mohammadin S, Schranz ME, Xiong Z, Leebens-Mack J, Meyers BC, Sytsma KJ, Koch MA, Al-Shehbaz IA, Pires JC.

Am J Bot. 2018 Mar;105(3):463-469. doi: 10.1002/ajb2.1040. Epub 2018 Mar 25.

PMID:
29574686
8.

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism.

Yang X, Hu R, Yin H, Jenkins J, Shu S, Tang H, Liu D, Weighill DA, Cheol Yim W, Ha J, Heyduk K, Goodstein DM, Guo HB, Moseley RC, Fitzek E, Jawdy S, Zhang Z, Xie M, Hartwell J, Grimwood J, Abraham PE, Mewalal R, Beltrán JD, Boxall SF, Dever LV, Palla KJ, Albion R, Garcia T, Mayer JA, Don Lim S, Man Wai C, Peluso P, Van Buren R, De Paoli HC, Borland AM, Guo H, Chen JG, Muchero W, Yin Y, Jacobson DA, Tschaplinski TJ, Hettich RL, Ming R, Winter K, Leebens-Mack JH, Smith JAC, Cushman JC, Schmutz J, Tuskan GA.

Nat Commun. 2017 Dec 1;8(1):1899. doi: 10.1038/s41467-017-01491-7.

9.

The asparagus genome sheds light on the origin and evolution of a young Y chromosome.

Harkess A, Zhou J, Xu C, Bowers JE, Van der Hulst R, Ayyampalayam S, Mercati F, Riccardi P, McKain MR, Kakrana A, Tang H, Ray J, Groenendijk J, Arikit S, Mathioni SM, Nakano M, Shan H, Telgmann-Rauber A, Kanno A, Yue Z, Chen H, Li W, Chen Y, Xu X, Zhang Y, Luo S, Chen H, Gao J, Mao Z, Pires JC, Luo M, Kudrna D, Wing RA, Meyers BC, Yi K, Kong H, Lavrijsen P, Sunseri F, Falavigna A, Ye Y, Leebens-Mack JH, Chen G.

Nat Commun. 2017 Nov 2;8(1):1279. doi: 10.1038/s41467-017-01064-8.

10.

Horizontal Transfer of Non-LTR Retrotransposons from Arthropods to Flowering Plants.

Gao D, Chu Y, Xia H, Xu C, Heyduk K, Abernathy B, Ozias-Akins P, Leebens-Mack JH, Jackson SA.

Mol Biol Evol. 2018 Feb 1;35(2):354-364. doi: 10.1093/molbev/msx275.

11.

The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants.

Bewick AJ, Niederhuth CE, Ji L, Rohr NA, Griffin PT, Leebens-Mack J, Schmitz RJ.

Genome Biol. 2017 May 1;18(1):65. doi: 10.1186/s13059-017-1195-1.

12.

Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.

Johnson KL, Cassin AM, Lonsdale A, Wong GK, Soltis DE, Miles NW, Melkonian M, Melkonian B, Deyholos MK, Leebens-Mack J, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Carpenter EJ, Bacic A, Doblin MS, Schultz CJ.

Plant Physiol. 2017 Jun;174(2):904-921. doi: 10.1104/pp.17.00295. Epub 2017 Apr 26.

13.

Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids.

Lin CS, Chen JJW, Chiu CC, Hsiao HCW, Yang CJ, Jin XH, Leebens-Mack J, de Pamphilis CW, Huang YT, Yang LH, Chang WJ, Kui L, Wong GK, Hu JM, Wang W, Shih MC.

Plant J. 2017 Jun;90(5):994-1006. doi: 10.1111/tpj.13525. Epub 2017 Apr 11.

14.

A Century of Sex Determination in Flowering Plants.

Harkess A, Leebens-Mack J.

J Hered. 2017 Jan;108(1):69-77. Epub 2016 Nov 14.

PMID:
27974487
15.

Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae).

McKain MR, McNeal JR, Kellar PR, Eguiarte LE, Pires JC, Leebens-Mack J.

Am J Bot. 2016 Oct;103(10):1717-1729. Epub 2016 Oct 20.

16.

The evolutionary ecology of "mutual services" in the 21st century.

Yoder JB, Leebens-Mack J.

Am J Bot. 2016 Oct;103(10):1712-1716. Epub 2016 Oct 26. No abstract available.

17.

The Evolution of HD2 Proteins in Green Plants.

Bourque S, Jeandroz S, Grandperret V, Lehotai N, Aimé S, Soltis DE, Miles NW, Melkonian M, Deyholos MK, Leebens-Mack JH, Chase MW, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Yan Z, Xie Y, Carpenter EJ, Wong GKS, Wendehenne D, Nicolas-Francès V.

Trends Plant Sci. 2016 Dec;21(12):1008-1016. doi: 10.1016/j.tplants.2016.10.001. Epub 2016 Oct 24. Review.

PMID:
27789157
18.

Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae).

Heyduk K, McKain MR, Lalani F, Leebens-Mack J.

Mol Phylogenet Evol. 2016 Dec;105:102-113. doi: 10.1016/j.ympev.2016.08.018. Epub 2016 Aug 30.

PMID:
27591171
19.

Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus.

Harkess A, Mercati F, Abbate L, McKain M, Pires JC, Sala T, Sunseri F, Falavigna A, Leebens-Mack J.

G3 (Bethesda). 2016 Sep 8;6(9):2679-85. doi: 10.1534/g3.116.030239.

20.

Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology.

Lane TS, Rempe CS, Davitt J, Staton ME, Peng Y, Soltis DE, Melkonian M, Deyholos M, Leebens-Mack JH, Chase M, Rothfels CJ, Stevenson D, Graham SW, Yu J, Liu T, Pires JC, Edger PP, Zhang Y, Xie Y, Zhu Y, Carpenter E, Wong GK, Stewart CN Jr.

BMC Biotechnol. 2016 May 31;16(1):47. doi: 10.1186/s12896-016-0277-6.

21.

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.

22.

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 Apr 21;8(4):1150-64. doi: 10.1093/gbe/evw060.

23.

Plant Comparative and Functional Genomics.

Yang X, Leebens-Mack J, Chen F, Yin Y.

Int J Genomics. 2015;2015:924369. doi: 10.1155/2015/924369. Epub 2015 Dec 31. No abstract available.

24.

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.

25.

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.

PMID:
26748268
26.

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.

27.

Gas exchange and leaf anatomy of a C3-CAM hybrid, Yucca gloriosa (Asparagaceae).

Heyduk K, Burrell N, Lalani F, Leebens-Mack J.

J Exp Bot. 2016 Mar;67(5):1369-79. doi: 10.1093/jxb/erv536. Epub 2015 Dec 29.

28.

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.

29.

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.

30.

Orchid phylogenomics and multiple drivers of their extraordinary diversification.

Givnish TJ, Spalink D, Ames M, Lyon SP, Hunter SJ, Zuluaga A, Iles WJ, Clements MA, Arroyo MT, Leebens-Mack J, Endara L, Kriebel R, Neubig KM, Whitten WM, Williams NH, Cameron KM.

Proc Biol Sci. 2015 Sep 7;282(1814). doi: 10.1098/rspb.2015.1553.

31.

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.

32.

Evolution of Asparagus L. (Asparagaceae): Out-of-South-Africa and multiple origins of sexual dimorphism.

Norup MF, Petersen G, Burrows S, Bouchenak-Khelladi Y, Leebens-Mack J, Pires JC, Linder HP, Seberg O.

Mol Phylogenet Evol. 2015 Nov;92:25-44. doi: 10.1016/j.ympev.2015.06.002. Epub 2015 Jun 14.

PMID:
26079131
33.

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.

34.

Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis).

Harkess A, Mercati F, Shan HY, Sunseri F, Falavigna A, Leebens-Mack J.

New Phytol. 2015 Aug;207(3):883-92. doi: 10.1111/nph.13389. Epub 2015 Mar 27.

35.

Data access for the 1,000 Plants (1KP) project.

Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GK.

Gigascience. 2014 Oct 27;3:17. doi: 10.1186/2047-217X-3-17. eCollection 2014. Review.

36.

Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants.

Zheng C, Kononenko A, Leebens-Mack J, Lyons E, Sankoff D.

BMC Genomics. 2014;15 Suppl 6:S8. doi: 10.1186/1471-2164-15-S6-S8. Epub 2014 Oct 17.

37.

Yucca aloifolia (Asparagaceae) opts out of an obligate pollination mutualism.

Rentsch JD, Leebens-Mack J.

Am J Bot. 2014 Dec;101(12):2062-7. doi: 10.3732/ajb.1400351. Epub 2014 Nov 26.

38.

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.

39.

Phylotranscriptomic analysis of the origin and early diversification of land plants.

Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GK, Leebens-Mack J.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4859-68. doi: 10.1073/pnas.1323926111. Epub 2014 Oct 29.

40.

Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes.

Cannon SB, McKain MR, Harkess A, Nelson MN, Dash S, Deyholos MK, Peng Y, Joyce B, Stewart CN Jr, Rolf M, Kutchan T, Tan X, Chen C, Zhang Y, Carpenter E, Wong GK, Doyle JJ, Leebens-Mack J.

Mol Biol Evol. 2015 Jan;32(1):193-210. doi: 10.1093/molbev/msu296. Epub 2014 Oct 27.

41.

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.

42.

Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach.

Panahiazar M, Sheth AP, Ranabahu A, Vos RA, Leebens-Mack J.

BMC Med Genomics. 2013;6 Suppl 3:S5. doi: 10.1186/1755-8794-6-S3-S5. Epub 2013 Nov 11.

43.

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.

44.

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
45.

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

Barrett CF, Specht CD, Leebens-Mack J, Stevenson DW, Zomlefer WB, Davis JI.

Ann Bot. 2014 Jan;113(1):119-33. doi: 10.1093/aob/mct264. Epub 2013 Nov 25.

46.

Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes.

Vitte C, Estep MC, Leebens-Mack J, Bennetzen JL.

Ann Bot. 2013 Sep;112(5):881-9. doi: 10.1093/aob/mct155. Epub 2013 Jul 25.

47.

Single nucleotide polymorphism isolated from a novel EST dataset in garden asparagus (Asparagus officinalis L.).

Mercati F, Riccardi P, Leebens-Mack J, Abenavoli MR, Falavigna A, Sunseri F.

Plant Sci. 2013 Apr;203-204:115-23. doi: 10.1016/j.plantsci.2013.01.002. Epub 2013 Jan 16.

PMID:
23415335
48.

Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies.

Bliss BJ, Wanke S, Barakat A, Ayyampalayam S, Wickett N, Wall PK, Jiao Y, Landherr L, Ralph PE, Hu Y, Neinhuis C, Leebens-Mack J, Arumuganathan K, Clifton SW, Maximova SN, Ma H, dePamphilis CW.

BMC Plant Biol. 2013 Jan 24;13:13. doi: 10.1186/1471-2229-13-13.

49.

Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes.

Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, Depamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, Jordon-Thaden I, Kutchan TM, Leebens-Mack J, Melkonian M, Miles N, Myburg H, Patterson J, Pires JC, Ralph P, Rolf M, Sage RF, Soltis D, Soltis P, Stevenson D, Stewart CN Jr, Surek B, Thomsen CJ, Villarreal JC, Wu X, Zhang Y, Deyholos MK, Wong GK.

PLoS One. 2012;7(11):e50226. doi: 10.1371/journal.pone.0050226. Epub 2012 Nov 21.

50.

Homoploid hybrid origin of Yucca gloriosa: intersectional hybrid speciation in Yucca (Agavoideae, Asparagaceae).

Rentsch JD, Leebens-Mack J.

Ecol Evol. 2012 Sep;2(9):2213-22. doi: 10.1002/ece3.328. Epub 2012 Aug 1.

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