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Items: 43

1.

Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff.

VanBuren R, Man Wai C, Wang X, Pardo J, Yocca AE, Wang H, Chaluvadi SR, Han G, Bryant D, Edger PP, Messing J, Sorrells ME, Mockler TC, Bennetzen JL, Michael TP.

Nat Commun. 2020 Feb 14;11(1):884. doi: 10.1038/s41467-020-14724-z.

2.

Building near-complete plant genomes.

Michael TP, VanBuren R.

Curr Opin Plant Biol. 2020 Jan 22;54:26-33. doi: 10.1016/j.pbi.2019.12.009. [Epub ahead of print] Review.

3.

Fusarium virguliform e Transcriptional Plasticity Is Revealed by Host Colonization of Maize versus Soybean.

Baetsen-Young A, Man Wai C, VanBuren R, Day B.

Plant Cell. 2020 Feb;32(2):336-351. doi: 10.1105/tpc.19.00697. Epub 2019 Dec 18.

4.

Transcriptome-Based Prediction of Complex Traits in Maize.

Azodi CB, Pardo J, VanBuren R, de Los Campos G, Shiu SH.

Plant Cell. 2020 Jan;32(1):139-151. doi: 10.1105/tpc.19.00332. Epub 2019 Oct 22.

5.

GingerRoot: A Novel DNA Transposon Encoding Integrase-Related Transposase in Plants and Animals.

Cerbin S, Wai CM, VanBuren R, Jiang N.

Genome Biol Evol. 2019 Nov 1;11(11):3181-3193. doi: 10.1093/gbe/evz230.

6.

The bracteatus pineapple genome and domestication of clonally propagated crops.

Chen LY, VanBuren R, Paris M, Zhou H, Zhang X, Wai CM, Yan H, Chen S, Alonge M, Ramakrishnan S, Liao Z, Liu J, Lin J, Yue J, Fatima M, Lin Z, Zhang J, Huang L, Wang H, Hwa TY, Kao SM, Choi JY, Sharma A, Song J, Wang L, Yim WC, Cushman JC, Paull RE, Matsumoto T, Qin Y, Wu Q, Wang J, Yu Q, Wu J, Zhang S, Boches P, Tung CW, Wang ML, Coppens d'Eeckenbrugge G, Sanewski GM, Purugganan MD, Schatz MC, Bennetzen JL, Lexer C, Ming R.

Nat Genet. 2019 Oct;51(10):1549-1558. doi: 10.1038/s41588-019-0506-8. Epub 2019 Sep 30.

PMID:
31570895
7.

A chromosome-scale assembly of the model desiccation tolerant grass Oropetium thomaeum.

VanBuren R, Wai CM, Keilwagen J, Pardo J.

Plant Direct. 2018 Nov 15;2(11):e00096. doi: 10.1002/pld3.96. eCollection 2018 Nov.

8.

Arabidopsis defense mutant ndr1-1 displays accelerated development and early flowering mediated by the hormone gibberellic acid.

Dhar N, Short DPG, Mamo BE, Corrion AJ, Wai CM, Anchieta A, VanBuren R, Day B, Ajwa H, Subbarao KV, Klosterman SJ.

Plant Sci. 2019 Aug;285:200-213. doi: 10.1016/j.plantsci.2019.04.006. Epub 2019 Apr 11.

PMID:
31203885
9.

Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album.

Wai CM, Weise SE, Ozersky P, Mockler TC, Michael TP, VanBuren R.

PLoS Genet. 2019 Jun 14;15(6):e1008209. doi: 10.1371/journal.pgen.1008209. eCollection 2019 Jun.

10.

Author Correction: Origin and evolution of the octoploid strawberry genome.

Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ.

Nat Genet. 2019 Apr;51(4):765. doi: 10.1038/s41588-019-0380-4.

PMID:
30842601
11.

Origin and evolution of the octoploid strawberry genome.

Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ.

Nat Genet. 2019 Mar;51(3):541-547. doi: 10.1038/s41588-019-0356-4. Epub 2019 Feb 25. Erratum in: Nat Genet. 2019 Apr;51(4):765.

12.

Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry.

Colle M, Leisner CP, Wai CM, Ou S, Bird KA, Wang J, Wisecaver JH, Yocca AE, Alger EI, Tang H, Xiong Z, Callow P, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Song GQ, Childs KL, Schilmiller A, Vorsa N, Buell CR, VanBuren R, Jiang N, Edger PP.

Gigascience. 2019 Mar 1;8(3). pii: giz012. doi: 10.1093/gigascience/giz012.

13.

Massive Tandem Proliferation of ELIPs Supports Convergent Evolution of Desiccation Tolerance across Land Plants.

VanBuren R, Pardo J, Man Wai C, Evans S, Bartels D.

Plant Physiol. 2019 Mar;179(3):1040-1049. doi: 10.1104/pp.18.01420. Epub 2019 Jan 2.

14.

Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat.

Mower JP, Ma PF, Grewe F, Taylor A, Michael TP, VanBuren R, Qiu YL.

New Phytol. 2019 Apr;222(2):1061-1075. doi: 10.1111/nph.15650. Epub 2019 Jan 24.

15.

Publisher Correction: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Zhang J, Zhang X, Tang H, Zhang Q, Hua X, Ma X, Zhu F, Jones T, Zhu X, Bowers J, Wai CM, Zheng C, Shi Y, Chen S, Xu X, Yue J, Nelson DR, Huang L, Li Z, Xu H, Zhou D, Wang Y, Hu W, Lin J, Deng Y, Pandey N, Mancini M, Zerpa D, Nguyen JK, Wang L, Yu L, Xin Y, Ge L, Arro J, Han JO, Chakrabarty S, Pushko M, Zhang W, Ma Y, Ma P, Lv M, Chen F, Zheng G, Xu J, Yang Z, Deng F, Chen X, Liao Z, Zhang X, Lin Z, Lin H, Yan H, Kuang Z, Zhong W, Liang P, Wang G, Yuan Y, Shi J, Hou J, Lin J, Jin J, Cao P, Shen Q, Jiang Q, Zhou P, Ma Y, Zhang X, Xu R, Liu J, Zhou Y, Jia H, Ma Q, Qi R, Zhang Z, Fang J, Fang H, Song J, Wang M, Dong G, Wang G, Chen Z, Ma T, Liu H, Dhungana SR, Huss SE, Yang X, Sharma A, Trujillo JH, Martinez MC, Hudson M, Riascos JJ, Schuler M, Chen LQ, Braun DM, Li L, Yu Q, Wang J, Wang K, Schatz MC, Heckerman D, Van Sluys MA, Souza GM, Moore PH, Sankoff D, VanBuren R, Paterson AH, Nagai C, Ming R.

Nat Genet. 2018 Dec;50(12):1754. doi: 10.1038/s41588-018-0293-7.

PMID:
30425353
16.

Desiccation Tolerance Evolved through Gene Duplication and Network Rewiring in Lindernia.

VanBuren R, Man Wai C, Pardo J, Giarola V, Ambrosini S, Song X, Bartels D.

Plant Cell. 2018 Dec;30(12):2943-2958. doi: 10.1105/tpc.18.00517. Epub 2018 Oct 25.

17.

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Zhang J, Zhang X, Tang H, Zhang Q, Hua X, Ma X, Zhu F, Jones T, Zhu X, Bowers J, Wai CM, Zheng C, Shi Y, Chen S, Xu X, Yue J, Nelson DR, Huang L, Li Z, Xu H, Zhou D, Wang Y, Hu W, Lin J, Deng Y, Pandey N, Mancini M, Zerpa D, Nguyen JK, Wang L, Yu L, Xin Y, Ge L, Arro J, Han JO, Chakrabarty S, Pushko M, Zhang W, Ma Y, Ma P, Lv M, Chen F, Zheng G, Xu J, Yang Z, Deng F, Chen X, Liao Z, Zhang X, Lin Z, Lin H, Yan H, Kuang Z, Zhong W, Liang P, Wang G, Yuan Y, Shi J, Hou J, Lin J, Jin J, Cao P, Shen Q, Jiang Q, Zhou P, Ma Y, Zhang X, Xu R, Liu J, Zhou Y, Jia H, Ma Q, Qi R, Zhang Z, Fang J, Fang H, Song J, Wang M, Dong G, Wang G, Chen Z, Ma T, Liu H, Dhungana SR, Huss SE, Yang X, Sharma A, Trujillo JH, Martinez MC, Hudson M, Riascos JJ, Schuler M, Chen LQ, Braun DM, Li L, Yu Q, Wang J, Wang K, Schatz MC, Heckerman D, Van Sluys MA, Souza GM, Moore PH, Sankoff D, VanBuren R, Paterson AH, Nagai C, Ming R.

Nat Genet. 2018 Nov;50(11):1565-1573. doi: 10.1038/s41588-018-0237-2. Epub 2018 Oct 8. Erratum in: Nat Genet. 2018 Dec;50(12):1754.

PMID:
30297971
18.

A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome.

VanBuren R, Wai CM, Colle M, Wang J, Sullivan S, Bushakra JM, Liachko I, Vining KJ, Dossett M, Finn CE, Jibran R, Chagné D, Childs K, Edger PP, Mockler TC, Bassil NV.

Gigascience. 2018 Aug 1;7(8). doi: 10.1093/gigascience/giy094.

19.

The causes and consequences of subgenome dominance in hybrids and recent polyploids.

Bird KA, VanBuren R, Puzey JR, Edger PP.

New Phytol. 2018 Oct;220(1):87-93. doi: 10.1111/nph.15256. Epub 2018 Jun 8. Review.

20.

Subgenome assignment in allopolyploids: challenges and future directions.

Edger PP, McKain MR, Bird KA, VanBuren R.

Curr Opin Plant Biol. 2018 Apr;42:76-80. doi: 10.1016/j.pbi.2018.03.006. Epub 2018 Apr 9. Review.

PMID:
29649616
21.

Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data.

Jibran R, Dzierzon H, Bassil N, Bushakra JM, Edger PP, Sullivan S, Finn CE, Dossett M, Vining KJ, VanBuren R, Mockler TC, Liachko I, Davies KM, Foster TM, Chagné D.

Hortic Res. 2018 Feb 7;5:8. doi: 10.1038/s41438-017-0013-y. eCollection 2018.

22.

Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla.

VanBuren R, Wai CM, Ou S, Pardo J, Bryant D, Jiang N, Mockler TC, Edger P, Michael TP.

Nat Commun. 2018 Jan 2;9(1):13. doi: 10.1038/s41467-017-02546-5.

23.

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity.

Edger PP, VanBuren R, Colle M, Poorten TJ, Wai CM, Niederhuth CE, Alger EI, Ou S, Acharya CB, Wang J, Callow P, McKain MR, Shi J, Collier C, Xiong Z, Mower JP, Slovin JP, Hytönen T, Jiang N, Childs KL, Knapp SJ.

Gigascience. 2018 Feb 1;7(2):1-7. doi: 10.1093/gigascience/gix124.

24.

Seed desiccation mechanisms co-opted for vegetative desiccation in the resurrection grass Oropetium thomaeum.

VanBuren R, Wai CM, Zhang Q, Song X, Edger PP, Bryant D, Michael TP, Mockler TC, Bartels D.

Plant Cell Environ. 2017 Oct;40(10):2292-2306. doi: 10.1111/pce.13027.

PMID:
28730594
25.

Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple.

Wai CM, VanBuren R, Zhang J, Huang L, Miao W, Edger PP, Yim WC, Priest HD, Meyers BC, Mockler T, Smith JAC, Cushman JC, Ming R.

Plant J. 2017 Oct;92(1):19-30. doi: 10.1111/tpj.13630. Epub 2017 Aug 21.

26.

Desiccation tolerance: Seedy origins of resurrection.

VanBuren R.

Nat Plants. 2017 Mar 27;3:17046. doi: 10.1038/nplants.2017.46. No abstract available.

PMID:
28346449
27.

Extremely low nucleotide diversity in the X-linked region of papaya caused by a strong selective sweep.

VanBuren R, Wai CM, Zhang J, Han J, Arro J, Lin Z, Liao Z, Yu Q, Wang ML, Zee F, Moore RC, Charlesworth D, Ming R.

Genome Biol. 2016 Nov 28;17(1):230.

28.

The genome of black raspberry (Rubus occidentalis).

VanBuren R, Bryant D, Bushakra JM, Vining KJ, Edger PP, Rowley ER, Priest HD, Michael TP, Lyons E, Filichkin SA, Dossett M, Finn CE, Bassil NV, Mockler TC.

Plant J. 2016 Sep;87(6):535-47. doi: 10.1111/tpj.13215. Epub 2016 Jul 20.

29.

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum.

VanBuren R, Bryant D, Edger PP, Tang H, Burgess D, Challabathula D, Spittle K, Hall R, Gu J, Lyons E, Freeling M, Bartels D, Ten Hallers B, Hastie A, Michael TP, Mockler TC.

Nature. 2015 Nov 26;527(7579):508-11. doi: 10.1038/nature15714. Epub 2015 Nov 11.

PMID:
26560029
30.

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.

31.

High-density interspecific genetic maps of kiwifruit and the identification of sex-specific markers.

Zhang Q, Liu C, Liu Y, VanBuren R, Yao X, Zhong C, Huang H.

DNA Res. 2015 Oct;22(5):367-75. doi: 10.1093/dnares/dsv019. Epub 2015 Sep 14.

32.

A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag(4) conferring resistance to the aphid Amphorophora agathonica.

Bushakra JM, Bryant DW, Dossett M, Vining KJ, VanBuren R, Gilmore BS, Lee J, Mockler TC, Finn CE, Bassil NV.

Theor Appl Genet. 2015 Aug;128(8):1631-46. doi: 10.1007/s00122-015-2541-x. Epub 2015 Jun 3.

33.

Origin and domestication of papaya Yh chromosome.

VanBuren R, Zeng F, Chen C, Zhang J, Wai CM, Han J, Aryal R, Gschwend AR, Wang J, Na JK, Huang L, Zhang L, Miao W, Gou J, Arro J, Guyot R, Moore RC, Wang ML, Zee F, Charlesworth D, Moore PH, Yu Q, Ming R.

Genome Res. 2015 Apr;25(4):524-33. doi: 10.1101/gr.183905.114. Epub 2015 Mar 11.

34.

Progress, challenges and the future of crop genomes.

Michael TP, VanBuren R.

Curr Opin Plant Biol. 2015 Apr;24:71-81. doi: 10.1016/j.pbi.2015.02.002. Epub 2015 Feb 19. Review.

PMID:
25703261
35.

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.

36.

Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map.

Zhang Q, Li L, VanBuren R, Liu Y, Yang M, Xu L, Bowers JE, Zhong C, Han Y, Li S, Ming R.

BMC Genomics. 2014 May 15;15:372. doi: 10.1186/1471-2164-15-372.

37.

Dynamic transposable element accumulation in the nascent sex chromosomes of papaya.

Vanburen R, Ming R.

Mob Genet Elements. 2013 Jan 1;3(1):e23462.

38.

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).

Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min XJ, Hudson KA, Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu Q, Mockler TC, Carroll A, Zheng Y, Sunkar R, Jia R, Chen N, Arro J, Wai CM, Wafula E, Spence A, Han Y, Xu L, Zhang J, Peery R, Haus MJ, Xiong W, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du C, Downie SR, Schuler MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, dePamphilis CW, Merchant SS, Paterson AH, Buchanan BB, Li S, Shen-Miller J.

Genome Biol. 2013 May 10;14(5):R41. doi: 10.1186/gb-2013-14-5-r41.

39.

Organelle DNA accumulation in the recently evolved papaya sex chromosomes.

VanBuren R, Ming R.

Mol Genet Genomics. 2013 Jun;288(5-6):277-84. doi: 10.1007/s00438-013-0747-7. Epub 2013 May 1.

PMID:
23636354
40.

Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar.

Yang M, Han Y, VanBuren R, Ming R, Xu L, Han Y, Liu Y.

BMC Genomics. 2012 Nov 21;13:653. doi: 10.1186/1471-2164-13-653.

41.

Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution.

Wang J, Na JK, Yu Q, Gschwend AR, Han J, Zeng F, Aryal R, VanBuren R, Murray JE, Zhang W, Navajas-Pérez R, Feltus FA, Lemke C, Tong EJ, Chen C, Wai CM, Singh R, Wang ML, Min XJ, Alam M, Charlesworth D, Moore PH, Jiang J, Paterson AH, Ming R.

Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13710-5. doi: 10.1073/pnas.1207833109. Epub 2012 Aug 6.

42.

Rapid divergence and expansion of the X chromosome in papaya.

Gschwend AR, Yu Q, Tong EJ, Zeng F, Han J, VanBuren R, Aryal R, Charlesworth D, Moore PH, Paterson AH, Ming R.

Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13716-21. doi: 10.1073/pnas.1121096109. Epub 2012 Aug 6.

43.

Genetic analysis of the Utah population: a comparison of STR and VNTR loci.

Jorde LB, Shortsleeve PA, Henry JW, Vanburen RT, Hutchinson LE, Rigley TM.

Hum Biol. 2000 Dec;72(6):927-36.

PMID:
11236864

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