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Items: 1 to 20 of 139

1.

Sequencing and assembly of the 22-gb loblolly pine genome.

Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marçais G, Puiu D, Roberts M, Wegrzyn JL, de Jong PJ, Neale DB, Salzberg SL, Yorke JA, Langley CH.

Genetics. 2014 Mar;196(3):875-90. doi: 10.1534/genetics.113.159715.

2.

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.

Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JF, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg SL, Langley CH.

Genome Biol. 2014 Mar 4;15(3):R59. doi: 10.1186/gb-2014-15-3-r59.

3.

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Jan 1;6(1):1-4. doi: 10.1093/gigascience/giw016. Erratum in: Gigascience. 2017 Oct 1;6(10):1.

4.

Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.

Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, Puiu D, Salzberg SL, Dejong PJ, Mockaitis K, Main D, Langley CH, Neale DB.

Genetics. 2014 Mar;196(3):891-909. doi: 10.1534/genetics.113.159996.

5.

Whole-exome targeted sequencing of the uncharacterized pine genome.

Neves LG, Davis JM, Barbazuk WB, Kirst M.

Plant J. 2013 Jul;75(1):146-156. doi: 10.1111/tpj.12193. Epub 2013 May 7.

6.

Timber! Felling the loblolly pine genome.

Hamilton JP, Buell CR.

Genome Biol. 2014 Mar 31;15(3):111. doi: 10.1186/gb4170.

7.

A high-density gene map of loblolly pine (Pinus taeda L.) based on exome sequence capture genotyping.

Neves LG, Davis JM, Barbazuk WB, Kirst M.

G3 (Bethesda). 2014 Jan 10;4(1):29-37. doi: 10.1534/g3.113.008714.

8.

Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis.

Perera D, Magbanua ZV, Thummasuwan S, Mukherjee D, Arick M 2nd, Chouvarine P, Nairn CJ, Schmutz J, Grimwood J, Dean JFD, Peterson DG.

Gene. 2018 Jul 15;663:165-177. doi: 10.1016/j.gene.2018.04.024. Epub 2018 Apr 12.

9.

Insights into the loblolly pine genome: characterization of BAC and fosmid sequences.

Wegrzyn JL, Lin BY, Zieve JJ, Dougherty WM, Martínez-García PJ, Koriabine M, Holtz-Morris A, deJong P, Crepeau M, Langley CH, Puiu D, Salzberg SL, Neale DB, Stevens KA.

PLoS One. 2013 Sep 4;8(9):e72439. doi: 10.1371/journal.pone.0072439. eCollection 2013.

10.

Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine.

Magbanua ZV, Ozkan S, Bartlett BD, Chouvarine P, Saski CA, Liston A, Cronn RC, Nelson CD, Peterson DG.

PLoS One. 2011 Jan 21;6(1):e16214. doi: 10.1371/journal.pone.0016214.

11.

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences.

Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB.

BMC Genomics. 2010 Jul 7;11:420. doi: 10.1186/1471-2164-11-420.

12.

Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.).

Lu M, Krutovsky KV, Nelson CD, Koralewski TE, Byram TD, Loopstra CA.

BMC Genomics. 2016 Sep 13;17(1):730. doi: 10.1186/s12864-016-3081-8. Erratum in: BMC Genomics. 2016 Nov 4;17 (1):869.

13.

From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana).

Crepeau MW, Langley CH, Stevens KA.

G3 (Bethesda). 2017 May 5;7(5):1563-1568. doi: 10.1534/g3.117.040055.

14.

Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species.

Asaf S, Khan AL, Khan MA, Shahzad R, Lubna, Kang SM, Al-Harrasi A, Al-Rawahi A, Lee IJ.

PLoS One. 2018 Mar 29;13(3):e0192966. doi: 10.1371/journal.pone.0192966. eCollection 2018.

15.

Genetic mapping of Pinus flexilis major gene (Cr4) for resistance to white pine blister rust using transcriptome-based SNP genotyping.

Liu JJ, Schoettle AW, Sniezko RA, Sturrock RN, Zamany A, Williams H, Ha A, Chan D, Danchok B, Savin DP, Kegley A.

BMC Genomics. 2016 Sep 23;17(1):753.

16.

Insights into conifer giga-genomes.

De La Torre AR, Birol I, Bousquet J, Ingvarsson PK, Jansson S, Jones SJ, Keeling CI, MacKay J, Nilsson O, Ritland K, Street N, Yanchuk A, Zerbe P, Bohlmann J.

Plant Physiol. 2014 Dec;166(4):1724-32. doi: 10.1104/pp.114.248708. Epub 2014 Oct 27. Review.

17.

Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Oct 1;6(10):1. doi: 10.1093/gigascience/gix072.

18.

ACC oxidase genes expressed in the wood-forming tissues of loblolly pine (Pinus taeda L.) include a pair of nearly identical paralogs (NIPs).

Yuan S, Wang Y, Dean JF.

Gene. 2010 Mar 15;453(1-2):24-36. doi: 10.1016/j.gene.2009.12.008. Epub 2010 Jan 4.

PMID:
20053371
19.

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine.

Chancerel E, Lepoittevin C, Le Provost G, Lin YC, Jaramillo-Correa JP, Eckert AJ, Wegrzyn JL, Zelenika D, Boland A, Frigerio JM, Chaumeil P, Garnier-Géré P, Boury C, Grivet D, González-Martínez SC, Rouzé P, Van de Peer Y, Neale DB, Cervera MT, Kremer A, Plomion C.

BMC Genomics. 2011 Jul 18;12:368. doi: 10.1186/1471-2164-12-368.

20.

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome.

Visser EA, Wegrzyn JL, Steenkmap ET, Myburg AA, Naidoo S.

BMC Genomics. 2015 Dec 12;16:1057. doi: 10.1186/s12864-015-2277-7.

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