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Items: 20

1.

Association mapping of ectomycorrhizal traits in loblolly pine (Pinus taeda L.).

Piculell BJ, Martínez-García PJ, Nelson CD, Hoeksema JD.

Mol Ecol. 2019 Jan 11. doi: 10.1111/mec.15013. [Epub ahead of print]

PMID:
30632641
2.

A new genomic tool for walnut (Juglans regia L.): development and validation of the high-density Axiom™ J. regia 700K SNP genotyping array.

Marrano A, Martínez-García PJ, Bianco L, Sideli GM, Di Pierro EA, Leslie CA, Stevens KA, Crepeau MW, Troggio M, Langley CH, Neale DB.

Plant Biotechnol J. 2018 Nov 22. doi: 10.1111/pbi.13034. [Epub ahead of print]

3.

DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing.

Prudencio ÁS, Werner O, Martínez-García PJ, Dicenta F, Ros RM, Martínez-Gómez P.

Int J Mol Sci. 2018 Nov 10;19(11). pii: E3542. doi: 10.3390/ijms19113542.

4.

Genomic Variation Among and Within Six Juglans Species.

Stevens KA, Woeste K, Chakraborty S, Crepeau MW, Leslie CA, Martínez-García PJ, Puiu D, Romero-Severson J, Coggeshall M, Dandekar AM, Kluepfel D, Neale DB, Salzberg SL, Langley CH.

G3 (Bethesda). 2018 Jul 2;8(7):2153-2165. doi: 10.1534/g3.118.200030.

5.

Novel Insights into Tree Biology and Genome Evolution as Revealed Through Genomics.

Neale DB, Martínez-García PJ, De La Torre AR, Montanari S, Wei XX.

Annu Rev Plant Biol. 2017 Apr 28;68:457-483. doi: 10.1146/annurev-arplant-042916-041049. Epub 2017 Feb 6. Review.

PMID:
28226237
6.

YeATSAM analysis of the walnut and chickpea transcriptome reveals key genes undetected by current annotation tools.

Chakraborty S, Martínez-García PJ, Dandekar AM.

F1000Res. 2016 Nov 17;5:2689. doi: 10.12688/f1000research.10040.1. eCollection 2016.

7.

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).

Gonzalez-Ibeas D, Martinez-Garcia PJ, Famula RA, Delfino-Mix A, Stevens KA, Loopstra CA, Langley CH, Neale DB, Wegrzyn JL.

G3 (Bethesda). 2016 Dec 7;6(12):3787-3802. doi: 10.1534/g3.116.032805.

8.

Sequence of the Sugar Pine Megagenome.

Stevens KA, Wegrzyn JL, Zimin A, Puiu D, Crepeau M, Cardeno C, Paul R, Gonzalez-Ibeas D, Koriabine M, Holtz-Morris AE, Martínez-García PJ, Sezen UU, Marçais G, Jermstad K, McGuire PE, Loopstra CA, Davis JM, Eckert A, de Jong P, Yorke JA, Salzberg SL, Neale DB, Langley CH.

Genetics. 2016 Dec;204(4):1613-1626. Epub 2016 Oct 28.

9.

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols.

Martínez-García PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT, Reagan RL, Chakraborty S, Walawage SL, Vasquez-Gross HA, Cardeno C, Famula RA, Pratt K, Kuruganti S, Aradhya MK, Leslie CA, Dandekar AM, Salzberg SL, Wegrzyn JL, Langley CH, Neale DB.

Plant J. 2016 Sep;87(5):507-32. doi: 10.1111/tpj.13207. Epub 2016 Jul 18.

10.

Deep RNA-Seq profile reveals biodiversity, plant-microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues.

Chakraborty S, Britton M, Martínez-García PJ, Dandekar AM.

AMB Express. 2016 Mar;6(1):12. doi: 10.1186/s13568-016-0182-3. Epub 2016 Feb 17.

11.

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut.

Chakraborty S, Britton M, Wegrzyn J, Butterfield T, Martínez-García PJ, Reagan RL, Rao BJ, Leslie CA, Aradhaya M, Neale D, Woeste K, Dandekar AM.

Version 2. F1000Res. 2015 Jun 17 [revised 2015 Jan 1];4:155. doi: 10.12688/f1000research.6617.2. eCollection 2015.

12.

A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda.

Westbrook JW, Chhatre VE, Wu LS, Chamala S, Neves LG, Muñoz P, Martínez-García PJ, Neale DB, Kirst M, Mockaitis K, Nelson CD, Peter GF, Davis JM, Echt CS.

G3 (Bethesda). 2015 Jun 11;5(8):1685-94. doi: 10.1534/g3.115.019588.

13.

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.

14.

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.

15.

Application of genomic and quantitative genetic tools to identify candidate resistance genes for brown rot resistance in peach.

Martínez-García PJ, Parfitt DE, Bostock RM, Fresnedo-Ramírez J, Vazquez-Lobo A, Ogundiwin EA, Gradziel TM, Crisosto CH.

PLoS One. 2013 Nov 11;8(11):e78634. doi: 10.1371/journal.pone.0078634. eCollection 2013.

16.

Heterogeneity in the entire genome for three genotypes of peach [Prunus persica (L.) Batsch] as distinguished from sequence analysis of genomic variants.

Fresnedo-Ramírez J, Martínez-García PJ, Parfitt DE, Crisosto CH, Gradziel TM.

BMC Genomics. 2013 Nov 1;14:750. doi: 10.1186/1471-2164-14-750.

17.

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.

18.

Effect prediction of identified SNPs linked to fruit quality and chilling injury in peach [Prunus persica (L.) Batsch].

Martínez-García PJ, Fresnedo-Ramírez J, Parfitt DE, Gradziel TM, Crisosto CH.

Plant Mol Biol. 2013 Jan;81(1-2):161-74. doi: 10.1007/s11103-012-9989-8. Epub 2012 Nov 25.

PMID:
23184287
19.

Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection.

Ahmad R, Parfitt DE, Fass J, Ogundiwin E, Dhingra A, Gradziel TM, Lin D, Joshi NA, Martinez-Garcia PJ, Crisosto CH.

BMC Genomics. 2011 Nov 22;12:569. doi: 10.1186/1471-2164-12-569.

20.

Disruption of endosperm development: an inbreeding effect in almond (Prunus dulcis).

Ortega E, Martínez-García PJ, Dicenta F, Egea J.

Sex Plant Reprod. 2010 Jun;23(2):135-40. doi: 10.1007/s00497-009-0117-0. Epub 2009 Oct 21.

PMID:
20490966

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