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De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes.

Ashrafi H, Hill T, Stoffel K, Kozik A, Yao J, Chin-Wo SR, Van Deynze A.

BMC Genomics. 2012 Oct 30;13:571. doi: 10.1186/1471-2164-13-571.


Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum).

Nicolaï M, Pisani C, Bouchet JP, Vuylsteke M, Palloix A.

Genet Mol Res. 2012 Aug 13;11(3):2295-300. doi: 10.4238/2012.August.13.3.


Transcriptome analysis of Capsicum annuum varieties Mandarin and Blackcluster: assembly, annotation and molecular marker discovery.

Ahn YK, Tripathi S, Kim JH, Cho YI, Lee HE, Kim DS, Woo JG, Cho MC.

Gene. 2014 Jan 10;533(2):494-9. doi: 10.1016/j.gene.2013.09.095.


The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.).

Raju NL, Gnanesh BN, Lekha P, Jayashree B, Pande S, Hiremath PJ, Byregowda M, Singh NK, Varshney RK.

BMC Plant Biol. 2010 Mar 11;10:45. doi: 10.1186/1471-2229-10-45.


Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68.

Lu FH, Cho MC, Park YJ.

Mol Biol Rep. 2012 Mar;39(3):3327-35. doi: 10.1007/s11033-011-1102-x.


De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity.

Iorizzo M, Senalik DA, Grzebelus D, Bowman M, Cavagnaro PF, Matvienko M, Ashrafi H, Van Deynze A, Simon PW.

BMC Genomics. 2011 Aug 2;12:389. doi: 10.1186/1471-2164-12-389.


SNP discovery by illumina-based transcriptome sequencing of the olive and the genetic characterization of Turkish olive genotypes revealed by AFLP, SSR and SNP markers.

Kaya HB, Cetin O, Kaya H, Sahin M, Sefer F, Kahraman A, Tanyolac B.

PLoS One. 2013 Sep 13;8(9):e73674. doi: 10.1371/journal.pone.0073674.


De novo assembly of transcriptome sequencing in Caragana korshinskii Kom. and characterization of EST-SSR markers.

Long Y, Wang Y, Wu S, Wang J, Tian X, Pei X.

PLoS One. 2015 Jan 28;10(1):e0115805. doi: 10.1371/journal.pone.0115805.


Identification and development of polymorphic EST-SSR markers by sequence alignment in pepper, Capsicum annuum (Solanaceae).

Kong Q, Zhang G, Chen W, Zhang Z, Zou X.

Am J Bot. 2012 Feb;99(2):e59-61. doi: 10.3732/ajb.1100347.


Exploitation of pepper EST-SSRs and an SSR-based linkage map.

Yi G, Lee JM, Lee S, Choi D, Kim BD.

Theor Appl Genet. 2006 Dec;114(1):113-30.


De novo transcriptome assembly in chili pepper (Capsicum frutescens) to identify genes involved in the biosynthesis of capsaicinoids.

Liu S, Li W, Wu Y, Chen C, Lei J.

PLoS One. 2013;8(1):e48156. doi: 10.1371/journal.pone.0048156.


Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa.

Shahin A, van Kaauwen M, Esselink D, Bargsten JW, van Tuyl JM, Visser RG, Arens P.

BMC Genomics. 2012 Nov 20;13:640. doi: 10.1186/1471-2164-13-640.


Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies.

Varshney RK, Kudapa H, Roorkiwal M, Thudi M, Pandey MK, Saxena RK, Chamarthi SK, Mohan SM, Mallikarjuna N, Upadhyaya H, Gaur PM, Krishnamurthy L, Saxena KB, Nigam SN, Pande S.

J Biosci. 2012 Nov;37(5):811-20. Review.


A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica.

Ueno S, Moriguchi Y, Uchiyama K, Ujino-Ihara T, Futamura N, Sakurai T, Shinohara K, Tsumura Y.

BMC Genomics. 2012 Apr 16;13:136. doi: 10.1186/1471-2164-13-136.


Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.

Hill TA, Ashrafi H, Reyes-Chin-Wo S, Yao J, Stoffel K, Truco MJ, Kozik A, Michelmore RW, Van Deynze A.

PLoS One. 2013;8(2):e56200. doi: 10.1371/journal.pone.0056200.


De novo assembly, gene annotation, and marker discovery in stored-product pest Liposcelis entomophila (Enderlein) using transcriptome sequences.

Wei DD, Chen EH, Ding TB, Chen SC, Dou W, Wang JJ.

PLoS One. 2013 Nov 14;8(11):e80046. doi: 10.1371/journal.pone.0080046.


Large scale in-silico identification and characterization of simple sequence repeats (SSRs) from de novo assembled transcriptome of Catharanthus roseus (L.) G. Don.

Kumar S, Shah N, Garg V, Bhatia S.

Plant Cell Rep. 2014 Jun;33(6):905-18. doi: 10.1007/s00299-014-1569-8.


Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae) transcriptome permits large-scale unigene assembly and SSR marker discovery.

Wang H, Jiang J, Chen S, Qi X, Peng H, Li P, Song A, Guan Z, Fang W, Liao Y, Chen F.

PLoS One. 2013 Apr 23;8(4):e62293. doi: 10.1371/journal.pone.0062293.


Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.

Kudapa H, Azam S, Sharpe AG, Taran B, Li R, Deonovic B, Cameron C, Farmer AD, Cannon SB, Varshney RK.

PLoS One. 2014 Jan 23;9(1):e86039. doi: 10.1371/journal.pone.0086039.

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