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Open Access Research article

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

Arwa Shahin1, Martijn van Kaauwen1, Danny Esselink1, Joachim W Bargsten123, Jaap M van Tuyl1, Richard GF Visser1 and Paul Arens1*

Author affiliations

1 Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, Wageningen, 6700 AJ, The Netherlands

2 Netherlands Bioinformatics Centre, Geert Grooteplein 28, Nijmegen, 6525 GA, The Netherlands

3 Applied Bioinformatics, Plant Research International, PO Box 619, Wageningen, 6700 AP, The Netherlands

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Citation and License

BMC Genomics 2012, 13:640  doi:10.1186/1471-2164-13-640

Published: 20 November 2012

Abstract

Background

Bulbous flowers such as lily and tulip (Liliaceae family) are monocot perennial herbs that are economically very important ornamental plants worldwide. However, there are hardly any genetic studies performed and genomic resources are lacking. To build genomic resources and develop tools to speed up the breeding in both crops, next generation sequencing was implemented. We sequenced and assembled transcriptomes of four lily and five tulip genotypes using 454 pyro-sequencing technology.

Results

Successfully, we developed the first set of 81,791 contigs with an average length of 514 bp for tulip, and enriched the very limited number of 3,329 available ESTs (Expressed Sequence Tags) for lily with 52,172 contigs with an average length of 555 bp. The contigs together with singletons covered on average 37% of lily and 39% of tulip estimated transcriptome. Mining lily and tulip sequence data for SSRs (Simple Sequence Repeats) showed that di-nucleotide repeats were twice more abundant in UTRs (UnTranslated Regions) compared to coding regions, while tri-nucleotide repeats were equally spread over coding and UTR regions. Two sets of single nucleotide polymorphism (SNP) markers suitable for high throughput genotyping were developed. In the first set, no SNPs flanking the target SNP (50 bp on either side) were allowed. In the second set, one SNP in the flanking regions was allowed, which resulted in a 2 to 3 fold increase in SNP marker numbers compared with the first set. Orthologous groups between the two flower bulbs: lily and tulip (12,017 groups) and among the three monocot species: lily, tulip, and rice (6,900 groups) were determined using OrthoMCL. Orthologous groups were screened for common SNP markers and EST-SSRs to study synteny between lily and tulip, which resulted in 113 common SNP markers and 292 common EST-SSR. Lily and tulip contigs generated were annotated and described according to Gene Ontology terminology.

Conclusions

Two transcriptome sets were built that are valuable resources for marker development, comparative genomic studies and candidate gene approaches. Next generation sequencing of leaf transcriptome is very effective; however, deeper sequencing and using more tissues and stages is advisable for extended comparative studies.

Keywords:
Flower bulb; Next generation sequencing; Gene ontology; SNP markers; SSRs; OrthoMCL; Comparative Genomics; Monocot