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De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing.
Sci Rep. 2019 02 28; 9(1):3047.SR

Abstract

Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, 'Chiang Mai Pink' and 'UB Snow 701', to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma.

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Authors+Show Affiliations

Taheri S
Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia. sima_taheri65@yahoo.com. Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia. sima_taheri65@yahoo.com.
Abdullah TL
Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia. thohirah@upm.edu.my.
Rafii MY
Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia. Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
Harikrishna JA
Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia. Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia.
Werbrouck SPO
Laboratory of Applied Science In Vitro Plant Biotechnology, Department of Plants and Crops, Faculty of Bioscience Engineering, University Ghent, Valentin Vaerwyckweg 1, BE-9000, Gent, Belgium.
Teo CH
Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia.
Sahebi M
Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
Azizi P
Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.

MeSH

CambodiaCurcumaDNA, PlantExpressed Sequence TagsFlowersGenes, PlantGenetic MarkersGingerHigh-Throughput Nucleotide SequencingMicrosatellite RepeatsMolecular Sequence AnnotationPlant BreedingRNA, PlantRNA-SeqThailandTranscriptome

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30816255

Citation

Taheri, Sima, et al. "De Novo Assembly of Transcriptomes, Mining, and Development of Novel EST-SSR Markers in Curcuma Alismatifolia (Zingiberaceae Family) Through Illumina Sequencing." Scientific Reports, vol. 9, no. 1, 2019, p. 3047.
Taheri S, Abdullah TL, Rafii MY, et al. De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing. Sci Rep. 2019;9(1):3047.
Taheri, S., Abdullah, T. L., Rafii, M. Y., Harikrishna, J. A., Werbrouck, S. P. O., Teo, C. H., Sahebi, M., & Azizi, P. (2019). De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing. Scientific Reports, 9(1), 3047. https://doi.org/10.1038/s41598-019-39944-2
Taheri S, et al. De Novo Assembly of Transcriptomes, Mining, and Development of Novel EST-SSR Markers in Curcuma Alismatifolia (Zingiberaceae Family) Through Illumina Sequencing. Sci Rep. 2019 02 28;9(1):3047. PubMed PMID: 30816255.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing. AU - Taheri,Sima, AU - Abdullah,Thohirah Lee, AU - Rafii,M Y, AU - Harikrishna,Jennifer Ann, AU - Werbrouck,Stefaan P O, AU - Teo,Chee How, AU - Sahebi,Mahbod, AU - Azizi,Parisa, Y1 - 2019/02/28/ PY - 2018/05/21/received PY - 2019/02/06/accepted PY - 2019/3/1/entrez PY - 2019/3/1/pubmed PY - 2020/9/22/medline SP - 3047 EP - 3047 JF - Scientific reports JO - Sci Rep VL - 9 IS - 1 N2 - Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, 'Chiang Mai Pink' and 'UB Snow 701', to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/30816255/De_novo_assembly_of_transcriptomes_mining_and_development_of_novel_EST_SSR_markers_in_Curcuma_alismatifolia__Zingiberaceae_family__through_Illumina_sequencing_ DB - PRIME DP - Unbound Medicine ER -