De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing

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 .

De novo transcriptome assembly and analysis of Phragmites karka, an invasive halophyte, to study the mechanism of salinity stress tolerance

“…The most abundant trinucleotide repeat was CCG/CGG followed by AGG/CCT. The results reiterate the observation that these motifs are common in monocots as reported in many previous studies 48 .…”

“…Therefore, the findings in our study are in agreement with previous reports. In addition, SSR markers are a valuable source of genomic variation and many transcriptomes have been screened to identify them in important plant species, including chinese hawthorn 45 Glycyrrhiza 46 , coriander 47 and Curcuma alismatifolia 48 In this study, about 31% of the P. karka unigenes contained SSR loci. Trinucleotide repeats were found to be most abundant, which is in keeping with a number of previous reports in monocots 49 .…”

Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

“…The application of EST-SSR markers for genetic diversity, phylogenetic analyses, the construction of genetic maps, and the marker-assisted selection of important traits has recently been reported for several plant species (Dutta et al, 2011;Jo et al, 2015;Huang et al, 2016;Vatanparast et al, 2016;Taheri et al, 2019). At present, the transcriptome sequencing technology (RNA-Seq) is a rapid, reliable, and cost-effective tool for the characterization of gene content, and the identification of polymorphic markers in non-model plants (Taheri et al, 2019;Zhang et al, 2019). An increasing number of successful examples have supported the FIGURE 2 | Dendrogram of Opisthopappus populations, generated using UPGMA (A) and NJ (B) cluster analysis.…”

“…strategy of using transcriptome data to predict SSR molecular markers (Zalapa et al, 2012;Han et al, 2018;Taheri et al, 2019). For our work, among 33,974 assembled unigene sequences, 2644 potential EST-SSRs were identified, which represented ∼7.78% of the transcriptomic sequences ( Supplementary Table S2), and the distribution density was one SSR per 10.30 kb.…”

De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

“…Transcriptome sequencing/analysis is very effective tool for gene identi cation [53][54][55][56] and to identify gene expression at different developmental stages or physiological conditions of a cell [47]. Illumina HiSeq™ 4000 technology is effective, timeless, affordable, trusty tool for transcriptome description and gene detection in non-model plants as well.…”