Sequencing and de novo assembly of a Dahlia hybrid cultivar transcriptome
نویسندگان
چکیده
Dahlia variabilis, with an exceptionally high diversity of floral forms and colors, is a popular flower amongst both commercial growers and hobbyists. Recently, some genetic controls of pigment patterns have been elucidated. These studies have been limited, however, by the lack of comprehensive transcriptomic resources for this species. Here we report the sequencing, assembly, and annotation of the transcriptome of the developing leaves, stems, and floral buds of D. variabilis. This resulted in 35,638 contigs, most of which seem to contain the complete coding sequence, and of which 20,881 could be successfully annotated by similarity to UniProt. Furthermore, we conducted a preliminary investigation to identify contigs with expression patterns consistent with tissue-specificity. These results will accelerate research into the genetic controls of pigmentation and floral form of D. variabilis.
منابع مشابه
Clustering of Short Read Sequences for de novo Transcriptome Assembly
Given the importance of transcriptome analysis in various biological studies and considering thevast amount of whole transcriptome sequencing data, it seems necessary to develop analgorithm to assemble transcriptome data. In this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. First, the contiguous sequencesare generated using de Bruijn graph with d...
متن کاملDe novo transcriptome assembly of a sour cherry cultivar, Schattenmorelle
Sour cherry (Prunus cerasus) in the genus Prunus in the family Rosaceae is one of the most popular stone fruit trees worldwide. Of known sour cherry cultivars, the Schattenmorelle is a famous old sour cherry with a high amount of fruit production. The Schattenmorelle was selected before 1650 and described in the 1800s. This cultivar was named after gardens of the Chateau de Moreille in which th...
متن کاملComparisons of De Novo Transcriptome Assemblers in Diploid and Polyploid Species Using Peanut (Arachis spp.) RNA-Seq Data
The narrow genetic base and limited genetic information on Arachis species have hindered the process of marker-assisted selection of peanut cultivars. However, recent developments in sequencing technologies have expanded opportunities to exploit genetic resources, and at lower cost. To use the genetic information for Arachis species available at the transcriptome level, it is important to have ...
متن کاملDe Novo transcriptome assembly of Zingiber officinale cv. Suruchi of Odisha
Zingiber officinale Rosc., known as ginger, is an Asian crop, popularly used in every household kitchen and commercially used in bakery, beverage, food and pharmaceutical industries. The present study deals with de novo transcriptome assembly of an elite ginger cultivar Suruchi by next generation sequencing methodology. From the analysis 10.9 GB raw data was obtained which can be available in N...
متن کاملSimultaneous Transcriptome Analysis of Sorghum and Bipolaris sorghicola by Using RNA-seq in Combination with De Novo Transcriptome Assembly
The recent development of RNA sequencing (RNA-seq) technology has enabled us to analyze the transcriptomes of plants and their pathogens simultaneously. However, RNA-seq often relies on aligning reads to a reference genome and is thus unsuitable for analyzing most plant pathogens, as their genomes have not been fully sequenced. Here, we analyzed the transcriptomes of Sorghum bicolor (L.) Moench...
متن کامل