| No. | Title | Authors | Journal |
|---|---|---|---|
| 64 | The developmental transcriptome atlas of the spoon worm Urechis unicinctus (Echiurida: Annelida) | 36. C. Park, YH. Han, SG. Lee, KB. Ryu, J. Oh, E. M. A. Kern, JK. Park, SJ. Cho | GigaScience. (2018) 7(3): 1-7 |
Abstract
Background
Echiurida is one of the most intriguing major subgroups of annelida, because unlike most other annelids, echiurids lack metameric body segmentation as adults. For this reason, transcriptome analyses from various developmental stages of echiurid species can be of substantial value for understanding precise expression levels and the complex regulatory networks during early and larval development.
Findings
A total of 914 million raw RNA-Seq reads were produced from 14 developmental stages of Urechis unicinctus, and were de novo assembled into contigs spanning 63,928,225 bp with an N50 length of 2,700 bp. The resulting comprehensive transcriptome database of the early developmental stages of U. unicinctus consists of 20,305 representative functional protein-coding transcripts. Approximately 66\% of unigenes were assigned to superphylum-level taxa, including Lophotrochozoa (40\%). The completeness of the transcriptome assembly was assessed using BUSCO and 75.7\% of the metazoan single-copy orthologs were presented in our transcriptome database. We observed three distinct patterns of global transcriptome profiles from 14 developmental stages and identified a total of 12,705 genes that showed dynamic regulation patterns during the differentiation and maturation of U. unicinctus cells.
Conclusions
We present the first large-scale developmental transcriptome dataset of U. unicinctus and provide a general overview of the dynamics of global gene expression changes during its early developmental stages. The analysis of time-course gene expression data is a first step toward understanding the complex developmental gene regulatory networks in U. unicinctus and will furnish a valuable resource for analyzing the functions of gene repertoires in various developmental phases.
Background
Echiurida is one of the most intriguing major subgroups of annelida, because unlike most other annelids, echiurids lack metameric body segmentation as adults. For this reason, transcriptome analyses from various developmental stages of echiurid species can be of substantial value for understanding precise expression levels and the complex regulatory networks during early and larval development.
Findings
A total of 914 million raw RNA-Seq reads were produced from 14 developmental stages of Urechis unicinctus, and were de novo assembled into contigs spanning 63,928,225 bp with an N50 length of 2,700 bp. The resulting comprehensive transcriptome database of the early developmental stages of U. unicinctus consists of 20,305 representative functional protein-coding transcripts. Approximately 66\% of unigenes were assigned to superphylum-level taxa, including Lophotrochozoa (40\%). The completeness of the transcriptome assembly was assessed using BUSCO and 75.7\% of the metazoan single-copy orthologs were presented in our transcriptome database. We observed three distinct patterns of global transcriptome profiles from 14 developmental stages and identified a total of 12,705 genes that showed dynamic regulation patterns during the differentiation and maturation of U. unicinctus cells.
Conclusions
We present the first large-scale developmental transcriptome dataset of U. unicinctus and provide a general overview of the dynamics of global gene expression changes during its early developmental stages. The analysis of time-course gene expression data is a first step toward understanding the complex developmental gene regulatory networks in U. unicinctus and will furnish a valuable resource for analyzing the functions of gene repertoires in various developmental phases.