Sequencing and analysis of the transcriptome of the acorn worm Ptychodera flava, an indirect developing hemichordate.
Hemichordates are the sister group of echinoderms, and together they are closely related to chordates within the deuterostome lineage. Therefore, hemichordates represent an important animal group for the understanding of both the evolution of developmental mechanisms in deuterostome animals and the origin of chordates. Recently, the majority of studies investigating hemichordates have focused on the direct-developing enteropneust hemichordate Saccoglossus kowalevskii; few have focused on the indirect-developing hemichordates, partly because of the lack of extensive genomic resources in these animals. In this study, we report the sequencing and analysis of a transcriptome from an indirect-developing enteropneust hemichordate Ptychodera flava. We sequenced a mixed cDNA library from six developmental stages using the Roche GS FLX Titanium System to generate more than 879,000 reads. These reads were assembled into 17,990 contigs with an average length of 1316bp. We found that 60% of the assembled contigs, along with 28% of the unassembled singleton reads, had significant hits to sequences in the NCBI database by a BLASTx search, and we also annotated these sequences and obtained Gene Ontology (GO) terms for 6744 contigs and 5802 singletons. We further identified candidate P. flava transcripts corresponding to genes involved in major developmental signaling pathways, including the Wnt, Notch and TGF-β signaling pathways. Using available genome/transcriptome datasets from the direct-developing hemichordate S. kowalevskii, the echinoderm Strongylocentrotus purpuratus and the chordate Branchiostoma floridae, we found that 90%, 80% and 73% of the annotated protein sequences in these respective species matched our P. flava transcriptome in a homology search. We also constructed a database for the P. flava transcriptome, and researchers can easily access this dataset online. Our dataset significantly increases the amount of available P. flava sequence data and can serve as a reference transcriptome for future studies using this species.
Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan.
Shu-Hwa
SH
Chen
Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan.
Kun-Lin
KL
Li
Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan.
I-Hsuan
IH
Lu
Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan.
Yu-Bin
YB
Wang
Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan.
Che-Huang
CH
Tung
Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan.
Hsiu-Chi
HC
Ting
Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
Ching-Yi
CY
Lin
Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan; Institute of Population Health Sciences, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan. Electronic address: yamatolin@gmail.com.
Chung-Yen
CY
Lin
Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan. Electronic address: yhsu@gate.sinica.edu.tw.
Yi-Hsien
YH
Su
Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Oceanography, National Taiwan University, Taipei, Taiwan. Electronic address: jkyu@gate.sinica.edu.tw.
Jr-Kai
JK
Yu
D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D019295:Computational Biology; D018076:DNA, Complementary / Q000235:genetics; D063990:Gene Ontology; D007448:Invertebrates / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*
D018076:DNA, Complementary
Development; Evolution; Hemichordate; Next generation sequencing; Signaling pathway; Transcriptome