title: Transcriptome analysis of tube foot and large scale marker discovery in sea cucumber, Apostichopus japonicus.
abstract: Tube foot as one of the ambulacral appendages types in Aspidochirote holothurioids, is known for their functions in locomotion, feeding, chemoreception, light sensitivity and respiration. In this study, we explored the characteristic of transcriptome in the tube foot of sea cucumber (Apostichopus japonicus). Our results showed that among 390 unigenes which specifically expressed in the tube foot, 190 of them were annotated. Based on the assembly transcriptome, we found 219,860 SNPs from 34,749 unigenes, 97,683, 53,624, 27,767 and 40,786 were located in CDSs, 5'-UTRs, 3'-UTRs and non-CDS separately. Furthermore, 12,114 SSRs were detected from 7394 unigenes. Target genes of four specifically expressed miRNAs (miR-29a, miR-29b, miR-278-3p and miR-2005) in tube foot were also predicted based on the transcriptome, which contain immune-related factors (MBL, VLRA, AjC3, MyD88, CFB), skin pigmentation (MITF), candidate regeneration factor (TRP) and holothurians autolysis-related factor (CL). These results develop a relatively large number of molecular markers and transcriptome resources, and will provide a foundation for further analyses on the function and molecular mechanisms underlying A. japonicas tube foot.
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China; College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian 116023, China.
authors.forename: Xiaoxu
authors.initials: X
authors.lastname: Zhou
authors.affiliation: College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian 116023, China.
authors.forename: Hongdi
authors.initials: H
authors.lastname: Wang
authors.affiliation: College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian 116023, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Cui
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China; College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian 116023, China.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Qiu
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China; College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian 116023, China.
authors.forename: Yaqing
authors.initials: Y
authors.lastname: Chang
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China; College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian 116023, China. Electronic address: xiuliwang417@sina.com.
authors.forename: Xiuli
authors.initials: X
authors.lastname: Wang
mesh_terms: D000818:Animals; D019295:Computational Biology; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012616:Sea Cucumbers / Q000235:genetics* / Q000254:growth & development; D059467:Transcriptome / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger
keywords: Large scale molecular markers; Sea cucumber (Apostichopus japonicus); Transcriptome analysis; Tube foot; qRT-PCR