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Author Hu, Li ♦ Zhao, YaE ♦ Yang, YuanJun ♦ Niu, DongLing ♦ Wang, RuiLing ♦ Cheng, Juan ♦ Yang, Fan
Source SpringerLink
Content type Text
Publisher Springer Berlin Heidelberg
File Format PDF
Copyright Year ©2016
Language English
Subject Domain (in DDC) Technology ♦ Medicine & health
Subject Keyword Sarcoptes scabiei canis ♦ RNA extraction ♦ RNA-Seq ♦ Functional prediction ♦ CD verification ♦ Medical Microbiology ♦ Microbiology ♦ Immunology
Abstract The transcriptomic data of Sarcoptes is still lacking in the public database due to the difficulty in extracting high-quality RNA from tiny mites with thick chitin. In this study, total RNA was extracted from live Sarcoptes mites for quality assessment, RNA-Seq, functional annotation, and coding region (CD) prediction and verification. The results showed that the sample JMQ-lngm was qualified for cDNA library construction. Firstly, Agilent 2100 detection showed that the RNA baseline was smooth and the 18S peak was single. Second, the Illumina platform generated 65.78M clean reads and 20,826 unigenes with 35.43M were assembled, occupying 62.98 % of the 56.26M genome. In total, 15,034 unigenes were annotated in seven functional databases. Finally, 13,122 CDs were detected in the 20,826 unigenes, of which 70 complete CDs were matched with Sarcoptes manually in non-redundant nucleotide (NT). Three CDs with indels ≥10 bp were verified. Those results indicated that peritrophin sequences of JMQ-lngm missed 35 bp during the assembly; the pressure-sensitive sodium channel sequences of all the six Sarcoptes scabiei canis isolates were confirmed to be 90 bp shorter than that of a Sarcoptes scabiei hominis isolate; three introns remained in PH chlorine ion channel gating sequences of JMQ-lngm. Moreover, the allergen gene prediction for JMQ-lngm indicated that 61 unigenes were matched with 19 allergen genes of Dermatophagoides, of which Der 1, Der 3, Der 8, and Der 10 had been confirmed in NT. In conclusion, this study successfully completed the RNA-Seq and functional annotation of S. s. canis for the first time, which provides molecular data for future studies on the identification and pathogenic genes of Sarcoptidae.
ISSN 09320113
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 2016-03-21
Publisher Place Berlin/Heidelberg
e-ISSN 14321955
Journal Parasitology Research
Volume Number 115
Issue Number 7
Page Count 10
Starting Page 2661
Ending Page 2670

Source: SpringerLink