کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
8388036 | 1543913 | 2018 | 6 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
De novo transcriptome assembly of the calanoid copepod Neocalanus flemingeri: A new resource for emergence from diapause
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موضوعات مرتبط
مهندسی و علوم پایه
علوم زمین و سیارات
علوم زمین و سیاره ای (عمومی)
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چکیده انگلیسی
Copepods, small planktonic crustaceans, are key links between primary producers and upper trophic levels, including many economically important fishes. In the subarctic North Pacific, the life cycle of copepods like Neocalanus flemingeri includes an ontogenetic migration to depth followed by a period of diapause (a type of dormancy) characterized by arrested development and low metabolic activity. The end of diapause is marked by the production of the first brood of eggs. Recent temperature anomalies in the North Pacific have raised concerns about potential negative effects on N. flemingeri. Since diapause is a developmental program, its progress can be tracked using through global gene expression. Thus, a reference transcriptome was developed as a first step towards physiological profiling of diapausing females using high-throughput Illumina sequencing. The de novo transcriptome, the first for this species was designed to investigate the diapause period. RNA-Seq reads were obtained for dormant to reproductive N. flemingeri females. A high quality de novo transcriptome was obtained by first assembling reads from each individual using Trinity software followed by clustering with CAP3 Assembly Program. This assembly consisted of 140,841transcripts (contigs). Bench-marking universal single-copy orthologs analysis identified 85% of core eukaryotic genes, with 79% predicted to be complete. Comparison with other calanoid transcriptomes confirmed its quality and degree of completeness. Trinity assembly of reads originating from multiple individuals led to fragmentation. Thus, the workflow applied here differed from the one recommended by Trinity, but was required to obtain a good assembly.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Marine Genomics - Volume 37, February 2018, Pages 114-119
Journal: Marine Genomics - Volume 37, February 2018, Pages 114-119
نویسندگان
Vittoria Roncalli, Matthew C. Cieslak, Stephanie A. Sommer, Russell R. Hopcroft, Petra H. Lenz,