title: Spliced leader RNA trans-splicing discovered in copepods.
abstract: Copepods are one of the most abundant metazoans in the marine ecosystem, constituting a critical link in aquatic food webs and contributing significantly to the global carbon budget, yet molecular mechanisms of their gene expression are not well understood. Here we report the detection of spliced leader (SL) trans-splicing in calanoid copepods. We have examined nine species of wild-caught copepods from Jiaozhou Bay, China that represent the major families of the calanoids. All these species contained a common 46-nt SL (CopepodSL). We further determined the size of CopepodSL precursor RNA (slRNA; 108-158 nt) through genomic analysis and 3'-RACE technique, which was confirmed by RNA blot analysis. Structure modeling showed that the copepod slRNA folded into typical slRNA secondary structures. Using a CopepodSL-based primer set, we selectively enriched and sequenced copepod full-length cDNAs, which led to the characterization of copepod transcripts and the cataloging of the complete set of 79 eukaryotic cytoplasmic ribosomal proteins (cRPs) for a single copepod species. We uncovered the SL trans-splicing in copepod natural populations, and demonstrated that CopepodSL was a sensitive and specific tool for copepod transcriptomic studies at both the individual and population levels and that it would be useful for metatranscriptomic analysis of copepods.
authors.affiliation: The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.|College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
authors.forename: Feifei
authors.initials: F
authors.lastname: Yang
authors.affiliation: The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.|College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
authors.forename: Donghui
authors.initials: D
authors.lastname: Xu
authors.affiliation: The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.|College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
authors.forename: Yunyun
authors.initials: Y
authors.lastname: Zhuang
authors.affiliation: The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.|College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Yi
authors.affiliation: The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.|College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
authors.forename: Yousong
authors.initials: Y
authors.lastname: Huang
authors.affiliation: The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.|College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
authors.forename: Hongju
authors.initials: H
authors.lastname: Chen
authors.affiliation: Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, USA.
authors.forename: Senjie
authors.initials: S
authors.lastname: Lin
authors.affiliation: Department of Microbiology, Immunology &Molecular Genetics, University of California, Los Angeles, California 90095, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Campbell
authors.affiliation: Department of Microbiology, Immunology &Molecular Genetics, University of California, Los Angeles, California 90095, USA.
authors.forename: Nancy R
authors.initials: NR
authors.lastname: Sturm
authors.affiliation: The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.|College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
authors.forename: Guangxing
authors.initials: G
authors.lastname: Liu
authors.affiliation: The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.|College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.|Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, USA.
authors.forename: Huan
authors.initials: H
authors.lastname: Zhang
mesh_terms: D000818:Animals; D033342:Copepoda / Q000235:genetics / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism*; D022821:RNA Splice Sites / Q000502:physiology*; D020040:Trans-Splicing / Q000502:physiology*
chemical_list: D012322:RNA Precursors; D022821:RNA Splice Sites