Bichir microRNA repertoire suggests a ray-finned fish affinity of Polypteriforme

Yang, Liandong; Zhang, Zhaolei; He, Shunping

doi:10.1016/j.gene.2015.04.058

Cited by 4 publications

(3 citation statements)

References 45 publications

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“…The miRNA showed higher level of conservation than protein-coding sequence, which had been confirmed by previous studies [ 20 , 31 , 40 , 42 ]. There are two important implications in this study.…”

Section: Discussionsupporting

confidence: 83%

The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau

et al. 2017

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Tibetan naked carp Gymnocypris przewalskii is an ideal model system to study highland adaptation of fish, because it evolved specific genetic and phenotypic characteristics to adapt to chronic cold and alkaline environments in Lake Qinghai. MicroRNAs (miRNAs) are small noncoding RNAs that regulating gene expression post-transcriptionally in a wide range of biological processes. In this study, we focus on the role of miRNAs in adaptation of G. przewalskii to extreme conditions in Lake Qinghai. We generate the first miRNAome of G. przewalskii in Schizothoracinae fish. Using several genomic resources, we inferred 341 conserved miRNAs belonged to 152 miRNA families and 43 novel miRNAs in G. przewalskii, and also identified 15 teleost-specific miRNAs. Using a large scale of conserved miRNAs, we constructed a high-confidence phylogenetic tree between teleost and mammals than mitochondria and nuclear genes. In addition, we found that several miRNA family (e.g. miR-10 and let-7) members highly expressed in G. przewalskii, which may function in multiple biological processes. Finally, we predicted a total of 34,258 miRNA targets genes. Conserved miRNAs target genes participating in signal transduction, cell differentiation and biosynthetic process, and showed signature of functional constraint. While novel miRNAs in a species displayed species-specific targets and involved in ion binding, transport and oxidoreductase activity, may affect the expression patterns of targets with signature of gene family expansion or positive selection under extreme environment. Taken together, this study demonstrated that miRNAs may involve into roles of adaptation of G. przewalskii to highland aquatic environment, and also provide insights into miRNA regulatory network in Schizothoracinae fish as a case study.

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Section: Discussionsupporting

confidence: 83%

The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau

et al. 2017

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“…Any miRNA that met the sequence homology criteria of Yang et al [35] and Jain et al [36] was considered a conserved miRNA gene. Through this analysis, we identified a total of 151 conserved miRNAs which belonging to 47 miRNA families in both camellia species (Additional file 1: Table S6).…”

Section: Resultsmentioning

confidence: 99%

“…All mature sequences, star sequences and precursor sequences cored by miRDeep2 were retained and regarded as putative miRNAs and used for further analysis to identify known and novel miRNAs [33, 34]. Known miRNAs were annotated by identifying their homologous imRNAs in miRBase database (http://www.mirbase.org/) using the following criteria: 1) seed region, nucleotides 2–7 must be identical; and 2) the remainder of the sequence alignment must contain no more than two mismatches [35, 36]. The putative miRNAs produced by miRDeep2 analysis were regarded as conservative miRNAs when it met the above criteria.…”

Section: Methodsmentioning

confidence: 99%

High throughput sequencing of small RNAs reveals dynamic microRNAs expression of lipid metabolism during Camellia oleifera and C. meiocarpa seed natural drying

et al. 2017

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BackgroundCamellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and quantity. MicroRNAs (miRNA) of lipid metabolism associated with camellia seed natural drying are unexplored. To obtain insight into the function of miRNAs in lipid metabolism during natural drying, Illumina sequencing of C. oleifera and C. meiocarpa small-RNA was conducted.ResultsA total of 274 candidate miRNAs were identified and 3733 target unigenes were annotated by performing a BLASTX. Through integrated GO and KEGG function annotation, 23 miRNA regulating 131 target genes were identified as lipid metabolism, regulating fatty acid biosynthesis, accumulation and catabolism. We observed one, two, and four miRNAs of lipid metabolism which were specially expressed in C. Meiocarpa, C. oleifera, and the two species collectively, respectively. At 30% moisture contents, C. meiocarpa and C. oleifer produced nine and eight significant differentially expressed miRNAs, respectively, with high fatty acid synthesis and accumulation activities. Across the two species, 12 significant differentially expressed miRNAs were identified at the 50% moisture content.ConclusionsSequencing of small-RNA revealed the presence of 23 miRNAs regulating lipid metabolism in camellia seed during natural drying and permitted comparative miRNA profiles between C. Meiocarpa and C. oleifera. Furthermore, this study successfully identified the best drying environment at which the quantity and quality of lipid in camellia seed are at its maximum.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3923-z) contains supplementary material, which is available to authorized users.

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Identification of the conserved and novel microRNAs by deep sequencing and prediction of their targets in Topmouth culter

Huang

Gong

Ren

et al. 2017

Gene

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Bichir microRNA repertoire suggests a ray-finned fish affinity of Polypteriforme

Cited by 4 publications

References 45 publications

The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau

The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau

High throughput sequencing of small RNAs reveals dynamic microRNAs expression of lipid metabolism during Camellia oleifera and C. meiocarpa seed natural drying

Identification of the conserved and novel microRNAs by deep sequencing and prediction of their targets in Topmouth culter

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