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Zhang C, Chen L, Zhou Y, Wang K, Chemnick LG, Ryder OA, Wang W, Zhang G, Qiu Q. Draft genome of the milu (Elaphurus davidianus). Gigascience 2018; 7:4757066. [PMID: 29267854 PMCID: PMC5824821 DOI: 10.1093/gigascience/gix130] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/12/2017] [Accepted: 12/15/2017] [Indexed: 11/13/2022] Open
Abstract
Background Milu, also known as Père David's deer (Elaphurus davidianus), was widely distributed in East Asia but recently experienced a severe bottleneck. Only 18 survived by the end of the 19th century, and the current population of 4500 individuals was propagated from just 11 kept by the 11th British Duke of Bedford. This species is known for its distinguishable appearance, the driving force behind which is still a mystery. To aid efforts to explore these phenomena, we constructed a draft genome of the species. Findings In total, we generated 321.86 gigabases (Gb) of raw DNA sequence from whole-genome sequencing of a male milu deer using an Illumina HiSeq 2000 platform. Assembly yielded a final genome with a scaffold N50 size of 3.03 megabases (Mb) and a total length of 2.52 Gb. Moreover, we identified 20 125 protein-coding genes and 988.1 Mb of repetitive sequences. In addition, homology-based searches detected 280 rRNA, 1335 miRNA, 1441 snRNA, and 893 tRNA sequences in the milu genome. The divergence time between E. davidianus and Bos taurus was estimated to be about 28.20 million years ago (Mya). We identified 167 species-specific genes and 293 expanded gene families in the milu lineage. Conclusions We report the first reference genome of milu, which will provide a valuable resource for studying the species' demographic history of severe bottleneck and the genetic mechanism(s) of special phenotypic evolution.
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Affiliation(s)
- Chenzhou Zhang
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, 710072, China
| | - Lei Chen
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, 710072, China
| | - Yang Zhou
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
- BGI-Shenzhen, Shenzhen 518083, China
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, 710072, China
| | - Leona G Chemnick
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, 710072, China
| | - Guojie Zhang
- China National Genebank, BGI-Shenzhen, Shenzhen 518083, China
- BGI-Shenzhen, Shenzhen 518083, China
- Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen 2100, Denmark
| | - Qiang Qiu
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi’an, 710072, China
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López MD, Alm Rosenblad M, Samuelsson T. Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components. Nucleic Acids Res 2008; 36:3001-10. [PMID: 18390578 PMCID: PMC2396436 DOI: 10.1093/nar/gkn142] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The RNA molecules of the spliceosome are critical for specificity and catalysis during splicing of eukaryotic pre-mRNA. In order to examine the evolution and phylogenetic distribution of these RNAs, we analyzed 149 eukaryotic genomes representing a broad range of phylogenetic groups. RNAs were predicted using high-sensitivity local alignment methods and profile HMMs in combination with covariance models. The results provide the most comprehensive view so far of the phylogenetic distribution of spliceosomal RNAs. RNAs were predicted in many phylogenetic groups where these RNA were not previously reported. Examples are RNAs of the major (U2-type) spliceosome in all fungal lineages, in lower metazoa and many protozoa. We also identified the minor (U12-type) spliceosomal U11 and U6atac RNAs in Acanthamoeba castellanii, where U12 spliceosomal RNA as well as minor introns were reported recently. In addition, minor-spliceosome-specific RNAs were identified in a number of phylogenetic groups where previously such RNAs were not observed, including the nematode Trichinella spiralis, the slime mold Physarum polycephalum and the fungal lineages Zygomycota and Chytridiomycota. The detailed map of the distribution of the U12-type RNA genes supports an early origin of the minor spliceosome and points to a number of occasions during evolution where it was lost.
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Affiliation(s)
- Marcela Dávila López
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, Box 440 and Department of Cell and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Göteborg, Sweden
| | - Magnus Alm Rosenblad
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, Box 440 and Department of Cell and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Göteborg, Sweden
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, Box 440 and Department of Cell and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Göteborg, Sweden
- *To whom correspondence should be addressed. +46 31 786 3468+46 31 41 6108
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Sierra-Montes JM, Freund AV, Ruiz LM, Szmulewicz MN, Rowold DJ, Herrera RJ. Multiple forms of U2 snRNA coexist in the silk moth Bombyx mori. Insect Mol Biol 2002; 11:105-114. [PMID: 11841508 DOI: 10.1046/j.0962-1075.2001.00313.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Eight U2 snRNA variants were isolated from several Bombyx mori U2-specific RT-PCR libraries. U2 sequences and secondary structures were generated and examined in terms of potential RNA and protein interactions. Analysis indicated that nucleotide changes occurred in both stem/loop and single-stranded areas. Changes in the double stranded areas were either compensatory, single substitutions (e.g. C <--> U) or prevented the double-stranded formation of one or two base pairs. The polymorphisms were clustered in moderately conserved regions. Some of the changes observed generated stronger base pairing. Inter-species conserved protein or RNA-binding sites were relatively unaffected. No polymorphic sites were found in known functional sequences. Bombyx mori and Drosophila melanogaster U2 sequences are 95% and 70% similar at the 5'- and the 3'-ends of the molecule, respectively. Phylogenetic analysis of the U2 sequences demonstrates remarkable conservation across species.
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Affiliation(s)
- J M Sierra-Montes
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
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Affiliation(s)
- W Filipowicz
- Friedrich Miescher Institute, P.O. Box 2543, CH-4002 Basel, Switzerland.
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Leader DJ, Clark GP, Watters J, Beven AF, Shaw PJ, Brown JW. Splicing-independent processing of plant box C/D and box H/ACA small nucleolar RNAs. Plant Mol Biol 1999; 39:1091-100. [PMID: 10380797 DOI: 10.1023/a:1006157022319] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are involved in various aspects of ribosome biogenesis and rRNA maturation. Plants have a unique organisation of snoRNA genes where multiple, different genes are tightly clustered at a number of different loci. The maize gene clusters studied here include genes from both of the two major classes of snoRNAs (box C/D and box H/ACA) and are transcribed as a polycistronic pre-snoRNA transcript from an upstream promoter. In contrast to vertebrate and yeast intron-encoded snoRNAs, which are processed from debranched introns by exonuclease activity, the particular organisation of plant snoRNA genes suggests a different mode of expression and processing. Here we show that single and multiple plant snoRNAs can be processed from both non-intronic and intronic transcripts such that processing is splicing-independent and requires endonucleolytic activity. Processing of these different snoRNAs from the same polycistronic transcript suggests that the processing machineries needed by each class are not spatially separated in the nucleolus/nucleus.
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MESH Headings
- Base Sequence
- Endonucleases/metabolism
- Genes/genetics
- Genes, Plant/genetics
- Genetic Vectors
- Introns/genetics
- Models, Genetic
- Plants, Toxic
- Promoter Regions, Genetic/genetics
- Protoplasts
- RNA Processing, Post-Transcriptional/genetics
- RNA Splicing
- RNA, Plant/analysis
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Nuclear/analysis
- RNA, Small Nuclear/classification
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Regulatory Sequences, Nucleic Acid/genetics
- Nicotiana/genetics
- Transfection
- Zea mays/enzymology
- Zea mays/genetics
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Affiliation(s)
- D J Leader
- Cell and Molecular Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, UK
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Pieńkowska J, Szweykowska-Kulińska Z. [Small nucleolar RNA]. Postepy Biochem 1998; 44:102-13. [PMID: 9770233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Lafontaine DL, Bousquet-Antonelli C, Henry Y, Caizergues-Ferrer M, Tollervey D. The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Genes Dev 1998; 12:527-37. [PMID: 9472021 PMCID: PMC316522 DOI: 10.1101/gad.12.4.527] [Citation(s) in RCA: 282] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many or all of the sites of pseudouridine (Psi) formation in eukaryotic rRNA are selected by site-specific base-pairing with members of the box H + ACA class of small nucleolar RNAs (snoRNAs). Database searches previously identified strong homology between the rat nucleolar protein Nap57p, its yeast homolog Cbf5p, and the Escherichia coli Psi synthase truB/P35. We therefore tested whether Cbf5p is required for synthesis of Psi in the yeast rRNA. After genetic depletion of Cbf5p, formation of Psi in the pre-rRNA is dramatically inhibited, resulting in accumulation of the unmodified rRNA. Protein A-tagged Cbf5p coprecipitates all tested members of the box H + ACA snoRNAs but not box C + D snoRNAs or other RNA species. Genetic depletion of Cbf5p leads to depletion of all box H + ACA snoRNAs. These include snR30, which is required for pre-rRNA processing. Depletion of Cbf5p also results in a pre-rRNA processing defect similar to that seen on depletion of snR30. We conclude that Cbf5p is likely to be the rRNA Psi synthase and is an integral component of the box H + ACA class of snoRNPs, which function to target the enzyme to its site of action.
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Affiliation(s)
- D L Lafontaine
- Institute of Cell and Molecular Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, UK
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Ganot P, Caizergues-Ferrer M, Kiss T. The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev 1997; 11:941-56. [PMID: 9106664 DOI: 10.1101/gad.11.7.941] [Citation(s) in RCA: 267] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Eukaryotic cells contain a large number of small nucleolar RNAs (snoRNAs). A major family of snoRNAs features a consensus ACA motif positioned 3 nucleotides from the 3' end of the RNA. In this study we have characterized nine novel human ACA snoRNAs (U64-U72). Structural probing of U64 RNA followed by systematic computer modeling of all known box ACA snoRNAs revealed that this class of snoRNAs is defined by a phylogenetically conserved secondary structure. The ACA snoRNAs fold into two hairpin structures connected by a single-stranded hinge region and followed by a short 3' tail. The hinge region carries an evolutionarily conserved sequence motif, called box H (consensus, AnAnnA). The H box, probably in concert with the flanking helix structures and the ACA box characterized previously, plays an essential role in the accumulation of human U64 intronic snoRNA. The correct processing of a yeast ACA snoRNA, snR36, in mammalian cells demonstrated that the cis- and trans-acting elements required for processing and accumulation of ACA snoRNAs are evolutionarily conserved. The notion that ACA snoRNAs share a common secondary structure and conserved box elements that likely function as binding sites for common proteins (e.g., GAR1) suggests that these RNAs possess closely related nucleolar functions.
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Affiliation(s)
- P Ganot
- Laboratoire de Biologie Moléculaire Eucaryote du Centre National de laRecherche (CNRS), Université Paul Sabatier, Toulouse, France
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Abstract
Among the small nuclear RNAs (snRNAs) involved in the spliceosomal processing of pre-mRNA, U6 is the most conserved. As a first evidence for the presence of the splicing machinery in the amitochondrial protozoan Entamoeba histolytica (Eh), we have cloned the u6 snRNA gene. We find that in this organism u6 is a single copy gene that is transcribed as a poly(A)- RNA molecule of approximately 105 nucleotides. We have mapped the 5' end of the U6 snRNA transcript, and identified typical elements of a putative polymerase III promoter. This is the first snRNA gene reported in Eh. Sequence analysis indicates that this gene contains all the conserved nucleotides known to be important for U6 snRNA function. These results, in conjunction with the earlier finding of genes that contain pre-mRNA introns, suggest that Eh has a functional spliceosomal complex.
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Affiliation(s)
- R Miranda
- Department of Molecular Recognition and Structural Biology, Instituto de Biotecnología-UNAM, Cuernavaca, Mor., Mexico
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10
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Abstract
We have discovered that all known yeast and vertebrate small nucleolar RNAs (snoRNAs), except for the MRP/7-2 RNA, fall into two major classes. One class is defined by conserved boxes C and D and the other by a novel element: a consensus ACA triplet positioned 3 nt before the 3' end of the RNA. A role for the ACA box is snoRNA stability has been established by mutational analysis of a yeast ACA snoRNA (snR 11). Full function of the box depends on the integrity of an adjacent upstream stem. All members of the yeast ACA family are associated with the GAR1 protein. Binding of this or another common small nucleolar ribonucleoprotein particle protein is predicted to be a critical entry point to snoRNA posttranscriptional life, including precise formation of the snoRNA 3' end.
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Affiliation(s)
- A G Balakin
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst 01003, USA
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11
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Affiliation(s)
- B Sollner-Webb
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185
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Abstract
We have studied the accumulation and localization of U1 RNA during mouse embryo development by in situ hybridization with a U1 RNA probe and immunofluorescence microscopy using a mouse monoclonal antibody to U1 snRNP. There is a substantial amount of U1 RNA present in the oocyte that is present in both the germinal vesicle and the cytoplasm although the concentration is higher in the nuclear compartment. Following the germinal vesicle breakdown that accompanies ovulation and meiotic maturation, the U1 RNA is uniformly distributed throughout the unfertilized oocyte. In the fertilized egg, the silver grain density from in situ hybridization is higher over pronuclei and this enrichment is maintained at the two-cell and later stages. Similar results were obtained for the distribution of the U1 snRNP as assayed by immunofluorescence microscopy: U1 RNA is predominantly localized in all nuclei except polar body nuclei. The U1 RNA in the oocyte and two-cell embryo is predominantly (greater than 85%) U1a RNA. By the eight-cell stage there is a two to three-fold increase in the amount of total U1 RNA and the proportion of U1b RNA has increased to about 40%. The amount of U1 RNA continues to increase through the blastocyst stage and the proportion of the U1b RNA increases to 60%.
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Affiliation(s)
- S M Lobo
- Department of Chemistry, Florida State University, Tallahassee 32306
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