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Fu Y, Fang X, Xiao Y, Mao B, Xu Z, Shen M, Wang X. Two chromosome-level genomes of Smittia aterrima and Smittia pratorum (Diptera, Chironomidae). Sci Data 2024; 11:165. [PMID: 38310146 PMCID: PMC10838273 DOI: 10.1038/s41597-024-03010-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/26/2024] [Indexed: 02/05/2024] Open
Abstract
Chironomids are one of the most abundant aquatic insects and are widely distributed in various biological communities. However, the lack of high-quality genomes has hindered our ability to study the evolution and ecology of this group. Here, we used Nanopore long reads and Hi-C data to produce two chromosome-level genomes from mixed genomic data. The genomes of Smittia aterrima (SateA) and Smittia pratorum (SateB) were assembled into three chromosomes, with sizes of 78.45 Mb and 71.56 Mb, scaffold N50 lengths of 25.73 and 23.53 Mb, and BUSCO completeness of 98.5% and 97.8% (n = 1,367), 5.68 Mb (7.24%) and 1.94 Mb (2.72%) of repetitive elements, and predicted 12,330 (97.70% BUSCO completeness) and 11,250 (97.40%) protein-coding genes, respectively. These high-quality genomes will serve as valuable resources for comprehending the evolution and environmental adaptation of chironomids.
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Affiliation(s)
- Yue Fu
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, Hubei, 438000, China.
| | - Xiangliang Fang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, Hubei, 438000, China
| | - Yunli Xiao
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, Hubei, 438000, China
| | - Bin Mao
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, Hubei, 438000, China
| | - Zigang Xu
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, Hubei, 438000, China
| | - Mi Shen
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, Hubei, 438000, China
| | - Xinhua Wang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
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Uddin M, Altmann GG, Leblond CP. Radioautographic visualization of differences in the pattern of [3H]uridine and [3H]orotic acid incorporation into the RNA of migrating columnar cells in the rat small intestine. J Cell Biol 1984; 98:1619-29. [PMID: 6202697 PMCID: PMC2113200 DOI: 10.1083/jcb.98.5.1619] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The epithelium of rat small intestine was radioautographed to examine whether RNA is synthesized by the salvage pathway as shown after [3H]uridine injection or by the de novo pathway as shown after [3H]orotic acid injection. The two modes of RNA synthesis were thus investigated during the migration of columnar cells from crypt base to villus top, and the rate of synthesis was assessed by counting silver grains over the nucleolus and nucleoplasm at six levels along the duodenal epithelium--that is, in the base, mid, and top regions of the crypts and in the base, mid, and top regions of the villi. Concomitant biochemical analyses established that, after injection of either [5-3H]uridine or [5-3H]orotic acid: (a) buffered glutaraldehyde fixative was as effective as perchloric acid or trichloracetic acid in insolubilizing the nucleic acids of rat small intestine; (b) a major fraction of the nucleic acid label was in RNA, that is, 91% after [3H]uridine and 72% after [3H]orotic acid, with the rest in DNA; and (c) a substantial fraction of the RNA label was in poly A+ RNA (presumed to be messenger RNA). In radioautographs of duodenum prepared after [3H] uridine injection, the count of silver grains was high over nucleolus and nucleoplasm in crypt base cells and gradually decreased at the upper levels up to the villus base. In the rest of the villus, the grain count over the nucleolus was negligible, while over the nucleoplasm it was low but significant. After [3H]-orotic acid injection, the number of silver grains over the nucleolus was negligible at all levels, whereas over the nucleoplasm the number was low in crypt cells, but high in villus cells with a peak in mid villus. The interpretation is that, except for a small amount of label incorporated into DNA from either precursor by crypt cells, the bulk of the label is incorporated into RNA as follows. In the crypts, cells make almost exclusive use of uridine, that is, of the salvage pathway, for the synthesis of ribosomal RNA in the nucleolus and of messenger and transfer RNA in the nucleoplasm. However, when cells pass from crypt to villus, they mainly utilize orotic acid--i.e., the de novo pathway--for the synthesis of messenger and transfer RNA within the nucleoplasm.
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Kumar D. Autoradiographic studies on RNA synthesis and transport in the salivary gland of Lygaeus sp. (Hemiptera-Lygaeidae). EXPERIENTIA 1981; 37:37-8. [PMID: 6162674 DOI: 10.1007/bf01965555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Autoradiographic studies using 3H-uridine in the salivary gland of adult Lygaeus sp. were carried out. The gland cell nuclei, particularly the multiple nucleoli, are the sites of incorporation of the label exhibiting RNA synthesis. The labelled molecules (RNA) are transported to the cell cytoplasm and then into the gland lumen in which no turnover of the radioactivity is observed.
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Noel JS, Dewey WC, Abel JH, Thompson RP. Ultrastructure of the nucleolus during the Chinese hamster cell cycle. J Biophys Biochem Cytol 1971; 49:830-47. [PMID: 4933472 PMCID: PMC2108503 DOI: 10.1083/jcb.49.3.830] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Changes in the structure of the nucleolus during the cell cycle of the Chinese hamster cell in vitro were studied. Quantitative electron microscopic techniques were used to establish the size and volume changes in nucleolar structures. In mitosis, nucleolar remnants, "persistent nucleoli," consisting predominantly of ribosome-like granular material, and a granular coating on the chromosomes were observed. Persistent nucleoli were also observed in some daughter nuclei as they were leaving telophase and entering G(1). During very early G(1), a dense, fibrous material characteristic of interphase nucleoli was noted in the nucleoplasm of the cells. As the cells progressed through G(1), a granular component appeared which was intimately associated with the fibrous material. By the middle of G(1), complete, mature nucleoli were present. The nucleolar volume enlarged by a factor of two from the beginning of G(1) to the middle of S primarily due to the accumulation of the granular component. During the G(2) period, there was a dissolution or breakdown of the nucleolus prior to the entry of the cells into mitosis. Correlations between the quantitative aspects of this study and biochemical and cytochemical data available in the literature suggest the following: nucleolar reformation following division results from the activation of the nucleolar organizer regions which transcribe for RNA first appearing in association with protein as a fibrous component (45S RNA) and then later as a granular component (28S and 32S RNA).
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