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Garrido P, Casas-Benito A, Larrayoz IM, Narro-Íñiguez J, Rubio-Mediavilla S, Zozaya E, Martín-Carnicero A, Martínez A. Expression of Mitochondrial Long Non-Coding RNAs, MDL1 and MDL1AS, Are Good Prognostic and/or Diagnostic Biomarkers for Several Cancers, Including Colorectal Cancer. Cancers (Basel) 2024; 16:960. [PMID: 38473321 DOI: 10.3390/cancers16050960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Non-coding RNAs provide new opportunities to identify biomarkers that properly classify cancer patients. Here, we study the biomarker status of the mitochondrial long non-coding RNAs, MDL1 and MDL1AS. Expression of these genes was studied in public transcriptomic databases. In addition, a cohort of 69 locally advanced rectal cancer (LARC) patients with a follow-up of more than 5 years was used to determine the prognostic value of these markers. Furthermore, cell lines of colorectal (HCT116) and breast (MDA-MB-231) carcinoma were employed to study the effects of downregulating MDL1AS in vitro. Expression of MDL1AS (but not MDL1) was significantly different in tumor cells than in the surrounding tissue in a tumor-type-specific context. Both MDL1 and MDL1AS were accurate biomarkers for the 5-year survival of LARC patients (p = 0.040 and p = 0.007, respectively) with promising areas under the curve in the ROC analyses (0.820 and 0.930, respectively). MDL1AS downregulation reduced mitochondrial respiration in both cell lines. Furthermore, this downregulation produced a decrease in growth and migration on colorectal cells, but the reverse effects on breast cancer cells. In summary, MDL1 and MDL1AS can be used as reliable prognostic biomarkers of LARC, and MDL1AS expression provides relevant information on the diagnosis of different cancers.
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Affiliation(s)
- Pablo Garrido
- Angiogenesis Group, Oncology Area, Center for Biomedical Research of La Rioja (CIBIR), 26006 Logroño, Spain
| | - Adrián Casas-Benito
- Angiogenesis Group, Oncology Area, Center for Biomedical Research of La Rioja (CIBIR), 26006 Logroño, Spain
| | - Ignacio M Larrayoz
- Department of Nursing, Biomarkers, Artificial Intelligence and Signaling (BIAS), University of La Rioja, 26004 Logroño, Spain
| | - Judit Narro-Íñiguez
- Angiogenesis Group, Oncology Area, Center for Biomedical Research of La Rioja (CIBIR), 26006 Logroño, Spain
| | | | - Enrique Zozaya
- Pathology Service, Hospital de Calahorra, 26500 Calahorra, Spain
| | | | - Alfredo Martínez
- Angiogenesis Group, Oncology Area, Center for Biomedical Research of La Rioja (CIBIR), 26006 Logroño, Spain
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2
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Ren B, Guan MX, Zhou T, Cai X, Shan G. Emerging functions of mitochondria-encoded noncoding RNAs. Trends Genet 2023; 39:125-139. [PMID: 36137834 DOI: 10.1016/j.tig.2022.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 01/27/2023]
Abstract
Mitochondria, organelles that harbor their own circular genomes, are critical for energy production and homeostasis maintenance in eukaryotic cells. Recent studies discovered hundreds of mitochondria-encoded noncoding RNAs (mt-ncRNAs), including novel subtypes of mitochondria-encoded circular RNAs (mecciRNAs) and mitochondria-encoded double-stranded RNAs (mt-dsRNAs). Here, we discuss the emerging field of mt-ncRNAs by reviewing their expression patterns, biogenesis, metabolism, regulatory roles, and functional mechanisms. Many mt-ncRNAs have regulatory roles in cellular physiology, and some are associated with, or even act as, causal factors in human diseases. We also highlight developments in technologies and methodologies and further insights into future perspectives and challenges in studying these noncoding RNAs, as well as their potential biomedical applications.
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Affiliation(s)
- Bingbing Ren
- Department of Pulmonary and Critical Care Medicine, Regional Medical Center for National Institute of Respiratory Disease, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; Cancer Center, Zhejiang University, Hangzhou 310058, China; Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Min-Xin Guan
- Division of Medical Genetics and Genomics, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China; Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Tianhua Zhou
- Cancer Center, Zhejiang University, Hangzhou 310058, China; Department of Cell Biology and Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, China
| | - Xiujun Cai
- Cancer Center, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Zhejiang University, Hangzhou 310016, China; Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Zhejiang University, Hangzhou 310016, China
| | - Ge Shan
- Department of Pulmonary and Critical Care Medicine, Regional Medical Center for National Institute of Respiratory Disease, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; Cancer Center, Zhejiang University, Hangzhou 310058, China; Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China; Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China.
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Chang J, Duan G, Li W, Yau TO, Liu C, Cui J, Xue H, Bu W, Hu Y, Gao S. The first discovery of Tc1 transposons in yeast. Front Microbiol 2023; 14:1141495. [PMID: 36876116 PMCID: PMC9977792 DOI: 10.3389/fmicb.2023.1141495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Background Identification of transposons without close homologs is still a difficult task. IS630/Tc1/mariner transposons, classified into a superfamily, are probably the most widespread DNA transposons in nature. Tc1/mariner transposons have been discovered in animals, plants, and filamentous fungi, however, not in yeast. Results In the present study, we report the discovery of two intact Tc1 transposons in yeast and filamentous fungi, respectively. The first one, named Tc1-OP1 (DD40E), represents Tc1 transposons in Ogataea parapolymorpha. The second one, named Tc1-MP1 (DD34E), represents Tc1 transposons in the Rhizopodaceae and Mucoraceae families. As a homolog of Tc1-OP1 and Tc1-MP1, IS630-AB1 (DD34E) was discovered as an IS630 transposon in Acinetobacter spp. Conclusion Tc1-OP1 is not only the first reported Tc1 transposon in yeast, but also the first reported nonclassical Tc1 transposon. Tc1-OP1 is the largest of IS630/Tc1/mariner transposons reported to date and significantly different from others. Notably, Tc1-OP1 encodes a serine-rich domain and a transposase, extending the current knowledge of Tc1 transposons. The phylogenetic relationships of Tc1-OP1, Tc1-MP1 and IS630-AB1 indicated that these transposons had evolved from a common ancestor. Tc1-OP1, Tc1-MP1 and IS630-AB1 can be used as reference sequences to facilitate the identification of IS630/Tc1/mariner transposons. More Tc1/mariner transposons will be identified in yeast, following our discovery.
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Affiliation(s)
- Jia Chang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Guangyou Duan
- School of Life Sciences, Qilu Normal University, Jinan, Shandong, China
| | - Wenjing Li
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Tung On Yau
- Department of Rural Land Use, Scotland's Rural College, Aberdeen, United Kingdom
| | - Chang Liu
- School of Medicine, Nankai University, Tianjin, China
| | - Jianlin Cui
- School of Medicine, Nankai University, Tianjin, China
| | - Huaijun Xue
- College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Yanping Hu
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, China
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Tian L, Yang W, Si C, Guo X, Zhang B. Complete Mitogenome Analysis of Five Leafhopper Species of Idiocerini (Hemiptera: Cicadellidae). Genes (Basel) 2022; 13:2000. [PMID: 36360236 PMCID: PMC9690763 DOI: 10.3390/genes13112000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 10/03/2023] Open
Abstract
Insect mitochondrial genomes (mitogenomes) are of great interest in exploring molecular evolution, phylogenetics, and biogeography. So far, only 12 mitogenomes of the leafhopper tribe Idiocerini have been released in GenBank, although the tribe comprises 488 known species including some agricultural, forestry, and horticultural pests. In order to compare and analyze the mitochondrial genome structure of Idiocerini and even the selective pressure of 13 protein-coding genes (PCGs) of the family Cicadellidae, the complete mitogenomes of five species including Nabicerus dentimus, Sahlbergotettix salicicola, Podulmorinus opacus, Podulmorinus consimilis, and a new species of a new genus were determined by next-generation sequencing. The size of the newly determined mitogenomes ranged from 14,733 bp to 15,044 bp, comprising the standard set of 13 PCGs, 22 transfer RNA genes, two ribosomal RNA genes, and a long non-coding control region (CR). The extent of purifying selection presented different pictures in the tribe and the family. The less pronounced genes (0.5 < dN/dS < 1) were nad5 and nad4l in Idiocerin, whereas in the family Cicadellidae including the sequences of Idiocerin, nad1-nad6 and cox1 genes were less pronounced. The codon encoding leucine was the most common in all species, and the codon encoding serine 1 was the most common in all species except for P. opacus. Interestingly, in P. opacus, another of the most common codons is that encoding serine 2. Among the 17 examined species of the Idiocerini, 14 species contained the tandem repeats, and 11 species of them contained the motif "TTATA". These findings will promote research on the structure and evolution of the mitochondrial genome and highlight the need for more mitogenomes in Cicadellidae.
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Affiliation(s)
- Lili Tian
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010022, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxin Yang
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010022, China
| | - Chengyan Si
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010022, China
| | - Xianguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Bin Zhang
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010022, China
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5
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Liang J, Chen R, Zhang F, Wang Q, Yang Y, Lv M, Yan S, Gao S. Full-length chloroplast genome of Dongxiang wild rice reveals small single-copy region switching. FRONTIERS IN PLANT SCIENCE 2022; 13:929352. [PMID: 36247578 PMCID: PMC9559570 DOI: 10.3389/fpls.2022.929352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Plant chloroplast DNA (cpDNA) typically has a circular structure, including a large single-copy region (LSC), a small single-copy region (SSC) and two inverted repeats (IR1 and IR2). The organization of these four elementary regions LSC-IR1-SSC-IR2 is highly conserved across all plant cpDNAs. Very few structural variations (SVs) occurring at the elementary-region level have been reported. RESULTS In the present study, we assembled the full-length cpDNA of Dongxiang wild rice line 159 (DXWR159). Using the long PacBio subreads, we discovered a large inversion of SSC and a large duplication of IR in DXWR159 cpDNAs. Significantly, we reported for the first time forward and reverse SSCs of cpDNAs in similar proportions and named the frequent inversion of a whole SSC as SSC switching. CONCLUSIONS Our study helps researchers to correctly assemble the chloroplast genomes. Our recombination model explained the formation of large SVs in cpDNAs and provided insights into a novel scientific question that if there are common mechanisms in the formation or translocation of all kinds of transposon-like elements (TLEs). We propose that: (1) large inversion is the most accepted mutation type of SVs in cpDNAs; (2) SSC switching ubiquitous occurs in plant cpDNAs; and (3) further investigation of molecular mechanism underlying SSC switching may reveal new driving forces for large SVs.
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Affiliation(s)
| | - Rui Chen
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
- Tianjin Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, China
| | - Qian Wang
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yingxia Yang
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Mingjie Lv
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Shuangyong Yan
- Tianjin Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, China
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6
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Liang G, Mi D, Chang J, On Yau T, Xu G, Ruan J, Bu W, Gao S. Precise annotation of Drosophila mitochondrial genomes leads to insights into AT-rich regions. Mitochondrion 2022; 65:145-149. [PMID: 35779797 DOI: 10.1016/j.mito.2022.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/24/2022] [Accepted: 06/26/2022] [Indexed: 11/16/2022]
Abstract
In the present study, we performed precise annotation of Drosophila melanogaster, D. simulans, D. grimshawi, Bactrocera oleae mitochondrial (mt) genomes using pan RNA-seq analysis. Using PacBio cDNA-seq data from D. simulans, we precisely annotated the Transcription Initiation Sites (TISs) of the mt Heavy and Light strands in Drosophila mt genomes and reported that the polyA(+) and polyA(-) motifs in the CRs are associated with TISs. The discovery of the conserved polyA(+) and polyA(-) motifs provides insights into many polyA and polyT sequences in CRs of insect mt genomes, leading to reveal the mt transcription and its regulation in invertebrates. Notably, we propose that: (1) polyA/polyT motifs in CRs function as signals to initiate mtDNA transcription; (2) the duplication, recombination or mutation of these polyA/polyT sequences formed the AT-rich regions during evolution; and (3) since CRs of many invertebrate species still contain many polyA/polyT sequences, there is a high probability that several TISs and TTSs exist in invertebrate mt genomes.
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Affiliation(s)
- Guangcai Liang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Dong Mi
- Department of Clinical Laboratory, Affiliated Maternity Hospital, Nankai University, Tianjin 300100, PR China
| | - Jia Chang
- College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, PR China
| | - Tung On Yau
- Department of Rural Land Use, Scotland's Rural College, Aberdeen AB21 9YA, United Kingdom
| | - Guofeng Xu
- College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, PR China
| | - Jishou Ruan
- School of Mathematical Sciences, Nankai University, Tianjin, Tianjin 300071, PR China
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, PR China.
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, PR China.
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7
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Liang J, Shi J, Chen S, Duan G, Yang F, Cheng Z, Li X, Ruan J, Mi D, Gao S. How the Replication and Transcription Complex Functions in Jumping Transcription of SARS-CoV-2. Front Genet 2022; 13:904513. [PMID: 35706445 PMCID: PMC9191571 DOI: 10.3389/fgene.2022.904513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/13/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although unprecedented efforts are underway to develop therapeutic strategies against this disease, scientists have acquired only a little knowledge regarding the structures and functions of the CoV replication and transcription complex (RTC). Ascertaining all the RTC components and the arrangement of them is an indispensably step for the eventual determination of its global structure, leading to completely understanding all of its functions at the molecular level. Results: The main results include: 1) hairpins containing the canonical and non-canonical NSP15 cleavage motifs are canonical and non-canonical transcription regulatory sequence (TRS) hairpins; 2) TRS hairpins can be used to identify recombination regions in CoV genomes; 3) RNA methylation participates in the determination of the local RNA structures in CoVs by affecting the formation of base pairing; and 4) The eventual determination of the CoV RTC global structure needs to consider METTL3 in the experimental design. Conclusions: In the present study, we proposed the theoretical arrangement of NSP12-15 and METTL3 in the global RTC structure and constructed a model to answer how the RTC functions in the jumping transcription of CoVs. As the most important finding, TRS hairpins were reported for the first time to interpret NSP15 cleavage, RNA methylation of CoVs and their association at the molecular level. Our findings enrich fundamental knowledge in the field of gene expression and its regulation, providing a crucial basis for future studies.
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Affiliation(s)
| | - Jinsong Shi
- National Clinical Research Center of Kidney Disease, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Shunmei Chen
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University, Kunming, China
| | - Guangyou Duan
- School of Life Sciences, Qilu Normal University, Jinan, China
| | - Fan Yang
- National Clinical Research Center of Kidney Disease, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Zhi Cheng
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xin Li
- College of Life Sciences, Nankai University, Tianjin, China
| | - Jishou Ruan
- School of Mathematical Sciences, Nankai University, Tianjin, China
| | - Dong Mi
- Department of Clinical Laboratory, Affiliated Maternity Hospital, Nankai University, Tianjin, China
- *Correspondence: Dong Mi, ; Shan Gao,
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, China
- *Correspondence: Dong Mi, ; Shan Gao,
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Complete Mitochondrial Genomes of Five Racerunners (Lacertidae: Eremias) and Comparison with Other Lacertids: Insights into the Structure and Evolution of the Control Region. Genes (Basel) 2022; 13:genes13050726. [PMID: 35627111 PMCID: PMC9141765 DOI: 10.3390/genes13050726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 12/04/2022] Open
Abstract
Comparative studies on mitochondrial genomes (mitogenomes) as well as the structure and evolution of the mitochondrial control region are few in the Lacertidae family. Here, the complete mitogenomes of five individuals of Eremias scripta (2 individuals), Eremias nikolskii, Eremias szczerbaki, and Eremias yarkandensis were determined using next-generation sequencing and were compared with other lacertids available in GenBank. The circular mitogenomes comprised the standard set of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and a long non-coding control region (CR). The extent of purifying selection was less pronounced for the COIII and ND2 genes in comparison with the rest of the PCGs. The codons encoding Leucine (CUN), Threonine, and Isolecucine were the three most frequently present. The secondary structure of rRNA of Lacertidae (herein, E. scripta KZL15 as an example) comprised four domains and 28 helices for 12S rRNA, with six domains and 50 helices for 16S rRNA. Five types and twenty-one subtypes of CR in Lacertidae were described by following the criteria of the presence and position of tandem repeats (TR), termination-associated sequence 1 (TAS1), termination-associated sequence 2 (TAS2), conserved sequence block 1 (CBS1), conserved sequence block 2 (CSB2), and conserved sequence block 3 (CSB3). The compositions of conserved structural elements in four genera, Acanthodactylus, Darevskia, Eremias, and Takydromus, were further explored in detail. The base composition of TAS2 – TATACATTAT in Lacertidae was updated. In addition, the motif “TAGCGGCTTTTTTG” of tandem repeats in Eremias and the motif ”GCGGCTT” in Takydromus were presented. Nucleotide lengths between CSB2 and CSB3 remained 35 bp in Eremias and Darevskia. The phylogenetic analyses of Lacertidae recovered the higher-level relationships among the three subfamilies and corroborated a hard polytomy in the Lacertinae phylogeny. The phylogenetic position of E. nikolskii challenged the monophyly of the subgenus Pareremias within Eremias. Some mismatches between the types of CR and their phylogeny demonstrated the complicated evolutionary signals of CR such as convergent evolution. These findings will promote research on the structure and evolution of the CR and highlight the need for more mitogenomes in Lacertidae.
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Liu X, Shan G. Mitochondria Encoded Non-coding RNAs in Cell Physiology. Front Cell Dev Biol 2021; 9:713729. [PMID: 34395442 PMCID: PMC8362354 DOI: 10.3389/fcell.2021.713729] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/12/2021] [Indexed: 01/05/2023] Open
Abstract
Mitochondria are the powerhouses of mammalian cells, which participate in series of metabolic processes and cellular events. Mitochondria have their own genomes, and it is generally acknowledged that human mitochondrial genome encodes 13 proteins, 2 rRNAs and 22 tRNAs. However, the complexity of mitochondria derived transcripts is just starting to be envisaged. Currently, there are at least 8 lncRNAs, some dsRNAs, various small RNAs, and hundreds of circRNAs known to be generated from mitochondrial genome. These non-coding RNAs either translocate into cytosol/nucleus or reside in mitochondria to play various biological functions. Here we present an overview of regulatory non-coding RNAs encoded by the mammalian mitochondria genome. For overall understandings of non-coding RNAs in mitochondrial function, a brief summarization of nuclear-encoded non-coding RNAs in mitochondria is also included. We discuss about roles of these non-coding RNAs in cellular physiology and the communication between mitochondria and the nucleus.
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Affiliation(s)
- Xu Liu
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Science and Medicine, Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, University of Science and Technology of China, Hefei, China
| | - Ge Shan
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Science and Medicine, Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, University of Science and Technology of China, Hefei, China
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10
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Li X, Cheng Z, Wang F, Chang J, Zhao Q, Zhou H, Liu C, Ruan J, Duan G, Gao S. A Negative Feedback Model to Explain Regulation of SARS-CoV-2 Replication and Transcription. Front Genet 2021; 12:641445. [PMID: 33719350 PMCID: PMC7954359 DOI: 10.3389/fgene.2021.641445] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/01/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although a preliminary understanding of the replication and transcription of SARS-CoV-2 has recently emerged, their regulation remains unknown. RESULTS By comprehensive analysis of genome sequence and protein structure data, we propose a negative feedback model to explain the regulation of CoV replication and transcription, providing a molecular basis of the "leader-to-body fusion" model. The key step leading to the proposal of our model was that the transcription regulatory sequence (TRS) motifs were identified as the cleavage sites of nsp15, a nidoviral RNA uridylate-specific endoribonuclease (NendoU). According to this model, nsp15 regulates the synthesis of subgenomic RNAs (sgRNAs), and genomic RNAs (gRNAs) by cleaving TRSs. The expression level of nsp15 controls the relative proportions of sgRNAs and gRNAs, which in turn change the expression level of nsp15 to reach equilibrium between the CoV replication and transcription. CONCLUSION The replication and transcription of CoVs are regulated by a negative feedback mechanism that influences the persistence of CoVs in hosts. Our findings enrich fundamental knowledge in the field of gene expression and its regulation, and provide new clues for future studies. One important clue is that nsp15 may be an important and ideal target for the development of drugs (e.g., uridine derivatives) against CoVs.
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Affiliation(s)
- Xin Li
- College of Life Sciences, Nankai University, Tianjin, China
- The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhi Cheng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Fang Wang
- The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Jia Chang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Qiang Zhao
- College of Life Sciences, Nankai University, Tianjin, China
| | - Hao Zhou
- College of Life Sciences, Nankai University, Tianjin, China
| | - Chang Liu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Jishou Ruan
- School of Mathematical Sciences, Nankai University, Tianjin, China
| | - Guangyou Duan
- School of Life Sciences, Qilu Normal University, Jinan, China
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, China
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11
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Complete mitochondrial genome of a blue-tailed skink Plestiodon capito (Reptilia, Squamata, Scincidae) and comparison with other Scincidae lizards. Genetica 2020; 148:229-241. [PMID: 33044712 DOI: 10.1007/s10709-020-00107-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 09/24/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
Vertebrate mitochondrial genomes (mitogenomes) are valuable for studying phylogeny, evolutionary genetics and genomics. To date, however, compared to other vertebrate groups, our knowledge about the mitogenomes of skinks (the family Scincidae), even of reptile, has been relatively limited. In the present study, we determined the complete mitogenome of a blue-tailed skink Plestiodon capito for the first time, and compared it with other skinks available in GenBank. The circular genome is 17,344 bp long, showing a typical vertebrate pattern with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region (CR). The gene organization, nucleotide composition, and codon usage are similar to those from skinks previously published. Twelve out of 13 PCGs initiates with canonical start codon (ATG), while COX1 starts with GTG. The codon usage analysis revealed a preferential use of the LeuCUN (Leu1), Pro, and Thr codons with the A/U ending. All tRNAs in P. capito were predicted to fold into typical clover-leaf secondary structure, except tRNA-Ser AGY. The secondary structures of 12S rRNA and 16S rRNA comprises 34 helices and 56 helices, respectively. The alignment of the Plesitodon species CRs exhibited high genetic variability and rich A + T content. Besides, variable types and numbers of tandem repeat units were also identified in the CR of Plestiodon. Phylogenetic analyses recovered P. capito as the sister species to P. tunganus; monophyly of the Scincidae is well supported. Our results will help to better understand structure and evolution of the mitochondrial DNA control region in reptiles as well as the evolutionary status of P. capito, and to lay foundation for further phylogenetic study of skinks in a mitogenomic framework.
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Xu X, Bei J, Xuan Y, Chen J, Chen D, Barker SC, Kelava S, Zhang X, Gao S, Chen Z. Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data. BMC Genomics 2020; 21:641. [PMID: 32938401 PMCID: PMC7493057 DOI: 10.1186/s12864-020-07060-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/10/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick virus (KITV), and Guangxi tick virus (GXTV)-evolutionarily related to MGTV-were reported. RESULTS In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China's Yunnan Province in 2016. We obtained the full-length genome sequence of this MGTV strain Yunnan2016 (GenBank: MT080097, MT080098, MT080099 and MT080100) and recommended it for its inclusion in the NCBI RefSeq database for future studies on MGTV, JMTV, KITV and GXTV. Phylogenetic analysis showed that MGTV, JMTV, KITV and GXTV are monophyletic and belong to a MGTV group. Furthermore, this MGTV group of viruses may be phylogenetically related to geographical regions that were formerly part of the supercontinents Gondwana and Laurasia. CONCLUSIONS To the best of our knowledge, this is the first study in which 5' and 3' sRNAs were used to generate full-length genome sequences of, but not limited to, RNA viruses. We also demonstrated the feasibility of using the sRNA-seq based method for the detection of viruses in pooled two and even possible one small ticks. MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the origin and evolution of RNA viruses. In addition, MGTV can be used as novel species for studies in phylogeography.
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Affiliation(s)
- Xiaofeng Xu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China
| | - Jinlong Bei
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Yibo Xuan
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China
| | - Jiayuan Chen
- College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, People's Republic of China
| | - Defu Chen
- College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, People's Republic of China
| | - Stephen C Barker
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Samuel Kelava
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xiaoai Zhang
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, People's Republic of China.
| | - Ze Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China.
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Chen Z, Xuan Y, Liang G, Yang X, Yu Z, Barker SC, Kelava S, Bu W, Liu J, Gao S. Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element. BMC Genomics 2020; 21:488. [PMID: 32680454 PMCID: PMC7367389 DOI: 10.1186/s12864-020-06906-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 07/10/2020] [Indexed: 02/07/2023] Open
Abstract
Background In the present study, we used long-PCR amplification coupled with Next-Generation Sequencing (NGS) to obtain complete mitochondrial (mt) genomes of individual ticks and unprecedently performed precise annotation of these mt genomes. We aimed to: (1) develop a simple, cost-effective and accurate method for the study of extremely high AT-content mt genomes within an individual animal (e.g. Dermacentor silvarum) containing miniscule DNA; (2) provide a high-quality reference genome for D. silvarum with precise annotation and also for future studies of other tick mt genomes; and (3) detect and analyze mt DNA variation within an individual tick. Results These annotations were confirmed by the PacBio full-length transcriptome data to cover both entire strands of the mitochondrial genomes without any gaps or overlaps. Moreover, two new and important findings were reported for the first time, contributing fundamental knowledge to mt biology. The first was the discovery of a transposon-like element that may eventually reveal much about mechanisms of gene rearrangements in mt genomes. Another finding was that Copy Number Variation (CNV) of Short Tandem Repeats (STRs) account for mitochondrial sequence diversity (heterogeneity) within an individual tick, insect, mouse or human, whereas SNPs were not detected. The CNV of STRs in the protein-coding genes resulted in frameshift mutations in the proteins, which can cause deleterious effects. Mitochondria containing these deleterious STR mutations accumulate in cells and can produce deleterious proteins. Conclusions We proposed that the accumulation of CNV of STRs in mitochondria may cause aging or diseases. Future tests of the CNV of STRs hypothesis help to ultimately reveal the genetic basis of mitochondrial DNA variation and its consequences (e.g., aging and diseases) in animals. Our study will lead to the reconsideration of the importance of STRs and a unified study of CNV of STRs with longer and shorter repeat units (particularly polynucleotides) in both nuclear and mt genomes.
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Affiliation(s)
- Ze Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China
| | - Yibo Xuan
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China.,College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, P. R. China
| | - Guangcai Liang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, Tianjin, 300350, P. R. China
| | - Xiaolong Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China
| | - Stephen C Barker
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Samuel Kelava
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, P. R. China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China.
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, P. R. China. .,School of Statistics and Data Science, Nankai University, Tianjin, Tianjin, 300071, P. R. China.
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Jin X, Cheng Z, Wang B, Yau TO, Chen Z, Barker SC, Chen D, Bu W, Sun D, Gao S. Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes leads to insight into mitochondrial transcription in mammals. RNA Biol 2020; 17:395-402. [PMID: 31905034 DOI: 10.1080/15476286.2019.1709746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
In the present study, we applied our 'precise annotation' to the mitochondrial (mt) genomes of human, chimpanzee, rhesus macaque and mouse using 5' and 3' end small RNAs. Our new annotations updated previous annotations. In particular, our new annotations led to two important novel findings: (1) the identification of five Conserved Sequence Blocks (CSB1, CSB2, CSB3, LSP and HSP) in the control regions; and (2) the annotation of Transcription Initiation and novel Transcription Termination Sites. Based on these annotations, we proposed a novel model of mt transcription which can account for the mt transcription and its regulation in mammals. According to our model, Transcription Termination Sites function as switches to regulate the production of short, long primary transcripts and uninterrupted transcription, rather than simply terminate the mt transcription. Moreover, the expression levels of mitochondrial transcription termination factors control the proportions of rRNAs, mRNAs and lncRNAs in total mt RNA. Our findings point to the existence of many other, as yet unidentified, Transcription Termination Sites in mammals.
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Affiliation(s)
- Xiufeng Jin
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| | - Zhi Cheng
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| | - Bo Wang
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, P.R.China
| | - Tung On Yau
- John Van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Ze Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, P.R. China
| | - Stephen C Barker
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Defu Chen
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| | - Daqing Sun
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, P.R.China
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, P.R.China
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Ji H, Xu X, Jin X, Yin H, Luo J, Liu G, Zhao Q, Chen Z, Bu W, Gao S. Using high-resolution annotation of insect mitochondrial DNA to decipher tandem repeats in the control region. RNA Biol 2019; 16:830-837. [PMID: 30870076 DOI: 10.1080/15476286.2019.1591035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
In this study, we used a small RNA sequencing (sRNA-seq) based method to annotate the mitochondrial genome of the insect Erthesina fullo Thunberg at 1 bp resolution. The high-resolution annotations cover both entire strands of the mitochondrial genome without any gaps or overlaps. Most of the new annotations were consistent with the previous annotations which had been obtained using PacBio full-length transcripts. Two important findings were that animals transcribe both entire strands of mitochondrial genomes and the tandem repeats in the control region of the E. fullo mitochondrial genome contains the repeated Transcription Initiation Sites (TISs) of the heavy strand. In addition, we found that the copy numbers of tandem repeats showed a great diversity within an individual, suggesting that mitochondrial DNA recombination occurs in an individual. In conclusion, the sRNA-seq based method uses 5' and 3' end small RNAs to annotate nuclear non-coding and mitochondrial genes at 1 bp resolution, and can be used to identify new steady RNAs, particularly long non-coding RNAs (lncRNAs). The high-resolution annotations of mitochondrial genomes can also be used to study the molecular phylogenetics and evolution of animals or to investigate mitochondrial gene transcription, RNA processing, RNA maturation and several other related topics. The complete mitochondrial genome sequence of E. fullo with the new annotations using the sRNA-seq based method is available at the NCBI GenBank database under the accession number MK374364. We publish our theories, methods, the high quality sRNA-seq and RNA-seq data (SRA: SRP174926) for extensive use.
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Affiliation(s)
- Haishuo Ji
- a College of Life Sciences , Nankai University , Tianjin , P.R.China
| | - Xiaofeng Xu
- b State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Science , Lanzhou , P.R.China
| | - Xiufeng Jin
- a College of Life Sciences , Nankai University , Tianjin , P.R.China
| | - Hong Yin
- b State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Science , Lanzhou , P.R.China.,c Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonose , Yangzhou , P.R.China
| | - Jianxun Luo
- b State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Science , Lanzhou , P.R.China
| | - Guangyuan Liu
- b State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Science , Lanzhou , P.R.China
| | - Qiang Zhao
- a College of Life Sciences , Nankai University , Tianjin , P.R.China
| | - Ze Chen
- b State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Science , Lanzhou , P.R.China
| | - Wenjun Bu
- a College of Life Sciences , Nankai University , Tianjin , P.R.China
| | - Shan Gao
- a College of Life Sciences , Nankai University , Tianjin , P.R.China
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