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Choi Y, Shin E, Lee M, Yeom JH, Lee K. Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species. PLoS One 2023; 18:e0289072. [PMID: 38051731 DOI: 10.1371/journal.pone.0289072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/10/2023] [Indexed: 12/07/2023] Open
Abstract
Heterogeneity of ribosomal RNA (rRNA) sequences has recently emerged as a mechanism that can lead to subpopulations of specialized ribosomes. Our previous study showed that ribosomes containing highly divergent rRNAs expressed from the rrnI operon (I-ribosomes) can preferentially translate a subset of mRNAs such as hspA and tpiA in the Vibrio vulnificus CMCP6 strain. Here, we explored the functional conservation of I-ribosomes across Vibrio species. Exogenous expression of the rrnI operon in another V. vulnificus strain, MO6-24/O, and in another Vibrio species, V. fischeri (strain MJ11), decreased heat shock susceptibility by upregulating HspA expression. In addition, we provide direct evidence for the preferential synthesis of HspA by I-ribosomes in the V. vulnificus MO6-24/O strain. Furthermore, exogenous expression of rrnI in V. vulnificus MO6-24/O cells led to higher mortality of infected mice when compared to the wild-type (WT) strain and a strain expressing exogenous rrnG, a redundant rRNA gene in the V. vulnificus CMCP6 strain. Our findings suggest that specialized ribosomes bearing heterogeneous rRNAs play a conserved role in translational regulation among Vibrio species. This study shows the functional importance of rRNA heterogeneity in gene expression control by preferential translation of specific mRNAs, providing another layer of specialized ribosome system.
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Affiliation(s)
- Younkyung Choi
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Eunkyoung Shin
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Minho Lee
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
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2
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Harl J, Himmel T, Ilgūnas M, Valkiūnas G, Weissenböck H. The 18S rRNA genes of Haemoproteus (Haemosporida, Apicomplexa) parasites from European songbirds with remarks on improved parasite diagnostics. Malar J 2023; 22:232. [PMID: 37563610 PMCID: PMC10416517 DOI: 10.1186/s12936-023-04661-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND The nuclear ribosomal RNA genes of Plasmodium parasites are assumed to evolve according to a birth-and-death model with new variants originating by duplication and others becoming deleted. For some Plasmodium species, it has been shown that distinct variants of the 18S rRNA genes are expressed differentially in vertebrate hosts and mosquito vectors. The central aim was to evaluate whether avian haemosporidian parasites of the genus Haemoproteus also have substantially distinct 18S variants, focusing on lineages belonging to the Haemoproteus majoris and Haemoproteus belopolskyi species groups. METHODS The almost complete 18S rRNA genes of 19 Haemoproteus lineages of the subgenus Parahaemoproteus, which are common in passeriform birds from the Palaearctic, were sequenced. The PCR products of 20 blood and tissue samples containing 19 parasite lineages were subjected to molecular cloning, and ten clones in mean were sequenced each. The sequence features were analysed and phylogenetic trees were calculated, including sequence data published previously from eight additional Parahaemoproteus lineages. The geographic and host distribution of all 27 lineages was visualised as CytB haplotype networks and pie charts. Based on the 18S sequence data, species-specific oligonucleotide probes were designed to target the parasites in host tissue by in situ hybridization assays. RESULTS Most Haemoproteus lineages had two or more variants of the 18S gene like many Plasmodium species, but the maximum distances between variants were generally lower. Moreover, unlike in most mammalian and avian Plasmodium species, the 18S sequences of all but one parasite lineage clustered into reciprocally monophyletic clades. Considerably distinct 18S clusters were only found in Haemoproteus tartakovskyi hSISKIN1 and Haemoproteus sp. hROFI1. The presence of chimeric 18S variants in some Haemoproteus lineages indicates that their ribosomal units rather evolve in a semi-concerted fashion than according to a strict model of birth-and-death evolution. CONCLUSIONS Parasites of the subgenus Parahaemoproteus contain distinct 18S variants, but the intraspecific variability is lower than in most mammalian and avian Plasmodium species. The new 18S data provides a basis for more thorough investigations on the development of Haemoproteus parasites in host tissue using in situ hybridization techniques targeting specific parasite lineages.
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Affiliation(s)
- Josef Harl
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Tanja Himmel
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | | | - Herbert Weissenböck
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
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3
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Gavrilova AA, Fefilova AS, Vishnyakov IE, Kuznetsova IM, Turoverov KK, Uversky VN, Fonin AV. On the Roles of the Nuclear Non-Coding RNA-Dependent Membrane-Less Organelles in the Cellular Stress Response. Int J Mol Sci 2023; 24:ijms24098108. [PMID: 37175815 PMCID: PMC10179167 DOI: 10.3390/ijms24098108] [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: 03/26/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
At the beginning of the 21st century, it became obvious that radical changes had taken place in the concept of living matter and, in particular, in the concept of the organization of intracellular space. The accumulated data testify to the essential importance of phase transitions of biopolymers (first of all, intrinsically disordered proteins and RNA) in the spatiotemporal organization of the intracellular space. Of particular interest is the stress-induced reorganization of the intracellular space. Examples of organelles formed in response to stress are nuclear A-bodies and nuclear stress bodies. The formation of these organelles is based on liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) and non-coding RNA. Despite their overlapping composition and similar mechanism of formation, these organelles have different functional activities and physical properties. In this review, we will focus our attention on these membrane-less organelles (MLOs) and describe their functions, structure, and mechanism of formation.
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Affiliation(s)
- Anastasia A Gavrilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Anna S Fefilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Innokentii E Vishnyakov
- Group of Molecular Cytology of Prokaryotes and Bacterial Invasion, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
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Cao L, Chen P, Hou X, Ma J, Yang N, Xu Y, Zhang Y, Zhao A, Zhang J, Li X, Huang H. Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) × Epinephelus polyphekadion (male). JOURNAL OF FISH BIOLOGY 2023; 102:328-339. [PMID: 36317644 DOI: 10.1111/jfb.15263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Hybridization is one of the primary methods used to cultivate farmed grouper species. The hybrid grouper derived from crossing Epinephelus fuscoguttatus (♀) and E. polyphekadion (♂) exhibits growth superiority over its parents. The genetic characteristics and growth patterns of the hybrid grouper have not yet been defined. This study confirms the ploidy level of the hybrid grouper (2n = 48) using chromosome count analysis and flow cytometry. The 5S rDNA family was used to evaluate genetic diversity. Only one 5S class (~400 bp) was detected in the hybrid grouper, which could be used to distinguish between two different types based on nucleotide sequences, likely representing homologous unit classes from the female and male parental species. Growth patterns of 5-8-month-old hybrid groupers were also monitored. In this phase, a positive allometric growth pattern in body mass with total length was found. Body height and body mass were significantly correlated based on correlation and path coefficient, suggesting that body height could serve as an excellent index to increase body mass. These results aid our understanding of the genetic evolution of the hybrid grouper and inform the development of improved rearing techniques.
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Affiliation(s)
- Liu Cao
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Pan Chen
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Xingrong Hou
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Jun Ma
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Ning Yang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
| | - Yanping Xu
- Hainan Tropical Ocean University, Sanya, China
| | | | - Anqi Zhao
- Hainan Tropical Ocean University, Sanya, China
| | | | - Xinyu Li
- Hainan Tropical Ocean University, Sanya, China
| | - Hai Huang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Sanya, China
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Sanya, China
- Yazhou Bay Innovation Institute, Sanya, China
- Hainan Tropical Ocean University, Sanya, China
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Choi Y, Joo M, Song W, Lee M, Hyeon H, Kim HL, Yeom JH, Lee K, Shin E. Transcript-specific selective translation by specialized ribosomes bearing genome-encoded heterogeneous rRNAs in V. vulnificus CMCP6. J Microbiol 2022; 60:1162-1167. [PMID: 36422844 DOI: 10.1007/s12275-022-2437-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Ribosomes composed of genome-encoded heterogeneous rRNAs are implicated in the rapid adaptation of bacterial cells to environmental changes. A previous study showed that ribosomes bearing the most heterogeneous rRNAs expressed from the rrnI operon (I-ribosomes) are implicated in the preferential translation of a subset of mRNAs, including hspA and tpiA, in Vibrio vulnificus CMCP6. In this study, we show that HspA nascent peptides were predominantly bound to I-ribosomes. Specifically, I-ribosomes were enriched more than two-fold in ribosomes that were pulled down by immunoprecipitation of HspA peptides compared with the proportion of I-ribosomes in crude ribosomes and ribosomes pulled down by immunoprecipitation of RNA polymerase subunit β peptides in the wild-type (WT) and rrnI-completed strains. Other methods that utilized the incorporation of an affinity tag in 23S rRNA or chimeric rRNA tethering 16S and 23S rRNAs, which generated specialized functional ribosomes in Escherichia coli, did not result in functional I-ribosomes in V. vulnificus CMCP6. This study provides direct evidence of the preferential translation of hspA mRNA by I-ribosomes.
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Affiliation(s)
- Younkyung Choi
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minju Joo
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Wooseok Song
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minho Lee
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, 24252, Republic of Korea
| | - Hana Hyeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyun-Lee Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Eunkyoung Shin
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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Volkov RA, Borisjuk N, Garcia S, Kovařík A, Sáez-Vásquez J. Editorial: Molecular organization, evolution, and function of ribosomal DNA. FRONTIERS IN PLANT SCIENCE 2022; 13:994380. [PMID: 35991440 PMCID: PMC9386555 DOI: 10.3389/fpls.2022.994380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Roman A. Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake and Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, School of Life Sciences, Huaiyin Normal University, Huai'an, China
| | - Sònia Garcia
- Institut Botànic de Barcelona - Consejo Superior de Investigaciones Cientificas(IBB-CSIC), Barcelona, Spain
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, Perpignan, France
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Tynkevich YO, Shelyfist AY, Kozub LV, Hemleben V, Panchuk II, Volkov RA. 5S Ribosomal DNA of Genus Solanum: Molecular Organization, Evolution, and Taxonomy. FRONTIERS IN PLANT SCIENCE 2022; 13:852406. [PMID: 35498650 PMCID: PMC9043955 DOI: 10.3389/fpls.2022.852406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
The Solanum genus, being one of the largest among high plants, is distributed worldwide and comprises about 1,200 species. The genus includes numerous agronomically important species such as Solanum tuberosum (potato), Solanum lycopersicum (tomato), and Solanum melongena (eggplant) as well as medical and ornamental plants. The huge Solanum genus is a convenient model for research in the field of molecular evolution and structural and functional genomics. Clear knowledge of evolutionary relationships in the Solanum genus is required to increase the effectiveness of breeding programs, but the phylogeny of the genus is still not fully understood. The rapidly evolving intergenic spacer region (IGS) of 5S rDNA has been successfully used for inferring interspecific relationships in several groups of angiosperms. Here, combining cloning and sequencing with bioinformatic analysis of genomic data available in the SRA database, we evaluate the molecular organization and diversity of IGS for 184 accessions, representing 137 species of the Solanum genus. It was found that the main mechanisms of IGS molecular evolution was step-wise accumulation of single base substitution or short indels, and that long indels and multiple base substitutions, which arose repeatedly during evolution, were mostly not conserved and eliminated. The reason for this negative selection seems to be association between indels/multiple base substitutions and pseudogenization of 5S rDNA. Comparison of IGS sequences allowed us to reconstruct the phylogeny of the Solanum genus. The obtained dendrograms are mainly congruent with published data: same major and minor clades were found. However, relationships between these clades and position of some species (S. cochoae, S. clivorum, S. macrocarpon, and S. spirale) were different from those of previous results and require further clarification. Our results show that 5S IGS represents a convenient molecular marker for phylogenetic studies on the Solanum genus. In particular, the simultaneous presence of several structural variants of rDNA in the genome enables the detection of reticular evolution, especially in the largest and economically most important sect. Petota. The origin of several polyploid species should be reconsidered.
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Affiliation(s)
- Yurij O. Tynkevich
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Antonina Y. Shelyfist
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Liudmyla V. Kozub
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Vera Hemleben
- Center of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Irina I. Panchuk
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
- Center of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Roman A. Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
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Joo M, Yeom JH, Choi Y, Jun H, Song W, Kim HL, Lee K, Shin E. Specialised ribosomes as versatile regulators of gene expression. RNA Biol 2022; 19:1103-1114. [PMID: 36255182 PMCID: PMC9586635 DOI: 10.1080/15476286.2022.2135299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The ribosome has long been thought to be a homogeneous cellular machine that constitutively and globally synthesises proteins from mRNA. However, recent studies have revealed that ribosomes are highly heterogeneous, dynamic macromolecular complexes with specialised roles in translational regulation in many organisms across the kingdoms. In this review, we summarise the current understanding of ribosome heterogeneity and the specialised functions of heterogeneous ribosomes. We also discuss specialised translation systems that utilise orthogonal ribosomes.
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Affiliation(s)
- Minju Joo
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Ji-Hyun Yeom
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Younkyung Choi
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyeon Jun
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Wooseok Song
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyun-Lee Kim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Eunkyoung Shin
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
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Spangenberg V, Losev M, Volkhin I, Smirnova S, Nikitin P, Kolomiets O. DNA Environment of Centromeres and Non-Homologous Chromosomes Interactions in Mouse. Cells 2021; 10:3375. [PMID: 34943883 PMCID: PMC8699862 DOI: 10.3390/cells10123375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
Although the pericentromeric regions of chromosomes that are enriched in tandemly repeated satellite DNA represent a significant part of eukaryotic genomes, they remain understudied, which is mainly due to interdisciplinary knowledge gaps. Recent studies suggest their important role in genome regulation, karyotype stability, and evolution. Thus, the idea of satellite DNA as a junk part of the genome has been refuted. The integration of data regarding molecular composition, chromosome behaviour, and the details of the in situ organization of pericentromeric regions is of great interest. The objective of this work was a cytogenetic analysis of the interactions between pericentromeric regions from non-homologous chromosomes in mouse spermatocytes using immuno-FISH. We analysed two events: the associations between centromeric regions of the X chromosome and autosomes and the associations between the centromeric regions of the autosomal bivalents that form chromocenters. We concluded that the X chromosome forms temporary synaptic associations with different autosomes in early meiotic prophase I, which can normally be found until the pachytene-diplotene, without signs of pachytene arrest. These associations are formed between the satellite-DNA-rich centromeric regions of the X chromosome and different autosomes but do not involve the satellite-DNA-poor centromeric region of the Y chromosome. We suggest the hypothetical model of X chromosome competitive replacement from such associations during synaptic correction. We showed that the centromeric region of the X chromosome in association remains free of γH2Ax-dependent chromatin inactivation, while the Y chromosome is completely inactivated. This finding highlights the predominant role of associations between satellite DNA-rich regions of different chromosomes, including the X chromosome. We suppose that X-autosomal transient associations are a manifestation of an additional synaptic disorder checkpoint. These associations are normally corrected before the late diplotene stage. We revealed that the intense spreading conditions that were applied to the spermatocyte I nuclei did not lead to the destruction of stretched chromatin fibers of elongated chromocenters enriched in satellite DNA. The tight associations that we revealed between the pericentromeric regions of different autosomal bivalents and the X chromosome may represent the basis for a mechanism for maintaining the repeats stability in the autosomes and in the X chromosome. The consequences of our findings are discussed.
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Affiliation(s)
- Victor Spangenberg
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (M.L.); (I.V.); (S.S.); (P.N.); (O.K.)
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10
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Haig D. Concerted evolution of ribosomal DNA: Somatic peace amid germinal strife: Intranuclear and cellular selection maintain the quality of rRNA. Bioessays 2021; 43:e2100179. [PMID: 34704616 DOI: 10.1002/bies.202100179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/12/2021] [Indexed: 11/10/2022]
Abstract
Most eukaryotes possess many copies of rDNA. Organismal selection alone cannot maintain rRNA function because the effects of mutations in one rDNA are diluted by the presence of many other rDNAs. rRNA quality is maintained by processes that increase homogeneity of rRNA within, and heterogeneity among, germ cells thereby increasing the effectiveness of cellular selection on ribosomal function. A successful rDNA repeat will possess adaptations for spreading within tandem arrays by intranuclear selection. These adaptations reside in the non-coding regions of rDNA. Single-copy genes are predicted to manage processes of intranuclear and cellular selection in the germline to maintain the quality of rRNA expressed in somatic cells of future generations.
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Affiliation(s)
- David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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11
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Regulatory roles of nucleolus organizer region-derived long non-coding RNAs. Mamm Genome 2021; 33:402-411. [PMID: 34436664 DOI: 10.1007/s00335-021-09906-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022]
Abstract
The nucleolus is the largest sub-nuclear domain, serving primarily as the place for ribosome biogenesis. A delicately regulated function of the nucleolus is vital to the cell not only for maintaining proper protein synthesis but is also tightly associated with responses to different types of cellular stresses. Recently, several long non-coding RNAs (lncRNAs) were found to be part of the regulatory network that modulate nucleolar functions. Several of these lncRNAs are encoded in the ribosomal DNA (rDNA) repeats or are transcribed from the genomic regions that are located near the nucleolus organizer regions (NORs). In this review, we first discuss the current understanding of the sequence of the NORs and variations between different NORs. We then focus on the NOR-derived lncRNAs in mammalian cells and their functions in rRNA transcription and the organization of nucleolar structure under different cellular conditions. The identification of these lncRNAs reveals great potential of the NORs in harboring novel genes involved in the regulation of nucleolar functions.
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Prahl RE, Khan S, Deo RC. The role of internal transcribed spacer 2 secondary structures in classifying mycoparasitic Ampelomyces. PLoS One 2021; 16:e0253772. [PMID: 34191835 PMCID: PMC8244850 DOI: 10.1371/journal.pone.0253772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/13/2021] [Indexed: 11/19/2022] Open
Abstract
Many fungi require specific growth conditions before they can be identified. Direct environmental DNA sequencing is advantageous, although for some taxa, specific primers need to be used for successful amplification of molecular markers. The internal transcribed spacer region is the preferred DNA barcode for fungi. However, inter- and intra-specific distances in ITS sequences highly vary among some fungal groups; consequently, it is not a solely reliable tool for species delineation. Ampelomyces, mycoparasites of the fungal phytopathogen order Erysiphales, can have ITS genetic differences up to 15%; this may lead to misidentification with other closely related unknown fungi. Indeed, Ampelomyces were initially misidentified as other pycnidial mycoparasites, but subsequent research showed that they differ in pycnidia morphology and culture characteristics. We investigated whether the ITS2 nucleotide content and secondary structure was different between Ampelomyces ITS2 sequences and those unrelated to this genus. To this end, we retrieved all ITS sequences referred to as Ampelomyces from the GenBank database. This analysis revealed that fungal ITS environmental DNA sequences are still being deposited in the database under the name Ampelomyces, but they do not belong to this genus. We also detected variations in the conserved hybridization model of the ITS2 proximal 5.8S and 28S stem from two Ampelomyces strains. Moreover, we suggested for the first time that pseudogenes form in the ITS region of this mycoparasite. A phylogenetic analysis based on ITS2 sequences-structures grouped the environmental sequences of putative Ampelomyces into a different clade from the Ampelomyces-containing clades. Indeed, when conducting ITS2 analysis, resolution of genetic distances between Ampelomyces and those putative Ampelomyces improved. Each clade represented a distinct consensus ITS2 S2, which suggested that different pre-ribosomal RNA (pre-rRNA) processes occur across different lineages. This study recommends the use of ITS2 S2s as an important tool to analyse environmental sequencing and unveiling the underlying evolutionary processes.
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Affiliation(s)
- Rosa E. Prahl
- School of Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia
- * E-mail:
| | - Shahjahan Khan
- School of Sciences, Centre for Health Research, Centre for Applied Climate Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Ravinesh C. Deo
- School of Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia
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Krak K, Caklová P, Kopecký D, Blattner FR, Mahelka V. Horizontally Acquired nrDNAs Persist in Low Amounts in Host Hordeum Genomes and Evolve Independently of Native nrDNA. FRONTIERS IN PLANT SCIENCE 2021; 12:672879. [PMID: 34079572 PMCID: PMC8165317 DOI: 10.3389/fpls.2021.672879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Nuclear ribosomal DNA (nrDNA) has displayed extraordinary dynamics during the evolution of plant species. However, the patterns and evolutionary significance of nrDNA array expansion or contraction are still relatively unknown. Moreover, only little is known of the fate of minority nrDNA copies acquired between species via horizontal transfer. The barley genus Hordeum (Poaceae) represents a good model for such a study, as species of section Stenostachys acquired nrDNA via horizontal transfer from at least five different panicoid genera, causing long-term co-existence of native (Hordeum-like) and non-native (panicoid) nrDNAs. Using quantitative PCR, we investigated copy number variation (CNV) of nrDNA in the diploid representatives of the genus Hordeum. We estimated the copy number of the foreign, as well as of the native ITS types (ribotypes), and followed the pattern of their CNV in relation to the genus' phylogeny, species' genomes size and the number of nrDNA loci. For the native ribotype, we encountered an almost 19-fold variation in the mean copy number among the taxa analysed, ranging from 1689 copies (per 2C content) in H. patagonicum subsp. mustersii to 31342 copies in H. murinum subsp. glaucum. The copy numbers did not correlate with any of the genus' phylogeny, the species' genome size or the number of nrDNA loci. The CNV was high within the recognised groups (up to 13.2 × in the American I-genome species) as well as between accessions of the same species (up to 4×). Foreign ribotypes represent only a small fraction of the total number of nrDNA copies. Their copy numbers ranged from single units to tens and rarely hundreds of copies. They amounted, on average, to between 0.1% (Setaria ribotype) and 1.9% (Euclasta ribotype) of total nrDNA. None of the foreign ribotypes showed significant differences with respect to phylogenetic groups recognised within the sect. Stenostachys. Overall, no correlation was found between copy numbers of native and foreign nrDNAs suggesting the sequestration and independent evolution of native and non-native nrDNA arrays. Therefore, foreign nrDNA in Hordeum likely poses a dead-end by-product of horizontal gene transfer events.
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Affiliation(s)
- Karol Krak
- Czech Academy of Sciences, Institute of Botany, Prùhonice, Czechia
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague 6, Czechia
| | - Petra Caklová
- Czech Academy of Sciences, Institute of Botany, Prùhonice, Czechia
| | - David Kopecký
- Czech Academy of Sciences, Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Frank R. Blattner
- Experimental Taxonomy, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- German Centre of Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig, Leipzig, Germany
| | - Václav Mahelka
- Czech Academy of Sciences, Institute of Botany, Prùhonice, Czechia
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14
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Macey JR, Pabinger S, Barbieri CG, Buring ES, Gonzalez VL, Mulcahy DG, DeMeo DP, Urban L, Hime PM, Prost S, Elliott AN, Gemmell NJ. Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization. Commun Biol 2021; 4:116. [PMID: 33514857 PMCID: PMC7846811 DOI: 10.1038/s42003-020-01639-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023] Open
Abstract
Animal mitochondrial genomic polymorphism occurs as low-level mitochondrial heteroplasmy and deeply divergent co-existing molecules. The latter is rare, known only in bivalvian mollusks. Here we show two deeply divergent co-existing mt-genomes in a vertebrate through genomic sequencing of the Tuatara (Sphenodon punctatus), the sole-representative of an ancient reptilian Order. The two molecules, revealed using a combination of short-read and long-read sequencing technologies, differ by 10.4% nucleotide divergence. A single long-read covers an entire mt-molecule for both strands. Phylogenetic analyses suggest a 7-8 million-year divergence between genomes. Contrary to earlier reports, all 37 genes typical of animal mitochondria, with drastic gene rearrangements, are confirmed for both mt-genomes. Also unique to vertebrates, concerted evolution drives three near-identical putative Control Region non-coding blocks. Evidence of positive selection at sites linked to metabolically important transmembrane regions of encoded proteins suggests these two mt-genomes may confer an adaptive advantage for an unusually cold-tolerant reptile.
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Affiliation(s)
- J Robert Macey
- Peralta Genomics Institute, Chancellor's Office, Peralta Community College District, 333 East 8th Street, Oakland, CA, 94606, USA.
| | - Stephan Pabinger
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Molecular Diagnostics, Giefinggasse 4, 1210, Vienna, Austria
| | - Charles G Barbieri
- Peralta Genomics Institute, Chancellor's Office, Peralta Community College District, 333 East 8th Street, Oakland, CA, 94606, USA
| | - Ella S Buring
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Ave., Washington, DC, 20560, USA
| | - Vanessa L Gonzalez
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Ave., Washington, DC, 20560, USA
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Ave., Washington, DC, 20560, USA
| | - Dustin P DeMeo
- Peralta Genomics Institute, Chancellor's Office, Peralta Community College District, 333 East 8th Street, Oakland, CA, 94606, USA
| | - Lara Urban
- Department of Anatomy, University of Otago, PO Box 913, Dunedin, 9054, New Zealand
| | - Paul M Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS, 66045, USA
| | - Stefan Prost
- LOEWE-Center for Translational Biodiversity Genomics, Senckenberg Museum, 60325, Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, 0184, South Africa
| | - Aaron N Elliott
- Peralta Genomics Institute, Chancellor's Office, Peralta Community College District, 333 East 8th Street, Oakland, CA, 94606, USA
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, PO Box 913, Dunedin, 9054, New Zealand
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15
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Mullis A, Lu Z, Zhan Y, Wang TY, Rodriguez J, Rajeh A, Chatrath A, Lin Z. Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance. Mol Biol Evol 2020; 37:455-468. [PMID: 31589316 PMCID: PMC6993855 DOI: 10.1093/molbev/msz229] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ribosomal protein (RP) genes encode structural components of ribosomes, the cellular machinery for protein synthesis. A single functional copy has been maintained in most of 78–80 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some fungal species have maintained duplicate copies in most RP families. The mechanisms by which the RP genes were duplicated and maintained and their functional significance are poorly understood. To address these questions, we identified all RP genes from 295 fungi and inferred the timing and nature of gene duplication events for all RP families. We found that massive duplications of RP genes have independently occurred by different mechanisms in three distantly related lineages: budding yeasts, fission yeasts, and Mucoromycota. The RP gene duplicates in budding yeasts and Mucoromycota were mainly created by whole genome duplication events. However, duplicate RP genes in fission yeasts were likely generated by retroposition, which is unexpected considering their dosage sensitivity. The sequences of most RP paralogs have been homogenized by repeated gene conversion in each species, demonstrating parallel concerted evolution, which might have facilitated the retention of their duplicates. Transcriptomic data suggest that the duplication and retention of RP genes increased their transcript abundance. Physiological data indicate that increased ribosome biogenesis allowed these organisms to rapidly consume sugars through fermentation while maintaining high growth rates, providing selective advantages to these species in sugar-rich environments.
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Affiliation(s)
- Alison Mullis
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Zhaolian Lu
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Yu Zhan
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Judith Rodriguez
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO
| | - Ahmad Rajeh
- Department of Biology, Saint Louis University, St. Louis, MO.,Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO
| | - Ajay Chatrath
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO
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16
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Løken SB, Skrede I, Schumacher T. The Helvella corium species aggregate in Nordic countries - phylogeny and species delimitation. Fungal Syst Evol 2020; 5:169-186. [PMID: 32467922 PMCID: PMC7250015 DOI: 10.3114/fuse.2020.05.11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mycologists have always been curious about the elaborate morphotypes and shapes of species of the genus Helvella. The small, black, cupulate Helvella specimens have mostly been assigned to Helvella corium, a broadly defined morpho-species. Recent phylogenetic analyses, however, have revealed an aggregate of species hidden under this name. We performed a multispecies coalescent analysis to re-assess species limits and evolutionary relationships of the Helvella corium species aggregate in the Nordic countries. To achieve this, we used morphology and phylogenetic evidence from five loci – heat shock protein 90 (hsp), translation elongation factor 1-alpha (tef), RNA polymerase II (rpb2), and the 5.8S and large subunit (LSU) of the nuclear ribosomal DNA. All specimens under the name Helvella corium in the larger university fungaria of Norway, Sweden and Denmark were examined and barcoded, using partial hsp and/or rpb2 as the preferential secondary barcodes in Helvella. Additional fresh specimens were collected in three years (2015–2018) to obtain in vivo morphological data to aid in species discrimination. The H. corium species aggregate consists of seven phylogenetically distinct species, nested in three divergent lineages, i.e. H. corium, H. alpina and H. pseudoalpina sp. nov. in the /alpina-corium lineage, H. alpestris, H. macrosperma and H. nannfeldtii in the /alpestris-nannfeldtii lineage, and H. alpicola as a weakly supported sister to the /alpestris-nannfeldtii lineage. Among the seven species, the ribosomal loci expressed substantial variation in evolutionary rates, suggesting care in the use of these regions alone in delimitation of Helvella species. Altogether, 469 out of 496 available fungarium specimens were successfully barcoded.
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Affiliation(s)
- S B Løken
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316 Oslo, Norway
| | - I Skrede
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316 Oslo, Norway
| | - T Schumacher
- Department of Biosciences, University of Oslo, P.O. Box 1066, 0316 Oslo, Norway
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17
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Chromosome Dynamics Regulating Genomic Dispersion and Alteration of Nucleolus Organizer Regions (NORs). Cells 2020; 9:cells9040971. [PMID: 32326514 PMCID: PMC7227013 DOI: 10.3390/cells9040971] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023] Open
Abstract
The nucleolus organizer regions (NORs) demonstrate differences in genomic dispersion and transcriptional activity among all organisms. I postulate that such differences stem from distinct genomic structures and their interactions from chromosome observations using fluorescence in situ hybridization and silver nitrate staining methods. Examples in primates and Australian bulldog ants indicate that chromosomal features indeed play a significant role in determining the properties of NORs. In primates, rDNA arrays that are located on the short arm of acrocentrics frequently form reciprocal associations ("affinity"), but they lack such associations ("non-affinity") with other repeat arrays-a binary molecular effect. These "rules" of affinity vs. non-affinity are extrapolated from the chromosomal configurations of meiotic prophase. In bulldog ants, genomic dispersions of rDNA loci expand much more widely following an increase in the number of acrocentric chromosomes formed by centric fission. Affinity appears to be a significantly greater force: associations likely form among rDNA and heterochromatin arrays of acrocentrics-thus, more acrocentrics bring about more rDNA loci. The specific interactions among NOR-related genome structures remain unclear and require further investigation. Here, I propose that there are limited and non-limited genomic dispersion systems that result from genomic affinity rules, inducing specific chromosomal configurations that are related to NORs.
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18
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Qing X, Bik H, Yergaliyev TM, Gu J, Fonderie P, Brown-Miyara S, Szitenberg A, Bert W. Widespread prevalence but contrasting patterns of intragenomic rRNA polymorphisms in nematodes: Implications for phylogeny, species delimitation and life history inference. Mol Ecol Resour 2019; 20:318-332. [PMID: 31721426 DOI: 10.1111/1755-0998.13118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 10/26/2019] [Accepted: 11/07/2019] [Indexed: 01/15/2023]
Abstract
Ribosomal RNA genes have long been a favoured locus in phylogenetic and metabarcoding studies. Within a genome, rRNA loci are organized as tandem repeated arrays and the copies are homogenized through the process of concerted evolution. However, some level of rRNA variation (intragenomic polymorphism) is known to persist and be maintained in the genomes of many species. In nematode worms, the extent of rRNA polymorphism (RP) across species and the evolutionary and life history factors that contribute to the maintenance of intragenomic RP is largely unknown. Here, we present an extensive analysis across 30 terrestrial nematode species representing a range of free-living and parasitic taxa isolated worldwide. Our results indicate that RP is common and widespread, ribosome function appears to be maintained despite mutational changes, and intragenomic variants are stable in the genome and neutrally evolving. However, levels of variation were varied widely across rRNA locus and species, with some taxa observed to lack RP entirely. Higher levels of RP were significantly correlated with shorter generation time and high reproductive rates, and population-level factors may play a role in the geographic and phylogenetic structuring of rRNA variants observed in genera such as Rotylenchulus and Pratylenchus. Although RP did not dramatically impact the clustering and recovery of taxa in mock metabarcoding analyses, the present study has significant implications for global biodiversity estimates of nematode species derived from environmental rRNA amplicon studies, as well as our understanding of the evolutionary and ecological factors shaping genetic diversity across the nematode Tree of Life.
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Affiliation(s)
- Xue Qing
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium.,Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion, Israel
| | - Holly Bik
- Department of Nematology, University of California-Riverside, Riverside, CA, USA
| | - Timur M Yergaliyev
- Dead Sea and Arava Science Center, Dead Sea Branch, Masada National Park, Tamar Regional Council, Tel Aviv, Israel.,A. Baitursynov Kostanay State University, Kostanay, Kazakhstan
| | - Jianfeng Gu
- Technical Center of Ningbo Customs (Ningbo Inspection and Quarantine Science Technology Academy), Ningbo, China
| | - Pamela Fonderie
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sigal Brown-Miyara
- Department of Entomology, Nematology and Chemistry Units, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion, Israel
| | - Amir Szitenberg
- Dead Sea and Arava Science Center, Dead Sea Branch, Masada National Park, Tamar Regional Council, Tel Aviv, Israel
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, Ghent, Belgium
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19
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Harl J, Himmel T, Valkiūnas G, Weissenböck H. The nuclear 18S ribosomal DNAs of avian haemosporidian parasites. Malar J 2019; 18:305. [PMID: 31481072 PMCID: PMC6724295 DOI: 10.1186/s12936-019-2940-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/27/2019] [Indexed: 01/19/2023] Open
Abstract
Background Plasmodium species feature only four to eight nuclear ribosomal units on different chromosomes, which are assumed to evolve independently according to a birth-and-death model, in which new variants originate by duplication and others are deleted throughout time. Moreover, distinct ribosomal units were shown to be expressed during different developmental stages in the vertebrate and mosquito hosts. Here, the 18S rDNA sequences of 32 species of avian haemosporidian parasites are reported and compared to those of simian and rodent Plasmodium species. Methods Almost the entire 18S rDNAs of avian haemosporidians belonging to the genera Plasmodium (7), Haemoproteus (9), and Leucocytozoon (16) were obtained by PCR, molecular cloning, and sequencing ten clones each. Phylogenetic trees were calculated and sequence patterns were analysed and compared to those of simian and rodent malaria species. A section of the mitochondrial CytB was also sequenced. Results Sequence patterns in most avian Plasmodium species were similar to those in the mammalian parasites with most species featuring two distinct 18S rDNA sequence clusters. Distinct 18S variants were also found in Haemoproteus tartakovskyi and the three Leucocytozoon species, whereas the other species featured sets of similar haplotypes. The 18S rDNA GC-contents of the Leucocytozoon toddi complex and the subgenus Parahaemoproteus were extremely high with 49.3% and 44.9%, respectively. The 18S sequences of several species from all three genera showed chimeric features, thus indicating recombination. Conclusion Gene duplication events leading to two diverged main sequence clusters happened independently in at least six out of seven avian Plasmodium species, thus supporting evolution according to a birth-and-death model like proposed for the ribosomal units of simian and rodent Plasmodium species. Patterns were similar in the 18S rDNAs of the Leucocytozoon toddi complex and Haemoproteus tartakovskyi. However, the 18S rDNAs of the other species seem to evolve in concerted fashion like in most eukaryotes, but the presence of chimeric variants indicates that the ribosomal units rather evolve in a semi-concerted manner. The new data may provide a basis for studies testing whether differential expression of distinct 18S rDNA also occurs in avian Plasmodium species and related haemosporidian parasites.
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Affiliation(s)
- Josef Harl
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Tanja Himmel
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | | | - Herbert Weissenböck
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria.
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20
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Hirai H, Hirai Y, Udono T, Matsubayashi K, Tosi AJ, Koga A. Structural variations of subterminal satellite blocks and their source mechanisms as inferred from the meiotic configurations of chimpanzee chromosome termini. Chromosome Res 2019; 27:321-332. [PMID: 31418128 DOI: 10.1007/s10577-019-09615-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/09/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
Abstract
African great apes have large constitutive heterochromatin (C-band) blocks in subtelomeric regions of the majority of their chromosomes, but humans lack these. Additionally, the chimpanzee meiotic cell division process demonstrates unique partial terminal associations in the first meiotic prophase (pachytene). These are likely formed as a result of interaction among subtelomeric C-band blocks. We thus conducted an extensive study to define the features in the subtelomeric heterochromatic regions of chimpanzee chromosomes undergoing mitotic metaphase and meiotic cell division. Molecular cytogenetic analyses with probes of both subterminal satellite DNA (a main component of C-band) and rDNA demonstrated principles of interaction among DNA arrays. The results suggest that homologous and ectopic recombination through persistent subtelomeric associations (post-bouquet association observed in 32% of spermatocytes in the pachytene stage) appears to create variability in heterochromatin patterns and simultaneously restrain subtelomeric genome polymorphisms. That is, the meeting of non-homologous chromosome termini sets the stage for ectopic pairing which, in turn, is the mechanism for generating variability and genomic dispersion of subtelomeric C-band blocks through a system of concerted evolution. Comparison between the present study and previous reports indicated that the chromosomal distribution rate of sutelomeric regions seems to have antagonistic correlation with arm numbers holding subterminal satellite blocks in humans, chimpanzees, and gorillas. That is, the increase of subterminal satellite blocks probably reduces genomic diversity in the subtelomeric regions. The acquisition vs. loss of the subtelomeric C-band blocks is postulated as the underlying engine of this chromosomal differentiation yielded by meiotic chromosomal interaction.
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Affiliation(s)
- Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan. .,The Unit of Human-Nature Interlaced Life Science, Kyoto University Research Coordination Alliance, Kyoto, Japan.
| | - Yuriko Hirai
- Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Toshifumi Udono
- Kumamoto Sanctuary, Wildlife Research Center, Kyoto University, Uto, Kumamoto, Japan
| | | | - Anthony J Tosi
- Department of Anthropology and School of Biomedical Science, Kent State University, Kent, OH, 44242, USA
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
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21
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Analysis of genetic diversity and phylogeny of Philosamia ricini (Lepidoptera: Saturniidae) by using RAPD and internal transcribed spacer DNA1. Mol Biol Rep 2019; 46:3035-3048. [PMID: 30868343 DOI: 10.1007/s11033-019-04740-8] [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: 10/20/2018] [Accepted: 03/03/2019] [Indexed: 10/27/2022]
Abstract
The Indian Eri silkworm, Philosamia ricini Hutt, a commercial silk producing insect, is believed to have originated in the Brahmaputra valley of Assam. In this study, the genetic diversity and phylogenetic relationships of six morphs of Eri silkworm viz. white plain, white zebra, white spotted, blue plain, blue zebra and blue spotted collected from different geographical locations of North-East India were investigated by using random amplified polymorphic DNA (RAPD) and the first internal transcribed spacer region (ITS1). This study revealed a low genetic diversity among the morphs of Eri silkworm. Twenty-eight random primers generated 199 bands. Out of these, 112 were polymorphic (56.28%) with an average of 7.1 bands per primer. The genetic similarity matrix ranged from 0.56 to 0.99. The morphs collected from same geographical area shared the same cluster in the dendrogram. The genetic diversity in case of ITS1 sequences (2.19%) was found to be less as compared to RAPD. The ITS1 sequences of the morphs collected from same geographical area were found to be identical. The information generated in this study will help in conservation and effective breeding program to improve its productivity.
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22
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Parks MM, Kurylo CM, Batchelder JE, Theresa Vincent C, Blanchard SC. Implications of sequence variation on the evolution of rRNA. Chromosome Res 2019; 27:89-93. [PMID: 30719681 PMCID: PMC6505490 DOI: 10.1007/s10577-018-09602-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/19/2018] [Accepted: 12/26/2018] [Indexed: 12/22/2022]
Abstract
The evolution of the multi-copy family of ribosomal RNA (rRNA) genes is unique in regard to its genetics and genome evolution. Paradoxically, rRNA genes are highly homogenized within and between individuals, yet they are globally distinct between species. Here, we discuss the implications for models of rRNA gene evolution in light of our recent discoveries that ribosomes bearing rRNA sequence variants can affect gene expression and physiology and that intra-individual rRNA alleles exhibit both context- and tissue-specific expression.
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Affiliation(s)
- Matthew M Parks
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Chad M Kurylo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - C Theresa Vincent
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, New York, NY, USA.
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23
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Buleu OG, Jetybayev IY, Chobanov DP, Bugrov AG. Comparative analysis of C-heterochromatin, ribosomal and telomeric DNA markers in chromosomes of Pamphagidae grasshoppers from Morocco. COMPARATIVE CYTOGENETICS 2019; 13:61-74. [PMID: 30854170 PMCID: PMC6403196 DOI: 10.3897/compcytogen.v13i1.32039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/30/2019] [Indexed: 05/19/2023]
Abstract
The karyotypes and the localization of C-bands, clusters of ribosomal DNA and telomeric repeats of 10 species of the family Pamphagidae from Morocco are described for the first time. The species studied belong to the subfamilies Pamphaginae and Thrinchinae. All species have karyotypes consisting of 19 and 20 acrocentric chromosomes and X0/XX sex chromosome system in males and females, respectively (2n♂=19, NF=19; 2n♀=20, NF=20). Despite the karyotype conservatism, we revealed differences in the location and size of C-heterochromatin blocks and ribosomal DNA clusters. A comparative analysis of these differences shows that karyotype divergences in this group is connected not to structural chromosome rearrangements, but to the evolution of repetitive DNA.
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Affiliation(s)
- Olesya G. Buleu
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, RussiaInstitute of Systematics and Ecology of Animals, Russian Academy of SciencesNovosibirskRussia
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, RussiaNovosibirsk State UniversityNovosibirskRussia
| | - Ilyas Y. Jetybayev
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, RussiaNovosibirsk State UniversityNovosibirskRussia
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Pr. Lavrentjeva 10, 630090 Novosibirsk, RussiaInstitute of Cytology and Genetics, Russian Academy of SciencesNovosibirskRussia
| | - Dragan P. Chobanov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Tsar Osvobodotel Boul. 1, Sofia 1000, BulgariaInstitute of Biodiversity and Ecosystem Research, Bulgarian Academy of SciencesSofiaBulgaria
| | - Alexander G. Bugrov
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, RussiaInstitute of Systematics and Ecology of Animals, Russian Academy of SciencesNovosibirskRussia
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, RussiaNovosibirsk State UniversityNovosibirskRussia
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O'Donnell K, Cigelnik E, Nirenberg HI. Molecular systematics and phylogeography of theGibberella fujikuroispecies complex. Mycologia 2018. [DOI: 10.1080/00275514.1998.12026933] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Kerry O'Donnell
- Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, Illinois 61604-3999
| | - Elizabeth Cigelnik
- Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, Illinois 61604-3999
| | - Helgard I. Nirenberg
- Biologische Bundesanstalt für Land- und Forstwirtschaft, Institut für Mikrobiologie, Königin-Luise-Straβe 19, D-14119 Berlin, Germany
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Kim JH, Dilthey AT, Nagaraja R, Lee HS, Koren S, Dudekula D, Wood Iii WH, Piao Y, Ogurtsov AY, Utani K, Noskov VN, Shabalina SA, Schlessinger D, Phillippy AM, Larionov V. Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing. Nucleic Acids Res 2018; 46:6712-6725. [PMID: 29788454 PMCID: PMC6061828 DOI: 10.1093/nar/gky442] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/08/2018] [Indexed: 12/31/2022] Open
Abstract
Despite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments from a single human chromosome 21 using transformation-associated recombination (TAR) cloning in yeast. Accurate long-read sequencing of 13 isolates covering ∼0.82 Mb of the chromosome 21 rDNA complement revealed substantial variation among tandem repeat rDNA copies, several palindromic structures and potential errors in the previous reference sequence. These clones revealed 101 variant positions in the 45S transcription unit and 235 in the intergenic spacer sequence. Approximately 60% of the 45S variants were confirmed in independent whole-genome or RNA-seq data, with 47 of these further observed in mature 18S/28S rRNA sequences. TAR cloning and long-read sequencing enabled the accurate reconstruction of multiple rDNA units and a new, high-quality 44 838 bp rDNA reference sequence, which we have annotated with variants detected from chromosome 21 of a single individual. The large number of variants observed reveal heterogeneity in human rDNA, opening up the possibility of corresponding variations in ribosome dynamics.
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MESH Headings
- Animals
- Cell Line
- Chromosomes, Human, Pair 21
- Cloning, Molecular
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- DNA, Ribosomal Spacer/chemistry
- Genes, rRNA
- Genetic Variation
- Humans
- Mice
- Nucleic Acid Conformation
- Nucleolus Organizer Region/chemistry
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Jung-Hyun Kim
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
| | - Alexander T Dilthey
- National Human Genome Research Institute, Computational and Statistical Genomics Branch, Bethesda, MD 20892, USA
| | - Ramaiah Nagaraja
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - Hee-Sheung Lee
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
| | - Sergey Koren
- National Human Genome Research Institute, Computational and Statistical Genomics Branch, Bethesda, MD 20892, USA
| | - Dawood Dudekula
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - William H Wood Iii
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - Yulan Piao
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20892, USA
| | - Koichi Utani
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
| | - Vladimir N Noskov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20892, USA
| | - David Schlessinger
- National Institute on Aging, Laboratory of Genetics and Genomics, Baltimore, MD 21224, USA
| | - Adam M Phillippy
- National Human Genome Research Institute, Computational and Statistical Genomics Branch, Bethesda, MD 20892, USA
| | - Vladimir Larionov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD 20892, USA
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Liu Q, Qi Y, Liang Q, Xu X, Hu F, Wang J, Xiao J, Wang S, Li W, Tao M, Qin Q, Zhao R, Yao Z, Liu S. The chimeric genes in the hybrid lineage of Carassius auratus cuvieri (♀)×Carassius auratus red var. (♂). SCIENCE CHINA-LIFE SCIENCES 2018; 61:1079-1089. [DOI: 10.1007/s11427-017-9306-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/06/2018] [Indexed: 12/30/2022]
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Zhang J, Di H, Luo K, Jahufer Z, Wu F, Duan Z, Stewart A, Yan Z, Wang Y. Coumarin Content, Morphological Variation, and Molecular Phylogenetics of Melilotus. Molecules 2018; 23:E810. [PMID: 29614822 PMCID: PMC6017091 DOI: 10.3390/molecules23040810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/22/2018] [Accepted: 03/28/2018] [Indexed: 12/14/2022] Open
Abstract
Melilotus albus and Melilotus officinalis are widely used in forage production and herbal medicine due to the biological activity of their coumarins, which have many biological and pharmacological activities, including anti-HIV and anti-tumor effects. To comprehensively evaluate M. albus and M. officinalis coumarin content (Cou), morphological variation, and molecular phylogeny, we examined the Cou, five morphological traits and the molecular characterization based on the trnL-F spacer and internal transcribed spacer (ITS) regions of 93 accessions. Significant (p < 0.05) variation was observed in the Cou and all five morphological traits in both species. Analysis of population differentiation (Pst) of the phenotypic traits showed that powdery mildew resistance (PMR) had the greatest Pst, meaning that this trait demonstrated the largest genetic differentiation among the accessions. The Pst values of dry matter yield (DMY) and Cou were relatively high. Biplot analysis identified accessions with higher DMY and higher and lower Cou. Analysis of molecular sequence variation identified seven haplotypes of the trnL-F spacer and 13 haplotypes of the ITS region. Based on haplotype and sequence analyses, the genetic variation of M. officinalis was higher than that of M. albus. Additionally, ITS sequence analysis showed that the variation among accessions was larger than that among species across three geographical areas: Asia, Europe, and North America. Similarly, variation among accessions for both the trnL-F and ITS sequences were larger than the differences between the geographical areas. Our results indicate that there has been considerable gene flow between the two Melilotus species. Our characterization of Cou and the morphological and genetic variations of these two Melilotus species may provide useful insights into germplasm improvement to enhance DMY and Cou.
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Affiliation(s)
- Jiyu Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Hongyan Di
- Agricultural Technology Extension and Training Center, Agricultural and Animal Husbandry of Zhongwei, Zhongwei 755000, China.
| | - Kai Luo
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Zulfi Jahufer
- AgResearch Ltd., Grasslands Research Center, Private Bag 11008, Palmerston North 11008, New Zealand.
| | - Fan Wu
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Zhen Duan
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Alan Stewart
- PGG Wrightson Seeds, P.O. Box 175, Lincoln, Christchurch 7640, New Zealand.
| | - Zhuanzhuan Yan
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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Kaur H, Gaba K. Cytogenetic characterization of three species of Antilochus (Hemiptera: Heteroptera: Pyrrhocoridae). THE NUCLEUS 2018. [DOI: 10.1007/s13237-018-0228-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Szlachetko DL, Kolanowska M, Naczk A, Górniak M, Dudek M, Rutkowski P, Chiron G. Taxonomy of Cyrtochilum-alliance (Orchidaceae) in the light of molecular and morphological data. BOTANICAL STUDIES 2017; 58:8. [PMID: 28510191 PMCID: PMC5430592 DOI: 10.1186/s40529-017-0164-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 01/08/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The generic separateness and specific composition of the orchid genus Cyrtochilum was discussed for almost two centuries. Over the years several smaller taxa were segregated from this taxon, but their separateness was recently questioned based on molecular studies outcomes. The aim of our study was to revise concepts of morphological-based generic delimitation in Cyrtochilum-alliance and to compare it with the results of genetic analysis. We used phylogenetic framework in combination with phenetical analysis to provide proposal of the generic delimitation within Cyrtochilum-alliance. Two molecular markers, ITS and matK were used to construct phylogenetic tree. A total of over 5000 herbarium specimens were included in the morphological examination and the phenetical analysis included 29 generative and vegetative characters. RESULTS Comparative morphology of the previously recognized genera: Buesiella, Dasyglossum, Neodryas, Rusbyella, Siederella and Trigonochilum is presented. A new species within the the latter genus is described. Fourteen new combinations are proposed. The key to the identification of the genera of the Cyrtochilum-alliance and morphological characteristics of each genus are provided. CONCLUSIONS A total of six separated genera are recognized within Cyrtochilum-alliance. The reasons of the incompatibility between morphological differences observed within studied taxa and phylogenetic tree are argued and the taxonomic implications of such inconsistency, resulting in fragmentation or lumping of taxonomic units, are discussed.
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Affiliation(s)
- Dariusz L. Szlachetko
- Department of Plant Taxonomy and Nature Conservation, The University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Marta Kolanowska
- Department of Plant Taxonomy and Nature Conservation, The University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
- Department of Biodiversity Research, Global Change Research Institute AS CR, Bělidla 4a., 603 00 Brno, Czech Republic
| | - Aleksandra Naczk
- Department of Molecular Evolution, The University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Marcin Górniak
- Department of Molecular Evolution, The University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Magdalena Dudek
- Department of Plant Taxonomy and Nature Conservation, The University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Piotr Rutkowski
- Department of Plant Taxonomy and Nature Conservation, The University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Guy Chiron
- Herbiers, Université de Lyon I, 69622 Villeurbanne Cedex, France
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30
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Montecinos AE, Guillemin ML, Couceiro L, Peters AF, Stoeckel S, Valero M. Hybridization between two cryptic filamentous brown seaweeds along the shore: analysing pre- and postzygotic barriers in populations of individuals with varying ploidy levels. Mol Ecol 2017; 26:3497-3512. [PMID: 28295812 DOI: 10.1111/mec.14098] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/07/2017] [Accepted: 02/07/2017] [Indexed: 01/17/2023]
Abstract
We aimed to study the importance of hybridization between two cryptic species of the genus Ectocarpus, a group of filamentous algae with haploid-diploid life cycles that include the principal genetic model organism for the brown algae. In haploid-diploid species, the genetic structure of the two phases of the life cycle can be analysed separately in natural populations. Such life cycles provide a unique opportunity to estimate the frequency of hybrid genotypes in diploid sporophytes and meiotic recombinant genotypes in haploid gametophytes allowing the effects of reproductive barriers preventing fertilization or preventing meiosis to be untangle. The level of hybridization between E. siliculosus and E. crouaniorum was quantified along the European coast. Clonal cultures (568 diploid, 336 haploid) isolated from field samples were genotyped using cytoplasmic and nuclear markers to estimate the frequency of hybrid genotypes in diploids and recombinant haploids. We identified admixed individuals using microsatellite loci, classical assignment methods and a newly developed Bayesian method (XPloidAssignment), which allows the analysis of populations that exhibit variations in ploidy level. Over all populations, the level of hybridization was estimated at 8.7%. Hybrids were exclusively observed in sympatric populations. More than 98% of hybrids were diploids (40% of which showed signs of aneuploidy) with a high frequency of rare alleles. The near absence of haploid recombinant hybrids demonstrates that the reproductive barriers are mostly postzygotic and suggests that abnormal chromosome segregation during meiosis following hybridization of species with different genome sizes could be a major cause of interspecific incompatibility in this system.
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Affiliation(s)
- Alejandro E Montecinos
- UMI, EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, PUC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688, Roscoff cedex, France
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Marie-Laure Guillemin
- UMI, EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, PUC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688, Roscoff cedex, France
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Lucia Couceiro
- UMI, EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, PUC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688, Roscoff cedex, France
| | - Akira F Peters
- Bezhin Rosko, 40 rue des pêcheurs, 29250, Santec, France
| | - Solenn Stoeckel
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Rennes, France
| | - Myriam Valero
- UMI, EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, PUC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688, Roscoff cedex, France
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Baker RJ, Davis SK, Bradley RD, Hamilton MJ, Bussche RAVD. RIBOSOMAL-DNA, MITOCHONDRIAL-DNA, CHROMOSOMAL, AND ALLOZYMIC STUDIES ON A CONTACT ZONE IN THE POCKET GOPHER, GEOMYS. Evolution 2017; 43:63-75. [DOI: 10.1111/j.1558-5646.1989.tb04207.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/1987] [Accepted: 07/20/1988] [Indexed: 11/28/2022]
Affiliation(s)
- Robert J. Baker
- Department of Biology and The Museum; Texas Tech University; Lubbock TX 79409
| | - Scott K. Davis
- Department of Biology; Washington University; St. Louis MO 63130
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Rabanal FA, Mandáková T, Soto-Jiménez LM, Greenhalgh R, Parrott DL, Lutzmayer S, Steffen JG, Nizhynska V, Mott R, Lysak MA, Clark RM, Nordborg M. Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana. Genome Biol 2017; 18:75. [PMID: 28464948 PMCID: PMC5414317 DOI: 10.1186/s13059-017-1209-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/06/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Ribosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arabidopsis thaliana, 45S rRNA genes are found in two large ribosomal DNA (rDNA) clusters and little is known about the contribution of each to the overall transcription pattern in the species. RESULTS By taking advantage of genome sequencing data from the 1001 Genomes Consortium, we characterize rRNA gene sequence variation within and among accessions. Notably, variation is not restricted to the pre-rRNA sequences removed during processing, but it is also present within the highly conserved ribosomal subunits. Through linkage mapping we assign these variants to a particular rDNA cluster unambiguously and use them as reporters of rDNA cluster-specific expression. We demonstrate that rDNA cluster-usage varies greatly among accessions and that rDNA cluster-specific expression and silencing is controlled via genetic interactions between entire rDNA cluster haplotypes (alleles). CONCLUSIONS We show that rRNA gene cluster expression is controlled via complex epistatic and allelic interactions between rDNA haplotypes that apparently regulate the entire rRNA gene cluster. Furthermore, the sequence polymorphism we discovered implies that the pool of rRNA in a cell may be heterogeneous, which could have functional consequences.
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Affiliation(s)
- Fernando A Rabanal
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Luz M Soto-Jiménez
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | | | - David L Parrott
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Stefan Lutzmayer
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Joshua G Steffen
- Department of Natural Sciences, Colby-Sawyer College, New London, NH, USA
| | - Viktoria Nizhynska
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Richard Mott
- Genetics Institute, University College London (UCL), Gower Street, London, WC1E 6BT, UK
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Richard M Clark
- Department of Biology, University of Utah, Salt Lake City, UT, USA
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, USA
| | - Magnus Nordborg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
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Giudicelli GC, Mäder G, Silva-Arias GA, Zamberlan PM, Bonatto SL, Freitas LB. Secondary structure of nrDNA Internal Transcribed Spacers as a useful tool to align highly divergent species in phylogenetic studies. Genet Mol Biol 2017; 40:191-199. [PMID: 28199443 PMCID: PMC5452138 DOI: 10.1590/1678-4685-gmb-2016-0042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 08/23/2016] [Indexed: 12/18/2022] Open
Abstract
Recently, it has been suggested that internal transcribed spacer (ITS) sequences are under selective constraints to preserve their secondary structure. Here, we investigate the patterns of the ITS nucleotide and secondary structure conservation across the Passiflora L. genus to evaluate the potential use of secondary structure data as a helpful tool for the alignment in taxonomically complex genera. Considering the frequent use of ITS, this study also presents a perspective on future analyses in other plant groups. The ITS1 and ITS2 sequences presented significant differences for mean values of the lowest energy state (LES) and for number of hairpins in different Passiflora subgenera. Statistical analyses for the subgenera separately support significant differences between the LES values and the total number of secondary structures for ITS. In order to evaluate whether the LES values of ITS secondary structures were related to selective constraints, we compared these results among 120 ITS sequences from Passiflora species and 120 randomly generated sequences. These analyses indicated that Passiflora ITS sequences present characteristics of a region under selective constraint to maintain the secondary structure showing to be a promising tool to improve the alignments and identify sites with non-neutral substitutions or those correlated evolutionary steps.
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Affiliation(s)
- Giovanna C Giudicelli
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Geraldo Mäder
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gustavo A Silva-Arias
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Priscilla M Zamberlan
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Sandro L Bonatto
- Laboratory of Genomic and Molecular Biology, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Volkov RA, Panchuk II, Borisjuk NV, Hosiawa-Baranska M, Maluszynska J, Hemleben V. Evolutional dynamics of 45S and 5S ribosomal DNA in ancient allohexaploid Atropa belladonna. BMC PLANT BIOLOGY 2017; 17:21. [PMID: 28114894 PMCID: PMC5260122 DOI: 10.1186/s12870-017-0978-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/17/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Polyploid hybrids represent a rich natural resource to study molecular evolution of plant genes and genomes. Here, we applied a combination of karyological and molecular methods to investigate chromosomal structure, molecular organization and evolution of ribosomal DNA (rDNA) in nightshade, Atropa belladonna (fam. Solanaceae), one of the oldest known allohexaploids among flowering plants. Because of their abundance and specific molecular organization (evolutionarily conserved coding regions linked to variable intergenic spacers, IGS), 45S and 5S rDNA are widely used in plant taxonomic and evolutionary studies. RESULTS Molecular cloning and nucleotide sequencing of A. belladonna 45S rDNA repeats revealed a general structure characteristic of other Solanaceae species, and a very high sequence similarity of two length variants, with the only difference in number of short IGS subrepeats. These results combined with the detection of three pairs of 45S rDNA loci on separate chromosomes, presumably inherited from both tetraploid and diploid ancestor species, example intensive sequence homogenization that led to substitution/elimination of rDNA repeats of one parent. Chromosome silver-staining revealed that only four out of six 45S rDNA sites are frequently transcriptionally active, demonstrating nucleolar dominance. For 5S rDNA, three size variants of repeats were detected, with the major class represented by repeats containing all functional IGS elements required for transcription, the intermediate size repeats containing partially deleted IGS sequences, and the short 5S repeats containing severe defects both in the IGS and coding sequences. While shorter variants demonstrate increased rate of based substitution, probably in their transition into pseudogenes, the functional 5S rDNA variants are nearly identical at the sequence level, pointing to their origin from a single parental species. Localization of the 5S rDNA genes on two chromosome pairs further supports uniparental inheritance from the tetraploid progenitor. CONCLUSIONS The obtained molecular, cytogenetic and phylogenetic data demonstrate complex evolutionary dynamics of rDNA loci in allohexaploid species of Atropa belladonna. The high level of sequence unification revealed in 45S and 5S rDNA loci of this ancient hybrid species have been seemingly achieved by different molecular mechanisms.
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MESH Headings
- Atropa belladonna/classification
- Atropa belladonna/genetics
- Atropa belladonna/metabolism
- Chromosomes, Plant/genetics
- Chromosomes, Plant/metabolism
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- Evolution, Molecular
- Phylogeny
- Polyploidy
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
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Affiliation(s)
- Roman A. Volkov
- Department of General Genetics, Center of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych University of Chernivtsi, Kotsiubynski str. 2, 58012 Chernivtsi, Ukraine
| | - Irina I. Panchuk
- Department of General Genetics, Center of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych University of Chernivtsi, Kotsiubynski str. 2, 58012 Chernivtsi, Ukraine
| | - Nikolai V. Borisjuk
- Department of General Genetics, Center of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
- Australian Centre for Plant Functional Genomics (ACPFG), The University of Adelaide, Hartley Grove, Urrbrae, SA 5064 Australia
- Current addres: School of Life Science, Huaiyin Normal University, 223300 Huaian, China
| | | | - Jolanta Maluszynska
- Department of Plant Anatomy and Cytology, University of Silesia, 40032 Katowice, Poland
| | - Vera Hemleben
- Department of General Genetics, Center of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
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35
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Against all odds: reconstructing the evolutionary history of Scrophularia (Scrophulariaceae) despite high levels of incongruence and reticulate evolution. ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-016-0316-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Goodall-Copestake WP. One tunic but more than one barcode: evolutionary insights from dynamic mitochondrial DNA inSalpa thompsoni(Tunicata: Salpida). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Dutrillaux AM, Carton B, Cacheux L, Dutrillaux B. Interstitial NORs, Fragile Sites, and Chromosome Evolution: A Not So Simple Relationship - The Example of Melolontha melolontha and Genus Protaetia (Coleoptera: Scarabaeidae). Cytogenet Genome Res 2016; 149:304-311. [DOI: 10.1159/000448931] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2016] [Indexed: 11/19/2022] Open
Abstract
In the present study, the origin of recurrent rearrangements involving chromosome 6 in 3.2% of cells of Melolontha melolontha (Coleoptera, Scarabaeidae) was investigated. Various chromosome staining techniques, including C-banding, Giemsa and silver staining, as well as fluorescence in situ hybridization with a human 28S rDNA probe, were applied to M. melolontha chromosome spreads. In addition, related species of the genera Melolontha and Protaetia were studied. On chromosome 6 of M. melolontha, there is a fragile site-like structure which corresponds to an interstitial nucleolus organizer region (NOR). Despite this instability, the NOR remains unique and interstitial in this species, as well as in the other species studied. It is proposed that the intercalary position of the NOR both facilitates the detection of its fragile site-like instability and correlates with its relative stability during evolution. We explain this apparent paradox by strong counter-selection for imbalances of the chromosome fragment distal to the interstitial NORs, which would recurrently occur in the progeny of translocation carriers. Thus, the frequent telomeric position of the NORs in most animal and plant taxa would have no functional rationale but would be the consequence of selection against the meiotic transmission of chromosome imbalances.
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Terraneo TI, Benzoni F, Arrigoni R, Berumen ML. Species delimitation in the coral genus Goniopora (Scleractinia, Poritidae) from the Saudi Arabian Red Sea. Mol Phylogenet Evol 2016; 102:278-94. [DOI: 10.1016/j.ympev.2016.06.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 06/15/2016] [Accepted: 06/16/2016] [Indexed: 10/21/2022]
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Dueñas LF, Tracey DM, Crawford AJ, Wilke T, Alderslade P, Sánchez JA. The Antarctic Circumpolar Current as a diversification trigger for deep-sea octocorals. BMC Evol Biol 2016; 16:2. [PMID: 26727928 PMCID: PMC4700699 DOI: 10.1186/s12862-015-0574-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 12/19/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Antarctica is surrounded by the Antarctic Circumpolar Current (ACC), the largest and strongest current in the world. Despite its potential importance for shaping biogeographical patterns, the distribution and connectivity of deep-sea populations across the ACC remain poorly understood. In this study we conducted the first assessment of phylogeographical patterns in deep-sea octocorals in the South Pacific and Southern Ocean, specifically a group of closely related bottlebrush octocorals (Primnoidae: Tokoprymno and Thourella), as a test case to study the effect of the ACC on the population structure of brooding species. We assessed the degree to which the ACC constitutes a barrier to gene flow between northern and southern populations and whether the onset of diversification of these corals coincides with the origin of the ACC (Oligocene-Miocene boundary). RESULTS Based on DNA sequences of two nuclear genes from 80 individuals and a combination of phylogeographic model-testing approaches we found a phylogenetic break corresponding to the spatial occurrence of the ACC. We also found significant genetic structure among our four regional populations. However, we uncovered shared haplotypes among certain population pairs, suggesting long-distance, asymmetrical migration. Our divergence time analyses indicated that the separation of amphi-ACC populations took place during the Middle Miocene around 12.6 million years ago, i.e., after the formation of the ACC. CONCLUSION We suggest that the ACC constitutes a semi-permeable barrier to these deep-sea octocorals capable of separating and structuring populations, while allowing short periods of gene flow. The fluctuations in latitudinal positioning of the ACC during the Miocene likely contributed to the diversification of these octocorals. Additionally, we provide evidence that the populations from each of our four sampling regions could actually constitute different species.
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Affiliation(s)
- Luisa F Dueñas
- Department of Biological Sciences, Universidad de los Andes, A.A. 4976, Bogotá, Colombia.
- Department of Animal Ecology & Systematics, Justus Liebig University, Giessen, Germany.
| | - Dianne M Tracey
- National Institute of Water and Atmospheric Research-NIWA, Wellington, New Zealand.
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, A.A. 4976, Bogotá, Colombia.
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Panama City, Republic of Panama.
| | - Thomas Wilke
- Department of Animal Ecology & Systematics, Justus Liebig University, Giessen, Germany.
| | - Phil Alderslade
- CSIRO Marine and Atmospheric Research, PO Box 1538, Hobart, Tasmania, 7001, Australia.
| | - Juan A Sánchez
- Department of Biological Sciences, Universidad de los Andes, A.A. 4976, Bogotá, Colombia.
- Department of Animal Ecology & Systematics, Justus Liebig University, Giessen, Germany.
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Bennett KL, Linton YM, Shija F, Kaddumukasa M, Djouaka R, Misinzo G, Lutwama J, Huang YM, Mitchell LB, Richards M, Tossou E, Walton C. Molecular Differentiation of the African Yellow Fever Vector Aedes bromeliae (Diptera: Culicidae) from Its Sympatric Non-vector Sister Species, Aedes lilii. PLoS Negl Trop Dis 2015; 9:e0004250. [PMID: 26641858 PMCID: PMC4671560 DOI: 10.1371/journal.pntd.0004250] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/29/2015] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Yellow fever continues to be a problem in sub-Saharan Africa with repeated epidemics occurring. The mosquito Aedes bromeliae is a major vector of yellow fever, but it cannot be readily differentiated from its non-vector zoophilic sister species Ae. lilii using morphological characters. Genetic differences have been reported between anthropophilic Ae. bromeliae and zoophilic Ae. lilii and between forest and domestic populations. However, due to the application of different molecular markers and non-overlapping populations employed in previous studies, interpretation of species delimitation is unclear. METHODOLOGY/PRINCIPLE FINDINGS DNA sequences were generated from specimens of Ae. simpsoni s.l. from the Republic of Benin, Tanzania and Uganda for two nuclear genes apolipophorin 2 (apoLp2) and cytochrome p450 (CYPJ92), the ribosomal internal transcribed spacer region (ITS) and the mitochondrial cytochrome c oxidase (COI) barcoding region. Nuclear genes apoLp2 and CYPJ92 were unable to differentiate between species Ae. bromeliae and Ae. lilii due to ancestral lineage sorting, while ITS sequence data provided clear topological separation on a phylogeny. The standard COI barcoding region was shown to be subject to species introgression and unable to clearly distinguish the two taxa. Here we present a reliable direct PCR-based method for differentiation of the vector species Ae. bromeliae from its isomorphic, sympatric and non-biomedically important sister taxon, Ae. lilii, based on the ITS region. Using molecular species verification, we describe novel immature habitats for Ae. lilii and report both sympatric and allopatric populations. Whereas only Ae. lilii is found in the Republic of Benin and only Ae. bromeliae in Tanzania, both species are sympatric in Uganda. CONCLUSIONS/SIGNIFICANCE Our accurate identification method will allow informed distribution and detailed ecological studies that will facilitate assessment of arboviral disease risk and development of future targeted vector control.
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Affiliation(s)
- Kelly Louise Bennett
- Computational Evolutionary Biology Group, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Centre, Suitland, Maryland, United States of America
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Uniformed Services University of Health Sciences, Bethesda, Maryland, United States of America
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Fortunate Shija
- Computational Evolutionary Biology Group, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- Department of Veterinary Microbiology and Parasitology, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Martha Kaddumukasa
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Rousseau Djouaka
- Agro-Eco-Health Platform for West and Central Africa, International Institute for Tropical Agriculture, Republic of Benin
| | - Gerald Misinzo
- Department of Veterinary Microbiology and Parasitology, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Julius Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infections, Uganda Virus Research Institute, Entebbe, Uganda
| | - Yiau-Min Huang
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Centre, Suitland, Maryland, United States of America
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Luke B. Mitchell
- Walter Reed Biosystematics Unit, Smithsonian Institution Museum Support Centre, Suitland, Maryland, United States of America
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Miriam Richards
- Department of Veterinary Microbiology and Parasitology, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Eric Tossou
- Agro-Eco-Health Platform for West and Central Africa, International Institute for Tropical Agriculture, Republic of Benin
| | - Catherine Walton
- Computational Evolutionary Biology Group, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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Scienski K, Fay JC, Conant GC. Patterns of Gene Conversion in Duplicated Yeast Histones Suggest Strong Selection on a Coadapted Macromolecular Complex. Genome Biol Evol 2015; 7:3249-58. [PMID: 26560339 PMCID: PMC4700949 DOI: 10.1093/gbe/evv216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We find evidence for interlocus gene conversion in five duplicated histone genes from six yeast species. The sequences of these duplicated genes, surviving from the ancient genome duplication, show phylogenetic patterns inconsistent with the well-resolved orthology relationships inferred from a likelihood model of gene loss after the genome duplication. Instead, these paralogous genes are more closely related to each other than any is to its nearest ortholog. In addition to simulations supporting gene conversion, we also present evidence for elevated rates of radical amino acid substitutions along the branches implicated in the conversion events. As these patterns are similar to those seen in ribosomal proteins that have undergone gene conversion, we speculate that in cases where duplicated genes code for proteins that are a part of tightly interacting complexes, selection may favor the fixation of gene conversion events in order to maintain high protein identities between duplicated copies.
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Affiliation(s)
- Kathy Scienski
- Division of Animal Sciences, University of Missouri, Columbia Present address: Genetics Graduate Program, Texas A&M University, College Station, TX
| | - Justin C Fay
- Department of Genetics, Washington University Center for Genome Sciences and Systems Biology, Washington University
| | - Gavin C Conant
- Division of Animal Sciences, University of Missouri, Columbia Informatics Institute, University of Missouri, Columbia
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Perera OP, Allen KC, Jain D, Purcell M, Little NS, Luttrell RG. Rapid identification of Helicoverpa armigera and Helicoverpa zea (Lepidoptera: Noctuidae) using ribosomal RNA internal transcribed spacer 1. JOURNAL OF INSECT SCIENCE (ONLINE) 2015; 15:155. [PMID: 26516166 PMCID: PMC4625950 DOI: 10.1093/jisesa/iev137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/10/2015] [Indexed: 05/31/2023]
Abstract
Rapid identification of invasive species is crucial for deploying management strategies to prevent establishment. Recent Helicoverpa armigera (Hübner) invasions and subsequent establishment in South America has increased the risk of this species invading North America. Morphological similarities make differentiation of H. armigera from the native Helicoverpa zea (Boddie) difficult. Characteristics of adult male genitalia and nucleotide sequence differences in mitochondrial DNA are two of the currently available methods to differentiate these two species. However, current methods are likely too slow to be employed as rapid detection methods. In this study, conserved differences in the internal transcribed spacer 1 (ITS1) of the ribosomal RNA genes were used to develop species-specific oligonucleotide primers that amplified ITS1 fragments of 147 and 334 bp from H. armigera and H. zea, respectively. An amplicon (83 bp) from a conserved region of 18S ribosomal RNA subunit served as a positive control. Melting temperature differences in ITS1 amplicons yielded species-specific dissociation curves that could be used in high resolution melt analysis to differentiate the two Helicoverpa species. In addition, a rapid and inexpensive procedure for obtaining amplifiable genomic DNA from a small amount of tissue was identified. Under optimal conditions, the process was able to detect DNA from one H. armigera leg in a pool of 25 legs. The high resolution melt analysis combined with rapid DNA extraction could be used as an inexpensive method to genetically differentiate large numbers of H. armigera and H. zea using readily available reagents.
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Affiliation(s)
| | - Kerry C Allen
- USDA-ARS Southern Insect Management Research Unit, Stoneville, MS 38776
| | - Devendra Jain
- Department of Molecular Biology and Biotechnology, Maharana Pratap University of Agriculture and Technology, Udaipur-313001, Rajasthan, India
| | - Matthew Purcell
- USDA-ARS Australian Biological Control Laboratory, CSIRO Biosecurity, GPO Box 2583 Brisbane, Queensland 4001, Australia
| | - Nathan S Little
- USDA-ARS Southern Insect Management Research Unit, Stoneville, MS 38776
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Tian RM, Cai L, Zhang WP, Cao HL, Qian PY. Rare Events of Intragenus and Intraspecies Horizontal Transfer of the 16S rRNA Gene. Genome Biol Evol 2015. [PMID: 26220935 PMCID: PMC4558861 DOI: 10.1093/gbe/evv143] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Horizontal gene transfer (HGT) of operational genes has been widely reported in prokaryotic organisms. However, informational genes such as those involved in transcription and translation processes are very difficult to be horizontally transferred, as described by Woese’s complexity hypothesis. Here, we analyzed all of the completed prokaryotic genome sequences (2,143 genomes) in the NCBI (National Center for Biotechnology Information) database, scanned for genomes with high intragenomic heterogeneity of 16S rRNA gene copies, and explored potential HGT events of ribosomal RNA genes based on the phylogeny, genomic organization, and secondary structures of the ribosomal RNA genes. Our results revealed 28 genomes with relatively high intragenomic heterogeneity of multiple 16S rRNA gene copies (lowest pairwise identity <98.0%), and further analysis revealed HGT events and potential donors of the heterogeneous copies (such as HGT from Chlamydia suis to Chlamydia trachomatis) and mutation events of some heterogeneous copies (such as Streptococcus suis JS14). Interestingly, HGT of the 16S rRNA gene only occurred at intragenus or intraspecies levels, which is quite different from the HGT of operational genes. Our results improve our understanding regarding the exchange of informational genes.
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Affiliation(s)
- Ren-Mao Tian
- Division of Life Science, Hong Kong University of Science and Technology, China
| | - Lin Cai
- Division of Life Science, Hong Kong University of Science and Technology, China
| | - Wei-Peng Zhang
- Division of Life Science, Hong Kong University of Science and Technology, China
| | - Hui-Luo Cao
- Division of Life Science, Hong Kong University of Science and Technology, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, China
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Di H, Duan Z, Luo K, Zhang D, Wu F, Zhang J, Liu W, Wang Y. Interspecific Phylogenic Relationships within Genus Melilotus Based on Nuclear and Chloroplast DNA. PLoS One 2015; 10:e0132596. [PMID: 26167689 PMCID: PMC4500581 DOI: 10.1371/journal.pone.0132596] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 06/16/2015] [Indexed: 12/19/2022] Open
Abstract
Melilotus comprises 19 species, while the phylogenetic relationships between species remain unclear. In the present work, three chloroplast genes, rbcL, matK, trnL-F, and one nuclear region, ITS (internal transcribed spacer) belonging to 48 populations of 18 species of Melilotus were sequenced and phylogenetic trees were constructed to study their interspecific relationships. Based on the phylogenetic tree generated in this study using rbcL analysis, the Melilotus genus is clearly monophyletic in the legume family. Both Bayesian and maximum-parsimony approaches were used to analyze the data. The nrDNA ITS provided more informative characteristics (9.8%) than cpDNA (3.0%). Melilotus contains two closely related groups, clade I and clade II. M. spicatus, M. indicus and M. segetalis have a close relationship. M. infestus, M. siculus and M. sulcatus are closely related. The comparing between molecular phylogeny and flower color classification in Melilotus showed that the flower color is not much informative for phylogenetics of this genus.
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Affiliation(s)
- Hongyan Di
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
| | - Zhen Duan
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
| | - Kai Luo
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
| | - Daiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
| | - Fan Wu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
- * E-mail:
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, China
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Dumont BL. Interlocus gene conversion explains at least 2.7% of single nucleotide variants in human segmental duplications. BMC Genomics 2015; 16:456. [PMID: 26077037 PMCID: PMC4467073 DOI: 10.1186/s12864-015-1681-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/01/2015] [Indexed: 01/24/2023] Open
Abstract
Background Interlocus gene conversion (IGC) is a recombination-based mechanism that results in the unidirectional transfer of short stretches of sequence between paralogous loci. Although IGC is a well-established mechanism of human disease, the extent to which this mutagenic process has shaped overall patterns of segregating variation in multi-copy regions of the human genome remains unknown. One expected manifestation of IGC in population genomic data is the presence of one-to-one paralogous SNPs that segregate identical alleles. Results Here, I use SNP genotype calls from the low-coverage phase 3 release of the 1000 Genomes Project to identify 15,790 parallel, shared SNPs in duplicated regions of the human genome. My approach for identifying these sites accounts for the potential redundancy of short read mapping in multi-copy genomic regions, thereby effectively eliminating false positive SNP calls arising from paralogous sequence variation. I demonstrate that independent mutation events to identical nucleotides at paralogous sites are not a significant source of shared polymorphisms in the human genome, consistent with the interpretation that these sites are the outcome of historical IGC events. These putative signals of IGC are enriched in genomic contexts previously associated with non-allelic homologous recombination, including clear signals in gene families that form tandem intra-chromosomal clusters. Conclusions Taken together, my analyses implicate IGC, not point mutation, as the mechanism generating at least 2.7 % of single nucleotide variants in duplicated regions of the human genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1681-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Beth L Dumont
- Initiative in Biological Complexity, North Carolina State University, 112 Derieux Place, 3510 Thomas Hall, Campus Box 7614, Raleigh, NC, 27695-7614, USA.
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Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes. Proc Natl Acad Sci U S A 2015; 112:2485-90. [PMID: 25583482 DOI: 10.1073/pnas.1416878112] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Tandemly repeated ribosomal DNA (rDNA) arrays are among the most evolutionary dynamic loci of eukaryotic genomes. The loci code for essential cellular components, yet exhibit extensive copy number (CN) variation within and between species. CN might be partly determined by the requirement of dosage balance between the 5S and 45S rDNA arrays. The arrays are nonhomologous, physically unlinked in mammals, and encode functionally interdependent RNA components of the ribosome. Here we show that the 5S and 45S rDNA arrays exhibit concerted CN variation (cCNV). Despite 5S and 45S rDNA elements residing on different chromosomes and lacking sequence similarity, cCNV between these loci is strong, evolutionarily conserved in humans and mice, and manifested across individual genotypes in natural populations and pedigrees. Finally, we observe that bisphenol A induces rapid and parallel modulation of 5S and 45S rDNA CN. Our observations reveal a novel mode of genome variation, indicate that natural selection contributed to the evolution and conservation of cCNV, and support the hypothesis that 5S CN is partly determined by the requirement of dosage balance with the 45S rDNA array. We suggest that human disease variation might be traced to disrupted rDNA dosage balance in the genome.
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The intraspecific variability of mitochondrial genes of Agaricus bisporus reveals an extensive group I intron mobility combined with low nucleotide substitution rates. Curr Genet 2014; 61:87-102. [DOI: 10.1007/s00294-014-0448-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 08/12/2014] [Accepted: 08/18/2014] [Indexed: 12/16/2022]
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Bertrand C, Janzen DH, Hallwachs W, Burns JM, Gibson JF, Shokralla S, Hajibabaei M. Mitochondrial and nuclear phylogenetic analysis with Sanger and next-generation sequencing shows that, in Área de Conservación Guanacaste, northwestern Costa Rica, the skipper butterfly named Urbanus belli (family Hesperiidae) comprises three morphologically cryptic species. BMC Evol Biol 2014; 14:153. [PMID: 25005355 PMCID: PMC4112655 DOI: 10.1186/1471-2148-14-153] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/17/2014] [Indexed: 11/22/2022] Open
Abstract
Background Skipper butterflies (Hesperiidae) are a relatively well-studied family of Lepidoptera. However, a combination of DNA barcodes, morphology, and natural history data has revealed several cryptic species complexes within them. Here, we investigate three DNA barcode lineages of what has been identified as Urbanus belli (Hesperiidae, Eudaminae) in Área de Conservación Guanacaste (ACG), northwestern Costa Rica. Results Although no morphological traits appear to distinguish among the three, congruent nuclear and mitochondrial lineage patterns show that “Urbanus belli” in ACG is a complex of three sympatric species. A single strain of Wolbachia present in two of the three cryptic species indicates that Urbanus segnestami Burns (formerly Urbanus belliDHJ01), Urbanus bernikerni Burns (formerly Urbanus belliDHJ02), and Urbanus ehakernae Burns (formerly Urbanus belliDHJ03) may be biologically separated by Wolbachia, as well as by their genetics. Use of parallel sequencing through 454-pyrosequencing improved the utility of ITS2 as a phylogenetic marker and permitted examination of the intra- and interlineage relationships of ITS2 variants within the species complex. Interlineage, intralineage and intragenomic compensatory base pair changes were discovered in the secondary structure of ITS2. Conclusion These findings corroborate the existence of three cryptic species. Our confirmation of a novel cryptic species complex, initially suggested by DNA barcode lineages, argues for using a multi-marker approach coupled with next-generation sequencing for exploration of other suspected species complexes.
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Affiliation(s)
| | | | | | | | | | | | - Mehrdad Hajibabaei
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Inácio V, Rocheta M, Morais-Cecílio L. Molecular organization of the 25S-18S rDNA IGS of Fagus sylvatica and Quercus suber: a comparative analysis. PLoS One 2014; 9:e98678. [PMID: 24893289 PMCID: PMC4043768 DOI: 10.1371/journal.pone.0098678] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 05/05/2014] [Indexed: 01/28/2023] Open
Abstract
The 35S ribosomal DNA (rDNA) units, repeated in tandem at one or more chromosomal loci, are separated by an intergenic spacer (IGS) containing functional elements involved in the regulation of transcription of downstream rRNA genes. In the present work, we have compared the IGS molecular organizations in two divergent species of Fagaceae, Fagus sylvatica and Quercus suber, aiming to comprehend the evolution of the IGS sequences within the family. Self- and cross-hybridization FISH was done on representative species of the Fagaceae. The IGS length variability and the methylation level of 18 and 25S rRNA genes were assessed in representatives of three genera of this family: Fagus, Quercus and Castanea. The intergenic spacers in Beech and Cork Oak showed similar overall organizations comprising putative functional elements needed for rRNA gene activity and containing a non-transcribed spacer (NTS), a promoter region, and a 5′-external transcribed spacer. In the NTS: the sub-repeats structure in Beech is more organized than in Cork Oak, sharing some short motifs which results in the lowest sequence similarity of the entire IGS; the AT-rich region differed in both spacers by a GC-rich block inserted in Cork Oak. The 5′-ETS is the region with the higher similarity, having nonetheless different lengths. FISH with the NTS-5′-ETS revealed fainter signals in cross-hybridization in agreement with the divergence between genera. The diversity of IGS lengths revealed variants from ∼2 kb in Fagus, and Quercus up to 5.3 kb in Castanea, and a lack of correlation between the number of variants and the number of rDNA loci in several species. Methylation of 25S Bam HI site was confirmed in all species and detected for the first time in the 18S of Q. suber and Q. faginea. These results provide important clues for the evolutionary trends of the rDNA 25S-18S IGS in the Fagaceae family.
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Affiliation(s)
- Vera Inácio
- Centre for Botany Applied to Agriculture (CBAA), Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
| | - Margarida Rocheta
- Centre for Botany Applied to Agriculture (CBAA), Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
| | - Leonor Morais-Cecílio
- Centre for Botany Applied to Agriculture (CBAA), Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
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Berríos S, Manieu C, López-Fenner J, Ayarza E, Page J, González M, Manterola M, Fernández-Donoso R. Robertsonian chromosomes and the nuclear architecture of mouse meiotic prophase spermatocytes. Biol Res 2014; 47:16. [PMID: 25027603 PMCID: PMC4101721 DOI: 10.1186/0717-6287-47-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 04/21/2014] [Indexed: 11/06/2022] Open
Abstract
Background The nuclear architecture of meiotic prophase spermatocytes is based on higher-order patterns of spatial associations among chromosomal domains from different bivalents. The meiotic nuclear architecture depends on the chromosome characteristics and consequently is prone to modification by chromosomal rearrangements. In this work, we consider Mus domesticus spermatocytes with diploid chromosome number 2n = 40, all telocentric, and investigate a possible modification of the ancestral nuclear architecture due to the emergence of derived Rb chromosomes, which may be present in the homozygous or heterozygous condition. Results In the 2n = 40 spermatocyte nuclei random associations mediated by pericentromeric heterochromatin among the 19 telocentric bivalents ocurr at the nuclear periphery. The observed frequency of associations among them, made distinguishable by specific probes and FISH, seems to be the same for pairs that may or may not form Rb chromosomes. In the homozygote Rb 2n = 24 spermatocytes, associations also mediated by pericentromeric heterochromatin occur mainly between the three telocentric or the eight metacentric bivalents themselves. In heterozygote Rb 2n = 32 spermatocytes all heterochromatin is localized at the nuclear periphery, yet associations are mainly observed among the three telocentric bivalents and between the asynaptic axes of the trivalents. Conclusions The Rb chromosomes pose sharp restrictions for interactions in the 2n = 24 and 2n = 32 spermatocytes, as compared to the ample possibilities for interactions between bivalents in the 2n = 40 spermatocytes. Undoubtedly the emergence of Rb chromosomes changes the ancestral nuclear architecture of 2n = 40 spermatocytes since they establish new types of interactions among chromosomal domains, particularly through centromeric and heterochromatic regions at the nuclear periphery among telocentric and at the nuclear center among Rb metacentric ones.
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