Partially Local Three-Way Alignments and the Sequence Signatures of Mitochondrial Genome Rearrangements
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Kaistella Soli Sp. Nov., Isolated from Oil-Contaminated Soil
A001 Kaistella soli sp. nov., Isolated from Oil-contaminated Soil Dhiraj Kumar Chaudhary1, Ram Hari Dahal2, Dong-Uk Kim3, and Yongseok Hong1* 1Department of Environmental Engineering, Korea University Sejong Campus, 2Department of Microbiology, School of Medicine, Kyungpook National University, 3Department of Biological Science, College of Science and Engineering, Sangji University A light yellow-colored, rod-shaped bacterial strain DKR-2T was isolated from oil-contaminated experimental soil. The strain was Gram-stain-negative, catalase and oxidase positive, and grew at temperature 10–35°C, at pH 6.0– 9.0, and at 0–1.5% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence analysis suggested that the strain DKR-2T was affiliated to the genus Kaistella, with the closest species being Kaistella haifensis H38T (97.6% sequence similarity). The chemotaxonomic profiles revealed the presence of phosphatidylethanolamine as the principal polar lipids;iso-C15:0, antiso-C15:0, and summed feature 9 (iso-C17:1 9c and/or C16:0 10-methyl) as the main fatty acids; and menaquinone-6 as a major menaquinone. The DNA G + C content was 39.5%. In addition, the average nucleotide identity (ANIu) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain DKR-2T and phylogenically closest members were below the threshold values for species delineation. The polyphasic taxonomic features illustrated in this study clearly implied that strain DKR-2T represents a novel species in the genus Kaistella, for which the name Kaistella soli sp. nov. is proposed with the type strain DKR-2T (= KACC 22070T = NBRC 114725T). [This study was supported by Creative Challenge Research Foundation Support Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF- 2020R1I1A1A01071920).] A002 Chitinibacter bivalviorum sp. -
Sequences Signature and Genome Rearrangements in Mitogenomes
Sequences Signature and Genome Rearrangements in Mitogenomes Von der Fakultät für Mathematik und Informatik der Universität Leipzig angenommene DISSERTATION zur Erlangung des akademischen Grades DOCTOR RERUM NATURALIUM (Dr. rer. nat.) im Fachgebiet Informatik vorgelegt von Msc. Marwa Al Arab geboren am 27. Mai 1988 in Ayyat, Libanon Die Annahme der Dissertation wurde empfohlen von: 1. Prof. Dr. Peter F. Stadler, Universität Leipzig 2. Prof. Dr. Burkhard Morgenstern, Universität Göttingen 3. Prof. Dr. Kifah R. Tout, Lebanese University Die Verleihung des akademischen Grades erfolgt mit Bestehen der Verteidigung am 6.2.2018 mit dem Gesamtprädikat magna cum laude. Abstract During the last decades, mitochondria and their DNA have become a hot topic of re- search due to their essential roles which are necessary for cells survival and pathology. In this study, multiple methods have been developed to help with the understanding of mitochondrial DNA and its evolution. These methods tackle two essential prob- lems in this area: the accurate annotation of protein-coding genes and mitochondrial genome rearrangements. Mitochondrial genome sequences are published nowadays with increasing pace, which creates the need for accurate and fast annotation tools that do not require manual intervention. In this work, an automated pipeline for fast de-novo annotation of mitochondrial protein-coding genes is implemented. The pipeline includes methods for enhancing multiple sequence alignment, detecting frameshifts and building pro- tein proles guided by phylogeny. The methods are tested on animal mitogenomes available in RefSeq, the comparison with reference annotations highlights the high quality of the produced annotations. Furthermore, the frameshift method predicted a large number of frameshifts, many of which were unknown. -
Identification of Invasive Alien Species Using DNA Barcodes
Identification of Invasive Alien Species using DNA barcodes Royal Belgian Institute of Natural Sciences Royal Museum for Central Africa Rue Vautier 29, Leuvensesteenweg 13, 1000 Brussels , Belgium 3080 Tervuren, Belgium +32 (0)2 627 41 23 +32 (0)2 769 58 54 General introduction to this factsheet The Barcoding Facility for Organisms and Tissues of Policy Concern (BopCo) aims at developing an expertise forum to facilitate the identification of biological samples of policy concern in Belgium and Europe. The project represents part of the Belgian federal contribution to the European Research Infrastructure Consortium LifeWatch. Non-native species which are being introduced into Europe, whether by accident or deliberately, can be of policy concern since some of them can reproduce and disperse rapidly in a new territory, establish viable populations and even outcompete native species. As a consequence of their presence, natural and managed ecosystems can be disrupted, crops and livestock affected, and vector-borne diseases or parasites might be introduced, impacting human health and socio-economic activities. Non-native species causing such adverse effects are called Invasive Alien Species (IAS). In order to protect native biodiversity and ecosystems, and to mitigate the potential impact on human health and socio-economic activities, the issue of IAS is tackled in Europe by EU Regulation 1143/2014 of the European Parliament and Council. The IAS Regulation provides for a set of measures to be taken across all member states. The list of Invasive Alien Species of Union Concern is regularly updated. In order to implement the proposed actions, however, methods for accurate species identification are required when suspicious biological material is encountered. -
Bayesian Node Dating Based on Probabilities of Fossil Sampling Supports Trans-Atlantic Dispersal of Cichlid Fishes
Supporting Information Bayesian Node Dating based on Probabilities of Fossil Sampling Supports Trans-Atlantic Dispersal of Cichlid Fishes Michael Matschiner,1,2y Zuzana Musilov´a,2,3 Julia M. I. Barth,1 Zuzana Starostov´a,3 Walter Salzburger,1,2 Mike Steel,4 and Remco Bouckaert5,6y Addresses: 1Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway 2Zoological Institute, University of Basel, Basel, Switzerland 3Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic 4Department of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand 5Department of Computer Science, University of Auckland, Auckland, New Zealand 6Computational Evolution Group, University of Auckland, Auckland, New Zealand yCorresponding author: E-mail: [email protected], [email protected] 1 Supplementary Text 1 1 Supplementary Text Supplementary Text S1: Sequencing protocols. Mitochondrial genomes of 26 cichlid species were amplified by long-range PCR followed by the 454 pyrosequencing on a GS Roche Junior platform. The primers for long-range PCR were designed specifically in the mitogenomic regions with low interspecific variability. The whole mitogenome of most species was amplified as three fragments using the following primer sets: for the region between position 2 500 bp and 7 300 bp (of mitogenome starting with tRNA-Phe), we used forward primers ZM2500F (5'-ACG ACC TCG ATG TTG GAT CAG GAC ATC C-3'), L2508KAW (Kawaguchi et al. 2001) or S-LA-16SF (Miya & Nishida 2000) and reverse primer ZM7350R (5'-TTA AGG CGT GGT CGT GGA AGT GAA GAA G-3'). The region between 7 300 bp and 12 300 bp was amplified using primers ZM7300F (5'-GCA CAT CCC TCC CAA CTA GGW TTT CAA GAT GC-3') and ZM12300R (5'-TTG CAC CAA GAG TTT TTG GTT CCT AAG ACC-3'). -
Mechanisms of Gene Rearrangement in 13 Bothids
Luo et al. BMC Genomics (2019) 20:792 https://doi.org/10.1186/s12864-019-6128-9 RESEARCH ARTICLE Open Access Mechanisms of gene rearrangement in 13 bothids based on comparison with a newly completed mitogenome of the threespot flounder, Grammatobothus polyophthalmus (Pleuronectiformes: Bothidae) Hairong Luo1,2, Xiaoyu Kong1* , Shixi Chen1,2 and Wei Shi1 Abstract Background: The mitogenomes of 12 teleost fish of the bothid family (order Pleuronectiformes) indicated that the genomic-scale rearrangements characterized in previous work. A novel mechanism of genomic rearrangement called the Dimer-Mitogenome and Non-Random Loss (DMNL) model was used to account for the rearrangement found in one of these bothids, Crossorhombus azureus. Results: The 18,170 bp mitogenome of G. polyophthalmus contains 37 genes, two control regions (CRs), and the origin of replication of the L-strand (OL). This mitogenome is characterized by genomic-scale rearrangements: genes located on the L-strand are grouped in an 8-gene cluster (Q-A-C-Y-S1-ND6-E-P) that does not include tRNA-N; genes found on the H-strand are grouped together (F-12S … CytB-T) except for tRNA-D that was translocated inside the 8- gene L-strand cluster. Compared to non-rearranged mitogenomes of teleost fishes, gene organization in the mitogenome of G. polyophthalmus and in that of the other 12 bothids characterized thus far is very similar. These rearrangements could be sorted into four types (Type I, II, III and IV), differing in the particular combination of the CR, tRNA-D gene and 8-gene cluster and the shuffling of tRNA-V. -
Evolution of Oxidative Metabolism in Fishes
EVOLUTION OF OXIDATIVE METABOLISM IN FISHES by Alexander George Little A thesis submitted to the Department of Biology In conformity with the requirements for the degree of Master of Science Queenʼs University Kingston, Ontario, Canada September, 2009 ©Alexander George Little, 2009 Abstract " My study investigated the evolution of oxidative metabolism in fishes. While intense selection for, or against, non-synonymous point mutations in coding sequence drives the evolution of mitochondrial OXPHOS genes, genome-specific mechanisms such as gene duplication events can play major roles in the evolution of nuclear OXPHOS genes. My thesis focused on the mitochondrial enzyme cytochrome c oxidase (COX), principally in fish because of their evolutionary origins and functional diversity in terms of energy metabolism. In the first part of my thesis, I examined a highly aerobic group of fishes (billfishes and tunas) to study the evolution of mitochondrial COX genes. Though the study began as a structure-function analysis of COX, my approach changed when my preliminary results called into question the accepted phylogenetic relationships of my species of interest. We generated a robust multigene phylogeny of this group to interpret data in a phylogenetically informative context. Phylogenetic analyses in this group provided us with a framework to study the evolution of mitochondrial OXPHOS genes, but unexpectedly revealed that: 1) billfishes are only distantly related to tunas, and share greater evolutionary affinities with flatfishes (Pleuronectiformes) and jacks (Carangidae), and 2) regional endothermy has evolved in a non-scombroid suborder in teleosts. These results collectively imply that regional endothermy has evolved independently at least twice within teleost fish. -
The Mitochondrial Genome Sequences of the Round Goby and the Sand
Adrian-Kalchhauser et al. BMC Genomics (2017) 18:177 DOI 10.1186/s12864-017-3550-8 RESEARCHARTICLE Open Access The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish Irene Adrian-Kalchhauser1* , Ola Svensson2,3, Verena E. Kutschera4, Magnus Alm Rosenblad3,5, Martin Pippel6, Sylke Winkler7, Siegfried Schloissnig6, Anders Blomberg3,8† and Patricia Burkhardt-Holm1,9† Abstract Background: Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb). Results: During genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16.4 kb), while the mitochondrial genome of the round goby is much larger than expected for a vertebrate. It is 19 kb in size and is thus one of the largest fish and even vertebrate mitochondrial genomes known to date. The expansion is attributable to a sequence insertion downstream of the putative transcriptional start site. This insertion carries traces of repeats from the control region, but is mostly novel. To get more information about this phenomenon, we gathered all available mitochondrial genomes of Gobiidae and of nine gobioid species, performed phylogenetic analyses, analysed gene arrangements, and compared gobiid mitochondrial genome sizes, ecological information and other species characteristics with respect to the mitochondrial phylogeny. This allowed us amongst others to identify a unique arrangement of tRNAs among Ponto-Caspian gobies. -
Comparative Mitogenomics of the Genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) Revealed Conserved Gene Rearrangement and High Sequence Variations
Int. J. Mol. Sci. 2015, 16, 25031-25049; doi:10.3390/ijms161025031 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article Comparative Mitogenomics of the Genus Odontobutis (Perciformes: Gobioidei: Odontobutidae) Revealed Conserved Gene Rearrangement and High Sequence Variations Zhihong Ma 1, Xuefen Yang 1,2, Miklos Bercsenyi 3, Junjie Wu 1, Yongyao Yu 1, Kaijian Wei 1,2, Qixue Fan 1,2 and Ruibin Yang 1,2,* 1 Key Lab of Freshwater Animal Breeding Certificated by Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; E-Mails: [email protected] (Z.M.); [email protected] (X.Y.); [email protected] (J.W.); [email protected] (Y.Y.); [email protected] (K.W.); [email protected] (Q.F.) 2 Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China 3 Georgikon Faculty, University of Pannonia, Keszthely 8360, Hungary; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +86-27-8728-2113; Fax: +86-27-8728-2114. Academic Editors: Jun Li and Li Lin Received: 16 August 2015 / Accepted: 14 October 2015 / Published: 20 October 2015 Abstract: To understand the molecular evolution of mitochondrial genomes (mitogenomes) in the genus Odontobutis, the mitogenome of Odontobutis yaluensis was sequenced and compared with those of another four Odontobutis species. Our results displayed similar mitogenome features among species in genome organization, base composition, codon usage, and gene rearrangement. The identical gene rearrangement of trnS-trnL-trnH tRNA cluster observed in mitogenomes of these five closely related freshwater sleepers suggests that this unique gene order is conserved within Odontobutis.