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      The mitochondrial genome of hydrothermal vent barnacle Eochionelasmus coreana (Cirripedia: Thoracica) from the Indian Ocean

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          Abstract

          Balanomorph Eochionelasmus species are hydrothermal vent endemic barnacles. In the genus Eochionelasmus, three species are known to date and they distribute at three different vent fields in Pacific and Indian Oceans, E. ohtai in the Southwest Pacific Ocean, E. paquensis in the East Pacific Ocean, and E. coreana in the Indian Ocean. Therefore, Eochionelasmus species are considered to be a meaningful model taxon to elucidate the evolutionary history of vent organism in relation to geotectonic events. Here, we characterized the partial mitogenome of a newly described vent barnacle Eochionelasmus coreana Chan et al., 2020 from the Solitaire vent field in the Indian Ocean. The length of mitogenome was 16,804 bp with 64.0% AT content. Its gene content and organization was identical to those of E. ohtai. There was one significant part in the mitogenome of E. coreana, which was a long intergenic region over 2 kb found between tRNA Pro and tRNA Thr. The phylogenetic tree suggested the monophyly of E. ohtai and E. coreana with high supporting values. In the future, additional mitogenome analysis of the last Eochionelasmus species, E. paquensis, could expand our understanding about the speciation and global distribution of Eochionelasmus species.

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          Most cited references 12

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          MITOS: improved de novo metazoan mitochondrial genome annotation.

          About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de. Copyright © 2012 Elsevier Inc. All rights reserved.
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            NOVOPlasty: de novo assembly of organelle genomes from whole genome data

            Abstract The evolution in next-generation sequencing (NGS) technology has led to the development of many different assembly algorithms, but few of them focus on assembling the organelle genomes. These genomes are used in phylogenetic studies, food identification and are the most deposited eukaryotic genomes in GenBank. Producing organelle genome assembly from whole genome sequencing (WGS) data would be the most accurate and least laborious approach, but a tool specifically designed for this task is lacking. We developed a seed-and-extend algorithm that assembles organelle genomes from whole genome sequencing (WGS) data, starting from a related or distant single seed sequence. The algorithm has been tested on several new (Gonioctena intermedia and Avicennia marina) and public (Arabidopsis thaliana and Oryza sativa) whole genome Illumina data sets where it outperforms known assemblers in assembly accuracy and coverage. In our benchmark, NOVOPlasty assembled all tested circular genomes in less than 30 min with a maximum memory requirement of 16 GB and an accuracy over 99.99%. In conclusion, NOVOPlasty is the sole de novo assembler that provides a fast and straightforward extraction of the extranuclear genomes from WGS data in one circular high quality contig. The software is open source and can be downloaded at https://github.com/ndierckx/NOVOPlasty.
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              Evolutionary and biogeographical patterns of barnacles from deep‐sea hydrothermal vents

              Abstract The characterization of evolutionary and biogeographical patterns is of fundamental importance to identify factors driving biodiversity. Due to their widespread but discontinuous distribution, deep‐sea hydrothermal vent barnacles represent an excellent model for testing biogeographical hypotheses regarding the origin, dispersal and diversity of modern vent fauna. Here, we characterize the global genetic diversity of vent barnacles to infer their time of radiation, place of origin, mode of dispersal and diversification. Our approach was to target a suite of multiple loci in samples representing seven of the eight described genera. We also performed restriction‐site associated DNA sequencing on individuals from each species. Phylogenetic inferences and topology hypothesis tests indicate that vent barnacles have colonized deep‐sea hydrothermal vents at least twice in history. Consistent with preliminary estimates, we find a likely radiation of barnacles in vent ecosystems during the Cenozoic. Our analyses suggest that the western Pacific was the place of origin of the major vent barnacle lineage, followed by circumglobal colonization eastwards through the Southern Hemisphere during the Neogene. The inferred time of radiation rejects the classic hypotheses of antiquity of vent taxa. The timing and the mode of origin, radiation and dispersal are consistent with recent inferences made for other deep‐sea taxa, including nonvent species, and are correlated with the occurrence of major geological events and mass extinctions. Thus, we suggest that the geological processes and dispersal mechanisms discussed here can explain the current distribution patterns of many other marine taxa and have played an important role shaping deep‐sea faunal diversity. These results also constitute the critical baseline data with which to assess potential effects of anthropogenic disturbances on deep‐sea ecosystems.
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                Author and article information

                Journal
                Mitochondrial DNA B Resour
                Mitochondrial DNA B Resour
                Mitochondrial DNA. Part B, Resources
                Taylor & Francis
                2380-2359
                15 March 2021
                2021
                : 6
                : 3
                : 710-712
                Affiliations
                [a ]Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology , Daejeon, Korea
                [b ]Biodiversity Research Center, Academia Sinica , Taipei, Taiwan
                [c ]Global Ocean Research Center, Korea Institute of Ocean Science and Technology , Busan, Korea
                [d ]Marine Biology Major, University of Science & Technology , Daejeon, Korea
                [e ]Marine Ecosystem Research Center, Korea Institute of Ocean Science and Technology , Busan, Korea
                Author notes
                CONTACT Se-Joo Kim biosejoo@ 123456kribb.re.kr Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology , 125 Gwahak-ro, Yuseong-gu, Daejeon34141, Korea
                Article
                1851153
                10.1080/23802359.2020.1851153
                7971211
                © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Page count
                Figures: 1, Tables: 0, Pages: 3, Words: 1566
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                Research Article
                Mitogenome Announcement

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