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Literature DB >> 25937221

Sequencing of the complete genome of an araphid pennate diatom Synedra acus subsp. radians from Lake Baikal.

Y P Galachyants¹, Yu R Zakharova, D P Petrova, A A Morozov, I A Sidorov, A M Marchenkov, M D Logacheva, M L Markelov, K V Khabudaev, Ye V Likhoshway, M A Grachev.

Abstract

High-throughput method of sequencing was applied to determine the complete nucleotide sequence of an araphid pennate diatom Synedra acus subsp. radians from Lake Baikal (East Siberia). The assembled genome has a total length of 98 Mbp, the mean coverage is 33x. Structure-functional annotation of the genome was performed.

Entities: Species

Mesh：

Year: 2015 PMID： 25937221 DOI： 10.1134/S1607672915020064

Source DB: PubMed Journal: Dokl Biochem Biophys ISSN： 1607-6729 Impact factor: 0.788

12 in total

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Authors: Nikolai V Ravin; Yuri P Galachyants; Andrey V Mardanov; Alexey V Beletsky; Darya P Petrova; Tatyana A Sherbakova; Yuliya R Zakharova; Yelena V Likhoshway; Konstantin G Skryabin; Mikhail A Grachev
Journal: Curr Genet Date: 2010-03-23 Impact factor: 3.886

3. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.

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Journal: Bioinformatics Date: 2007-03-01 Impact factor: 6.937

4. The silica balance in the world ocean: a reestimate.

Authors: P Tréguer; D M Nelson; A J Van Bennekom; D J Demaster; A Leynaert; B Quéguiner
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5. CORRELATED EVOLUTION OF GENOME SIZE AND CELL VOLUME IN DIATOMS (BACILLARIOPHYCEAE)(1).

Authors: Jessica A Connolly; Matthew J Oliver; Jeremy M Beaulieu; Charles A Knight; Lars Tomanek; Mark A Moline
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Journal: Nature Date: 2008-10-15 Impact factor: 49.962

7. OrthoMCL: identification of ortholog groups for eukaryotic genomes.

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8. iTRAQ-based proteomic analysis of the metabolism mechanism associated with silicon response in the marine diatom Thalassiosira pseudonana.

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9. InterProScan 5: genome-scale protein function classification.

Authors: Philip Jones; David Binns; Hsin-Yu Chang; Matthew Fraser; Weizhong Li; Craig McAnulla; Hamish McWilliam; John Maslen; Alex Mitchell; Gift Nuka; Sebastien Pesseat; Antony F Quinn; Amaia Sangrador-Vegas; Maxim Scheremetjew; Siew-Yit Yong; Rodrigo Lopez; Sarah Hunter
Journal: Bioinformatics Date: 2014-01-21 Impact factor: 6.937

10. High-throughput functional annotation and data mining with the Blast2GO suite.

Authors: Stefan Götz; Juan Miguel García-Gómez; Javier Terol; Tim D Williams; Shivashankar H Nagaraj; María José Nueda; Montserrat Robles; Manuel Talón; Joaquín Dopazo; Ana Conesa
Journal: Nucleic Acids Res Date: 2008-04-29 Impact factor: 16.971

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2. Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome.

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3. Unique configuration of genes of silicon transporter in the freshwater pennate diatom Synedra acus subsp. radians.

Authors: A M Marchenkov; A A Bondar; D P Petrova; K V Habudaev; Yu P Galachyants; Yu R Zakharova; N A Volokitina; M A Grachev
Journal: Dokl Biochem Biophys Date: 2017-01-06 Impact factor: 0.788

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Journal: Mar Biotechnol (NY) Date: 2022-04-09 Impact factor: 3.619

5. Re-examination of two diatom reference genomes using long-read sequencing.

Authors: Gina V Filloramo; Bruce A Curtis; Emma Blanche; John M Archibald
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6. Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes.

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Journal: Proc Natl Acad Sci U S A Date: 2021-01-26 Impact factor: 12.779

7. The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms.

Authors: Gust Bilcke; Emmelien Vancaester; Cristina Maria Osuna-Cruz; Sam De Decker; Atle M Bones; Per Winge; Nicole Poulsen; Petra Bulankova; Bram Verhelst; Sien Audoor; Darja Belisova; Aikaterini Pargana; Monia Russo; Frederike Stock; Emilio Cirri; Tore Brembu; Georg Pohnert; Gwenael Piganeau; Maria Immacolata Ferrante; Thomas Mock; Lieven Sterck; Koen Sabbe; Lieven De Veylder; Wim Vyverman; Klaas Vandepoele
Journal: Nat Commun Date: 2020-07-03 Impact factor: 14.919

8. A family of silicon transporter structural genes in a pennate diatom Synedra ulna subsp. danica (Kütz.) Skabitsch.

Authors: Artyom M Marchenkov; Darya P Petrova; Alexey A Morozov; Yulia R Zakharova; Michael A Grachev; Alexander A Bondar
Journal: PLoS One Date: 2018-08-29 Impact factor: 3.240

9. Extensive chloroplast genome rearrangement amongst three closely related Halamphora spp. (Bacillariophyceae), and evidence for rapid evolution as compared to land plants.

Authors: Sarah E Hamsher; Kyle G Keepers; Cloe S Pogoda; Joshua G Stepanek; Nolan C Kane; J Patrick Kociolek
Journal: PLoS One Date: 2019-07-03 Impact factor: 3.240

10. De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal.

Authors: Yuri Pavlovich Galachyants; Yulia Robertovna Zakharova; Nadezda Antonovna Volokitina; Alexey Anatolyevich Morozov; Yelena Valentinovna Likhoshway; Mikhail Aleksandrovich Grachev
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