Complete Mitogenome Sequencing, Annotation, and Phylogeny of Grateloupia turuturu, a Red Alga with Intronic cox1 Gene

The mitochondrial genome (mitogenome) is essential for identifying species and tracing genetic variation, gene patterns, and evolutionary studies. Here, the mitogenome of Grateloupia turuturu was sequenced on the Illumina sequencing platform. This circular mitogenome (28,265 bp) contains 49 genes, including three rRNAs, twenty transfer RNAs (tRNAs), and twenty-six protein-coding genes (PCGs). Nucleotide composition indicates biased AT (68.8%) content. A Group II intronic sequence was identified between two exons of the cox1 gene, and this sequence comprises an open reading frame (ORF) that encodes a hypothetical protein. The gene content, annotation, and genetic makeup are identical to those of Halymeniaceae members. The complete mitogenome sequences of the Grateloupia and Polyopes species were used in a phylogenetic analysis, which revealed that these two genera are monophyletic and that G. turuturu and G. elliptica are closely related. This newly constructed mitogenome will help us better understand the general trends in the development of cox1 introns in Halymeniaceae, as well as the evolution of red algal mitogenomes within the Rhodophyta and among diverse algal species.

[1]  J. West,et al.  Origin of minicircular mitochondrial genomes in red algae , 2023, Nature communications.

[2]  Jong-Oh Kim,et al.  The complete sequence of the mitochondrial DNA and phylogenetic analysis of the marine red alga Grateloupia elliptica (Rhodophyta: Halymeniales) , 2023, Mitochondrial DNA. Part B, Resources.

[3]  Yongjin He,et al.  The complete mitochondrial genome of Isochrysis galbana harbors a unique repeat structure and a specific trans-spliced cox1 gene , 2022, Frontiers in Microbiology.

[4]  Yafei Cai,et al.  Life barcoded by DNA barcodes , 2022, Conservation Genetics Resources.

[5]  Jong-Oh Kim,et al.  Complete mitochondrial genome and phylogenetic analysis of the marine red alga Polyopes affinis (Rhodophyta: Halymeniales) , 2022, Mitochondrial DNA. Part B, Resources.

[6]  C. Cho,et al.  Group II intron and repeat-rich red algal mitochondrial genomes demonstrate the dynamic recent history of autocatalytic RNAs , 2022, BMC biology.

[7]  Sudhir Kumar,et al.  MEGA11: Molecular Evolutionary Genetics Analysis Version 11 , 2021, Molecular biology and evolution.

[8]  S. Y. Kim,et al.  Complete mitochondrial genome of Polyopes lancifolius and comparison with related species in Halymeniales (Rhodophyta) , 2021, Mitochondrial DNA Part B: Resources.

[9]  Lu Sun,et al.  NCBI Taxonomy: a comprehensive update on curation, resources and tools , 2020, Database J. Biol. Databases Curation.

[10]  R. Bock,et al.  OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes , 2019, bioRxiv.

[11]  H. Yoon,et al.  Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements , 2018, BMC Genomics.

[12]  Maria Dyah Nur Meinita,et al.  Complete sequences of the mitochondrial DNA of the Grateloupia filicina (Rhodophyta) , 2018, Mitochondrial DNA. Part B, Resources.

[13]  C. Lane,et al.  Red Algal Mitochondrial Genomes Are More Complete than Previously Reported , 2016, Genome biology and evolution.

[14]  Patricia P. Chan,et al.  tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes , 2016, Nucleic Acids Res..

[15]  S. Y. Kim,et al.  Highly Conserved Mitochondrial Genomes among Multicellular Red Algae of the Florideophyceae , 2015, Genome biology and evolution.

[16]  D. Bhattacharya,et al.  The Mitochondrial Genome of Grateloupia taiwanensis (Halymeniaceae, Rhodophyta) and Comparative Mitochondrial Genomics of Red Algae , 2014, The Biological Bulletin.

[17]  S. Y. Kim,et al.  Complete mitochondrial genome of the marine red alga Grateloupia angusta (Halymeniales) , 2014, Mitochondrial DNA.

[18]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[19]  Paul Medvedev,et al.  Informed and automated k-mer size selection for genome assembly , 2013, Bioinform..

[20]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[21]  B. Lang,et al.  Mitochondrial introns: a critical view. , 2007, Trends in genetics : TIG.

[22]  S. Adl,et al.  The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists , 2005, The Journal of eukaryotic microbiology.

[23]  B. Lang,et al.  The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b. , 2003, Nucleic acids research.

[24]  Julie D Thompson,et al.  Multiple Sequence Alignment Using ClustalW and ClustalX , 2003, Current protocols in bioinformatics.

[25]  P Stothard,et al.  The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. , 2000, BioTechniques.

[26]  B F Lang,et al.  Complete Sequence of the Mitochondrial DNA of the Red Alga Porphyra purpurea: Cyanobacterial Introns and Shared Ancestry of Red and Green Algae , 1999, Plant Cell.

[27]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[28]  David J. States,et al.  Identification of protein coding regions by database similarity search , 1993, Nature Genetics.

[29]  R. Bock,et al.  Genomics of Chloroplasts and Mitochondria , 2012, Advances in Photosynthesis and Respiration.

[30]  J. Felsenstein Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[31]  Nicole T. Perna,et al.  Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes , 2004, Journal of Molecular Evolution.

[32]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.