Abebe M., Candales M. A., Duong A., Hood K. S., Li T., Neufeld R. A. et al. 2013 A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank. Mobile DNA 4, 1–9.
Adl S. M., Simpson A. G., Farmer M. A., Andersen R. A., Anderson O. R., Barta J. R. et al. 2005 The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol. 52, 399–451.
Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W. et al. 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.
Article CAS PubMed PubMed Central Google Scholar
Andrews S. 2010 FastQC: A quality control tool for high throughput sequence data, Babraham Institute, Cambridge.
Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S. et al. 2012 SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477.
Article CAS PubMed PubMed Central Google Scholar
Beck N., Lang B. 2010 MFannot, organelle genome annotation webserver, Université de Montréal QC, Canada.
Benson G. 1999 Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580.
Article CAS PubMed PubMed Central Google Scholar
Burger G., and Nedelcu A. M. 2012 Mitochondrial genomes of algae. In Genomics of Chloroplasts and Mitochondria (Advances in photosynthesis and respiration, vol 35.) (ed. R. Bock, and V. Knoop ) pp. 127–157. Springer, Dordrecht.
Burger G., Lang B. F., Braun H. P. and Marx S. 2003 The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b. Nucleic Acids Res. 31, 2353–2360.
Article CAS PubMed PubMed Central Google Scholar
Chikhi R. and Medvedev P. 2014 Informed and automated k-mer size selection for genome assembly. Bioinformatics 30, 31–37.
Article CAS PubMed Google Scholar
Dawson E. Y. 1958 Notes on Pacific coast marine algae, VII. Bulletin, Southern California Academy of Sciences 57, 65–80.
DePriest M. S., Bhattacharya D. and Lopez-Bautista J. M. 2014 The mitochondrial genome of Grateloupia taiwanensis (Halymeniaceae, Rhodophyta) and comparative mitochondrial genomics of red algae. Biol. Bull. 227, 191–200.
Article CAS PubMed Google Scholar
Enyeart P. J., Mohr G., Ellington A. D. and Lambowitz A. M. 2014 Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis. Mobile DNA 5, 1–19.
Felsenstein J. 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376.
Article CAS PubMed Google Scholar
Gargiulo G. M., Morabito M. and Manghisi A. 2013 A re-assessment of reproductive anatomy and postfertilization development in the systematics of Grateloupia (Halymeniales, Rhodophyta). Cryptogam. Algol. 34, 3–35.
Gish W. and States D. J. 1993 Identification of protein coding regions by database similarity search. Nat. Genet. 3, 266–272.
Article CAS PubMed Google Scholar
Greiner S., Lehwark P. and Bock R. 2019 OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 47, W59–W64.
Article CAS PubMed PubMed Central Google Scholar
Guiry M. D. and Guiry G. M. 2017 AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. https://www.algaebase.org/about/; searched on 6 June 2023.
Gurgel C. F. D. and Lopez-Bautista J. 2007 Red algae. Encyclopedia of life science, Wiley, Hoboken.
Jung S. W. and Choi C. G. 2020 Characteristics of marine algal communities in the spring at Gijang-gun, Busan. J. Korean Soc. Mar. Environ. Saf. 26, 175–185.
Kang J. W. 1966 On the geographical distribution of marine algae in Korea. Bull. Pusan Fish Coll. 7, 1–125.
Kawabata S. 1954 On the structure of the frond, and the reproductive organ of Pachymeniopsis lanceolate Yamada (Aeodes Ianceolata Okamura). Bull. Jpn. Soc. Phycol. 2, 67–71.
Kawaguchi S. 1997 Taxonomic notes on the Halymeniaceae (Gigartinales, Rhodophyta) from Japan. III. Synonymization of Pachymeniopsis Yamada in Kawabata with Grateloupia C. Agardh. Phycol. Res. 45, 9–21.
Kim S. Y., Manghisi A., Morabito M., Yang E. C., Yoon H. S., Miller K. A. et al. 2014a Genetic diversity and haplotype distribution of Pachymeniopsis gargiuli sp. nov. and P. lanceolata (Halymeniales, Rhodophyta) in Korea, with notes on their non-native distributions. J. Phycol. 50, 885–896.
Article CAS PubMed Google Scholar
Kim S. Y., Yang E. C., Boo S. M. and Yoon H. S. 2014b Complete mitochondrial genome of the marine red alga Grateloupia angusta (Halymeniales). Mitochondrial DNA 25, 269–270.
Article CAS PubMed Google Scholar
Kim J. I., Yoon H. S., Yi G., Shin W. and Archibald J. M. 2018 Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements. BMC Genomics 19, 1–14.
Kim S. Y., Cho C. H., Yang E. C., Yoon H. S. and Kim M. S. 2021 Complete mitochondrial genome of Polyopes lancifolius and comparison with related species in Halymeniales (Rhodophyta). Mitochondrial DNA Part B 6, 1365–1366.
Article PubMed PubMed Central Google Scholar
Kim D., Lee J., Cho C. H., Kim E. J., Bhattacharya D. and Yoon H. S. 2022 Group II intron and repeat-rich red algal mitochondrial genomes demonstrate the dynamic recent history of autocatalytic RNAs. BMC Biol. 20, 2.
Article CAS PubMed PubMed Central Google Scholar
Kozhenkova S. I. 2020 Checklist of marine benthic algae from the Russian continental coast of the Sea of Japan. Phytotaxa 437, 177–205.
Lang B. F., Laforest M. J. and Burger G. 2007 Mitochondrial introns: a critical view. Trends Genet. 23, 119–125.
Article CAS PubMed Google Scholar
Lee Y., and Kang S. 2001 A catalogue of the seaweeds in Korea, pp. 473–474. Cheju National University Press, Jeju.
Lee J. I., Kim H. K., Yoo K. D., Yoon H. D. and Kim Y. H. 2015 Benthic marine algal community on the mid-east coast of Korea. J. Korean Soc. Mar. Environ. Saf. 21, 119–129.
Lee Y., Cho C. H., Noh C., Yang J. H., Park S. I., Lee Y. M. et al. 2023 Origin of minicircular mitochondrial genomes in red algae. Nat. Commun. 14, 3363.
Article CAS PubMed PubMed Central Google Scholar
Li Y., Meinita M. D. N., Liu T., Chi S. and Yin H. 2018 Complete sequences of the mitochondrial DNA of the Grateloupia filicina (Rhodophyta). Mitochondrial DNA Part b. 3, 76–77.
Article PubMed PubMed Central Google Scholar
Martin M. 2011 Cutadapt removes adapter sequences from high-throughput sequencing reads. Embnet J. 17, 10–12.
Ohta N., Sato N. and Kuroiwa T. 1998 Structure and organization of the mitochondrial genome of the unicellular red alga Cyanidioschyzon merolae deduced from the complete nucleotide sequence. Nucleic Acids Res. 26, 5190–5198.
Article CAS PubMed PubMed Central Google Scholar
Okamura K. 1934 Icons of Japanese algae, vol. 7, pp. 39–48. Kazamashobo, Tokyo.
Patil M. P., Kim J. O., Kim K., Kim Y. R. and Yoon S. 2022 Complete mitochondrial genome and phylogenetic analysis of the marine red alga Polyopes affinis (Rhodophyta: Halymeniales). Mitochondrial DNA Part B 7, 1387–1388.
Article PubMed PubMed Central Google Scholar
Patil M. P., Kim J. O., Kim K. and Kim Y. R. 2023a The complete sequence of the mitochondrial DNA and phylogenetic analysis of the marine red alga Grateloupia elliptica (Rhodophyta: Halymeniales). Mitochondrial DNA Part B 8, 222–223.
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