Cite this paper:
Fangru NAN, Juan LI, Jia FENG, Junping LÜ, Qi LIU, Xudong LIU, Shulian XIE. Comparison and phylogeny on mitochondrial genome of marine and freshwater taxa of genus Hildenbrandia (Florideophyceae, Rhodophyta)[J]. Journal of Oceanology and Limnology, 2023, 41(6): 2324-2335

Comparison and phylogeny on mitochondrial genome of marine and freshwater taxa of genus Hildenbrandia (Florideophyceae, Rhodophyta)

Fangru NAN, Juan LI, Jia FENG, Junping LÜ, Qi LIU, Xudong LIU, Shulian XIE
School of Life Science, Shanxi University, Taiyuan 030006, China
Hildenbrandia is an early diverged lineage in Florideophyceae, Rhodophyta. The species diversity of this genus is still unresolved due to the simple morphology and limited molecular information. The mitochondrial genome of freshwater H. jigongshanensis was determined in this study. The freshwater H. jigongshanensis had a larger mitochondrial genome than the marine H. rubra and GC content was higher. Collinear alignment structure was observed between the mitochondrial genomes of H. jigongshanensis and H. rubra, except for one block that was encoded on the complement strand. More introns were found in mitochondrial genome of H. jigongshanensis than in H. rubra, and H. jigongshanensis shares the common feature with Bangiophyceae that two introns were distributed in cox1. Comparison of mitochondrial genome organization suggests that H. jigongshanensis preserves characters that could be hypothetically more similar to the ancestor of Bangiophyceae and Florideophyceae, which differ with previous studies based on chloroplast, and nuclear markers. More mitochondrial genomes and phylogenetic analyses combing nuclear, chloroplast and mitochondrial genomes are needed to clarify this discrepancy. Mitochondrion-based phylogeny in this study resulted in better solution at both the deep and recent derived nodes than single-gene phylogenies. Most protein-coding genes between H. jigongshanensis and H. rubra were identical except atp8, which was present in H. jigongshanensis while absent from H. rubra. This finding follows the trend that high Ka/Ks ratio genes are more frequently lost than low Ka/Ks ratio ones in red algae.
Key words:    red algae|organelle genome|freshwater species|phylogenomics   
Received: 2022-03-30   Revised:
PDF (4882 KB) Free
Print this page
Add to favorites
Email this article to others
Articles by Fangru NAN
Articles by Juan LI
Articles by Jia FENG
Articles by Junping LÜ
Articles by Qi LIU
Articles by Xudong LIU
Articles by Shulian XIE
Adams K L, Palmer J D.2003.Evolution of mitochondrial gene content:gene loss and transfer to the nucleus.Molecular Phylogenetics and Evolution, 29(3):380-395,
Adams K L, Qiu Y L, Stoutemyer M et al.2002.Punctuated evolution of mitochondrial gene content:high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution.Proceedings of the National Academy of Sciences, 99(15):9905-9912,
Bankevich A, Nurk S, Antipov D et al.2012.SPAdes:a new genome assembly algorithm and its applications to single-cell sequencing.Journal of Computational Biology, 19(5):455-477,
Bi G Q, Mao Y X, Xing Q K et al.2018."HomBlocks":a multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching.Genomics, 110(1):18-22,
Burger G, Lang B F, Braun H P et al.2003.The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b.Nucleic Acids Research, 31(9):2353-2360,
Cho C H, Park S I, Ciniglia C et al.2020.Potential causes and consequences of rapid mitochondrial genome evolution in thermoacidophilic Galdieria (Rhodophyta).BMC Evolutionary Biology, 20(1):112,
Darling A C E, Mau B, Blattner F R et al.2004.Mauve:multiple alignment of conserved genomic sequence with rearrangements.Genome Research, 14(7):1394-1403,
Denovan-Wright E M, Nedelcu A M, Lee R W.1998.Complete sequence of the mitochondrial DNA of Chlamydomonas eugametos.Plant Molecular Biology, 36(2):285-295,
Felsenstein J.1981.Evolutionary trees from DNA sequences:a maximum likelihood approach.Journal of Molecular Evolution, 17(6):368-376,
Gray M W, Lang B F, Cedergren R et al.1998.Genome structure and gene content in protist mitochondrial DNAs.Nucleic Acids Research, 26(4):865-878,
Hancock L, Goff L, Lane C.2010.Red algae lose key mitochondrial genes in response to becoming parasitic.Genome Biology and Evolution, 2:897-910,
Iha C, Grassa C J, de M Lyra G et al.2018.Organellar genomics:a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta).Journal of Phycology, 54(6):775-787,
Langmead B, Salzberg S L.2012.Fast gapped-read alignment with Bowtie 2.Nature Methods, 9(4):357-359,
Le Gall L, Saunders G W.2007.A nuclear phylogeny of the Florideophyceae (Rhodophyta) inferred from combined EF2, small subunit and large subunit ribosomal DNA:establishing the new red algal subclass Corallinophycidae.Molecular Phylogenetics and Evolution, 43(3):1118-1130,
Lee J M, Cho C H, Park S I et al.2016.Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants.BMC Biology, 14(1):75,
Lee J M, Song H J, Park S I et al.2018.Mitochondrial and plastid genomes from coralline red algae provide insights into the incongruent evolutionary histories of organelles.Genome Biology and Evolution, 10(11):2961-2972,
Nan F R, Feng J, Lv J P et al.2017a.Hildenbrandia jigongshanensis (Hildenbrandiaceae, Rhodophyta), a new freshwater species described from Jigongshan Mountain, China.Phytotaxa, 292(3):243-252,
Nan F R, Feng J, Lv J P et al.2017b.Origin and evolutionary history of freshwater Rhodophyta:further insights based on phylogenomic evidence.Scientific Reports, 7(1):2934,
Nan F R, Han J F, Feng J et al.2019.Morphological and molecular investigation of freshwater Hildenbrandia (Hildenbrandiales, Rhodophyta) with a new species reported from Japan.Phytotaxa, 423(2):68-74,
Okonechnikov K, Golosova O, Fursov M et al.2012.Unipro UGENE:a unified bioinformatics toolkit.Bioinformatics, 28(8):1166-1167,
Oliveira M C, Repetti S I, Iha C et al.2018.High-throughput sequencing for algal systematics.European Journal of Phycology, 53(3):256-272,
Paiano M O, Del Cortona A, Costa J F et al.2018.Complete mitochondrial genomes of six species of the freshwater red algal order Batrachospermales (Rhodophyta).Mitochondrial DNA Part B, 3(2):607-610,
Posada D, Buckley T R.2004.Model selection and model averaging in phylogenetics:advantages of akaike information criterion and Bayesian approaches over likelihood ratio tests.Systematic Biology, 53(5):793-808,
Rannala B, Yang Z H.1996.Probability distribution of molecular evolutionary trees:a new method of phylogenetic inference.Journal of Molecular Evolution,43(3):304-311,
Ronquist F, Teslenko M, Van Der Mark P et al.2012.MrBayes 3.2:efficient Bayesian phylogenetic inference and model choice across a large model space.Systematic Biology, 61(3):539-542,
Ruby J G, Bellare P, DeRisi J L.2013.PRICE:software for the targeted assembly of components of (Meta) genomic sequence data.G3:Genes, Genomes, Genetics, 3(5):865-880,
Saunders G W.1993.Gel purification of red algal genomic DNA:an inexpensive and rapid method for the isolation of polymerase chain reaction-friendly DNA.Journal of Phycology, 29(2):251-254,
Sherwood A R, Shea T B, Sheath R G.2002.European freshwater Hildenbrandia (Hildenbrandiales, Rhodophyta) has not been derived from multiple invasions from marine habitats.Phycologia, 41(1):87-95,
Sherwood A R, Sheath R G.1999.Biogeography and systematics of Hildenbrandia (Rhodophyta, Hildenbrandiales) in North America:inferences from morphometrics and rbcL and 18S rRNA gene sequence analyses.European Journal of Phycology, 34(5):523-532,
Sherwood A R, Sheath R G.2000.Biogeography and systematics of Hildenbrandia (Rhodophyta, Hildenbrandiales) in Europe:inferences from morphometrics and rbc L and 18S rRNA gene sequence analyses.European Journal of Phycology, 35(2):143-152,
Sherwood A R, Sheath R G.2003.Systematics of the Hildenbrandiales (Rhodophyta):gene sequence and morphometric analyses of global collections.Journal of Phycology, 39(2):409-422,
Slamovits C H, Saldarriaga J F, Larocque A et al.2007.The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes.Journal of Molecular Biology, 372(2):356-368,
Stamatakis A.2014.RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies.Bioinformatics, 30(9):1312-1313,
Tamura K, Peterson D, Peterson N et al.2011.MEGA5:molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.Molecular Biology and Evolution, 28(10):2731-2739,
Vieira C, Akita S, Kim Y S et al.2021a.First record of the genus Hildenbrandia (Florideophyceae:Hildenbrandiales) from French Polynesia and description of H.tahitiensis sp.nov.Journal of Asia-Pacific Biodiversity, 14(4):607-612,
Vieira C, Akita S, Uwai S et al.2021b.Hildenbrandia (Hildenbrandiales, Florideophyceae) from Japan and taxonomic lumping of H.jigongshanensis and H.japananensis.Phycological Research, 69(3):166-170,
Vis M L, Sheath R G.1997.Biogeography of Batrachospermum gelatinosum (Batrachospermales, Rhodophyta) in North America based on molecular and morphological data.Journal of Phycology, 33(3):520-526,
Wang D P, Zhang Y B, Zhang Z et al.2010.KaKs_Calculator 2.0:a toolkit incorporating gamma-series methods and sliding window strategies.Genomics, Proteomics & Bioinformatics, 8(1):77-80,
Yang E C, Boo S M, Bhattacharya D et al.2016.Divergence time estimates and the evolution of major lineages in the florideophyte red algae.Scientific Reports, 6:21361,
Yang E C, Kim K M, Kim S Y et al.2015.Highly conserved mitochondrial genomes among multicellular red algae of the Florideophyceae.Genome Biology and Evolution, 7(8):2394-2406,
Yoon H S, Müller K M, Sheath R G et al.2006.Defining the major lineages of red algae (Rhodophyta).Journal of Phycology, 42(2):482-492,
Copyright © Haiyang Xuebao