Comparison and phylogeny on mitochondrial genome of marine and freshwater taxa of genus <italic style="font-style: italic">Hildenbrandia </italic>(Florideophyceae, Rhodophyta)

Fangru NAN; Juan LI; Jia FENG; Junping LÜ; Qi LIU; Xudong LIU; Shulian XIE

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

Biology | Updated：2024-10-12

- Comparison and phylogeny on mitochondrial genome of marine and freshwater taxa of genus Hildenbrandia (Florideophyceae, Rhodophyta)
- Comparison and phylogeny on mitochondrial genome of marine and freshwater taxa of genus Hildenbrandia (Florideophyceae, Rhodophyta)
- 海洋湖沼学报(英文) 2023年41卷第6期页码：2324-2335
- Affiliations：
  
  School of Life Science, Shanxi University, Taiyuan 030006, China
- Author bio：
  
  xiesl@sxu.edu.cn
- Funds：
  
  the National Natural Science Foundation of China (No. 31800172 to F. R. NAN, No. 32170204 to S. L. XIE)
- DOI：
  中图分类号：
- 收稿：2022-03-30，
  
  录用：2022-06-27，
  
  网络首发：2022-09-15，
  
  纸质出版：2023-11-01
- Accepted：
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Comparison and phylogeny on mitochondrial genome of marine and freshwater taxa of genus Hildenbrandia (Florideophyceae, Rhodophyta)[J]. 海洋湖沼学报(英文), 2023,41(6):2324-2335.

NAN Fangru,LI Juan,FENG Jia,et al.Comparison and phylogeny on mitochondrial genome of marine and freshwater taxa of genus Hildenbrandia (Florideophyceae, Rhodophyta)[J].Journal of Oceanology and Limnology,2023,41(06):2324-2335.
Comparison and phylogeny on mitochondrial genome of marine and freshwater taxa of genus Hildenbrandia (Florideophyceae, Rhodophyta)[J]. 海洋湖沼学报(英文), 2023,41(6):2324-2335. DOI：

NAN Fangru,LI Juan,FENG Jia,et al.Comparison and phylogeny on mitochondrial genome of marine and freshwater taxa of genus Hildenbrandia (Florideophyceae, Rhodophyta)[J].Journal of Oceanology and Limnology,2023,41(06):2324-2335. DOI：

摘要

Abstract

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

jigongshanensis

was determined in this study. The freshwater

jigongshanensis

had a larger mitochondrial genome than the marine

rubra

and GC content was higher. Collinear alignment structure was observed between the mitochondrial genomes of

jigongshanensis

and

rubra

except for one block that was encoded on the complement strand. More introns were found in mitochondrial genome of

jigongshanensis

than in

rubra

and

jigongshanensis

shares the common feature with Bangiophyceae that two introns were distributed in

cox

1. Comparison of mitochondrial genome organization suggests that

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

jigongshanensis

and

rubra

were identical except

atp

which was present in

jigongshanensis

while absent from

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.

关键词

Keywords

references

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 , https://doi.‍org/‍10.‍1016/S1055-7903(03)00194-5 https://doi.‍org/‍10.‍1016/S1055-7903(03)00194-5 . https://do 10.1016/s1055-7903(03)00194-5 http://dx.doi.org/10.1016/s1055-7903(03)00194-5

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 , https://doi.‍org/‍10.1073/pnas.‍042694899 https://doi.‍org/‍10.1073/pnas.‍042694899 . https://do 10.1073/pnas.042694899 http://dx.doi.org/10.1073/pnas.042694899

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 , https://doi.‍org/10.1089/cmb.‍2012.0021 https://doi.‍org/10.1089/cmb.‍2012.0021 . https://do 10.1089/cmb.2012.0021 http://dx.doi.org/10.1089/cmb.2012.0021

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 , https://doi.org/‍10.1016/j.ygeno.2017.08.001 https://doi.org/‍10.1016/j.ygeno.2017.08.001 .

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 , https://doi.org/10.‍1093/nar/gkg326 https://doi.org/10.‍1093/nar/gkg326 .

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 , https://doi.‍org/10.‍1186/s12862-020-01677-6 https://doi.‍org/10.‍1186/s12862-020-01677-6 . https://do 10.1186/s12862-020-01677-6 http://dx.doi.org/10.1186/s12862-020-01677-6

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 , https://doi.‍org/10.‍1101/gr.2289704 https://doi.‍org/10.‍1101/gr.2289704 . https://do 10.1101/gr.2289704 http://dx.doi.org/10.1101/gr.2289704

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 , https://doi.org/10.1023/A:1005995718091 https://doi.org/10.1023/A:1005995718091 .

Felsenstein J . 1981 . Evolutionary trees from DNA sequences: a maximum likelihood approach . Journal of Molecular Evolution , 17 ( 6 ): 368 - 376 , https://doi.‍org/10.1007/BF01734359 https://doi.‍org/10.1007/BF01734359 . https://do 10.1007/bf01734359 http://dx.doi.org/10.1007/bf01734359

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 , https://doi.‍org/10.1093/nar/26.4.865 https://doi.‍org/10.1093/nar/26.4.865 . https://do 10.1093/nar/26.4.865 http://dx.doi.org/10.1093/nar/26.4.865

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 , https://doi.org/10.1093/gbe/evq075 https://doi.org/10.1093/gbe/evq075 .

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 , https://doi.‍‍org/10.1111/jpy.12765 https://doi.‍‍org/10.1111/jpy.12765 . https://do 10.1111/jpy.12765 http://dx.doi.org/10.1111/jpy.12765

Langmead B , Salzberg S L . 2012 . Fast gapped-read alignment with Bowtie 2 . Nature Methods , 9 ( 4 ): 357 - 359 , https://doi.‍org/‍10.1038/nmeth.1923 https://doi.‍org/‍10.1038/nmeth.1923 . https://do 10.1038/nmeth.1923 http://dx.doi.org/10.1038/nmeth.1923

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 , https://doi.org/10.1016/j.ympev.2006.11.012 https://doi.org/10.1016/j.ympev.2006.11.012 .

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 , https://doi.org/‍10.1186/s12915-016-0299-5 https://doi.org/‍10.1186/s12915-016-0299-5 .

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 , https://doi.org/10.1093/gbe/evy222 https://doi.org/10.1093/gbe/evy222 .

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 , https://doi.‍‍org/10.‍11646/phytotaxa.292.3.4 https://doi.‍‍org/10.‍11646/phytotaxa.292.3.4 .

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 , https://doi.‍org/10.‍1038/s41598-017-03235-5 https://doi.‍org/10.‍1038/s41598-017-03235-5 .

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 , https://doi.org/10.‍11646/phytotaxa.423.2.2 https://doi.org/10.‍11646/phytotaxa.423.2.2 .

Okonechnikov K , Golosova O , Fursov M et al . 2012 . Unipro UGENE: a unified bioinformatics toolkit . Bioinformatics , 28 ( 8 ): 1166 - 1167 , https://doi.‍org/10.‍1093/bioinformatics/bts091 https://doi.‍org/10.‍1093/bioinformatics/bts091 . https://do 10.1093/bioinformatics/bts091 http://dx.doi.org/10.1093/bioinformatics/bts091

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 , https://doi.‍org/10.‍1080/09670262.2018.1441446 https://doi.‍org/10.‍1080/09670262.2018.1441446 . https://do 10.1080/09670262.2018.1441446 http://dx.doi.org/10.1080/09670262.2018.1441446

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 , https://doi.org/10.1080%2F23802359.2018.1473734 https://doi.org/10.1080%2F23802359.2018.1473734 .

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 , https://doi.‍org/10.1080/10635150490522304 https://doi.‍org/10.1080/10635150490522304 . https://do 10.1080/10635150490522304 http://dx.doi.org/10.1080/10635150490522304

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 , https://doi.org/10.1007/BF02338839 https://doi.org/10.1007/BF02338839 .

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 , https://doi.‍org/10.1093/sysbio/sys029 https://doi.‍org/10.1093/sysbio/sys029 . https://do 10.1093/sysbio/sys029 http://dx.doi.org/10.1093/sysbio/sys029

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 , https://doi.org/10.1534/g3.113.005967 https://doi.org/10.1534/g3.113.005967 .

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 , https://doi.org/10.1111/j.0022-3646.1993.00251.x https://doi.org/10.1111/j.0022-3646.1993.00251.x .

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 , https://doi.org/10.2216/i0031-8884-41-1-87.1 https://doi.org/10.2216/i0031-8884-41-1-87.1 .

Sherwood A R , Sheath R G . 1999 . Biogeography and systematics of Hildenbrandia (Rhodophyta, Hildenbrandiales) in North America: inferences from morphometrics and rbc L and 18S rRNA gene sequence analyses . European Journal of Phycology , 34 ( 5 ): 523 - 532 , https://doi.‍org/10.‍1080/09541449910001718881 https://doi.‍org/10.‍1080/09541449910001718881 . https://do 10.1080/09541449910001718881 http://dx.doi.org/10.1080/09541449910001718881

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 , https://doi.org/10.1080/09670260010001735731 https://doi.org/10.1080/09670260010001735731 .

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 , https://doi.‍org/10.‍1046/j.‍1529-8817.2003.01050.x https://doi.‍org/10.‍1046/j.‍1529-8817.2003.01050.x . https://do 10.1046/j.1529-8817.2003.01050.x http://dx.doi.org/10.1046/j.1529-8817.2003.01050.x

Slamovits C H , Saldarriaga J F , Larocque A et al . 2007 . The highly reduced and f ragmented 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 , https://doi.‍org/10.1016/j.jmb.2007.06.085 https://doi.‍org/10.1016/j.jmb.2007.06.085 . https://do 10.1016/j.jmb.2007.06.085 http://dx.doi.org/10.1016/j.jmb.2007.06.085

Stamatakis A . 2014 . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies . Bioinformatics , 30 ( 9 ): 1312 - 1313 , https://doi.‍org/10.1093/bioinformatics/btu033 https://doi.‍org/10.1093/bioinformatics/btu033 . https://do 10.1093/bioinformatics/btu033 http://dx.doi.org/10.1093/bioinformatics/btu033

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 , https://doi.org/10.1093/molbev/msr121 https://doi.org/10.1093/molbev/msr121 .

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 , https://doi.org/10.1016/j.japb.2021.07.008 https://doi.org/10.1016/j.japb.2021.07.008 .

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 , https://doi.‍org/10.1111/pre.‍12456 https://doi.‍org/10.1111/pre.‍12456 . https://do 10.1111/pre.12456 http://dx.doi.org/10.1111/pre.12456

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 , https://doi.org/10.1111/j.0022-3646.1997.00520.x https://doi.org/10.1111/j.0022-3646.1997.00520.x .

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 , https://doi.‍org/10.1016/S1672-0229(10)60008-3 https://doi.‍org/10.1016/S1672-0229(10)60008-3 . https://do 10.1016/s1672-0229(10)60008-3 http://dx.doi.org/10.1016/s1672-0229(10)60008-3

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 , https://doi.org/10.1038/srep21361 https://doi.org/10.1038/srep21361 .

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 , https://doi.‍org/10.1093/gbe/evv147 https://doi.‍org/10.1093/gbe/evv147 . https://do 10.1093/gbe/evv147 http://dx.doi.org/10.1093/gbe/evv147

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 , https://doi.‍org/10.1111/j.1529-8817.2006.00210.x https://doi.‍org/10.1111/j.1529-8817.2006.00210.x . https://do 10.1111/j.1529-8817.2006.00210.x http://dx.doi.org/10.1111/j.1529-8817.2006.00210.x

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

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

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