New insights into the phylogeny of Stephanodiscaceae based on plastome

Yandan XIANG; Xudong LIU; Fangru NAN; Yang LIU; Shulian XIE; Xinjie JIN; John Patrick KOCIOLEK; Qi LIU

doi:10.1007/s00343-025-4286-y

Your Location：

Home >

Browse articles >

New insights into the phylogeny of Stephanodiscaceae based on plastome

Biology | Updated：2026-03-26

- New insights into the phylogeny of Stephanodiscaceae based on plastome
- New insights into the phylogeny of Stephanodiscaceae based on plastome
- 海洋湖沼学报(英文) 2026年44卷第1期页码：284-306
- Affiliations：
  
  1.School of Life Science, Shanxi University, Taiyuan 030006, China
  2.Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan 030006, China
  3.College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
  4.Museum of Natural History, University of Colorado, Boulder CO80309, USA
  5.Department of Ecology and Evolutionary Biology, University of Colorado, Boulder CO80309, USA
- Author bio：
  
  liuqi317@126.com
- Funds：
  
  the National Natural Science Foundation of China(31970217);the Scientific and Technological Innovation Programs of Higher Education Institution in Shanxi(2019L0070)
- DOI：10.1007/s00343-025-4286-y
  中图分类号：
- 收稿：2024-10-29，
  
  录用：2024-12-31，
  
  网络首发：2025-03-05，
  
  纸质出版：2026-01-01
- Accepted：
Scan QR Code
Yandan XIANG, Xudong LIU, Fangru NAN, 等. New insights into the phylogeny of Stephanodiscaceae based on plastome[J]. 海洋湖沼学报(英文), 2026,44(1):284-306.

XIANG Yandan,LIU Xudong,NAN Fangru,et al.New insights into the phylogeny of Stephanodiscaceae based on plastome[J].Journal of Oceanology and Limnology,2026,44(01):284-306.
Yandan XIANG, Xudong LIU, Fangru NAN, 等. New insights into the phylogeny of Stephanodiscaceae based on plastome[J]. 海洋湖沼学报(英文), 2026,44(1):284-306. DOI： 10.1007/s00343-025-4286-y.

XIANG Yandan,LIU Xudong,NAN Fangru,et al.New insights into the phylogeny of Stephanodiscaceae based on plastome[J].Journal of Oceanology and Limnology,2026,44(01):284-306. DOI： 10.1007/s00343-025-4286-y.

摘要

Abstract

Stephanodiscaceae is one of the most diverse family of the freshwater centric diatoms. However

the scarcity of whole plastome data poses a significant challenge to the undertaking of genomic studies on this taxonomic group. We collected data on the plastid genomes from 33 members of the Stephanodiscaceae and its close relatives

including 12 newly-sequenced genomes and 21 deposited in National Center for Biotechnology Information (NCBI). Phylogenetic trees are yielded five major clades based on homologous genes. The features of the plastid genomes

including repeat sequences

codon usage

and selection pressure for each clade

are analyzed. The paper makes a contribution to the field of diatom genomics by describing the structural characteristics of the plastid genomes in the Stephanodiscaceae and its closely related species

complemented by related analyses. It provides crucial data that will serve as indispensable references for future research.

关键词

Keywords

references

Ács É , Ari E , Duleba M et al . 2016 . Pantocsekiella , a new centric diatom genus based on morphological and genetic studies . Fottea , 16 ( 1 ): 56 - 78 , https://doi.org/10.5507/fot.2015.028 https://doi.org/10.5507/fot.2015.028 .

Alverson A J , Beszteri B , Julius M L et al . 2011 . The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella . BMC Evolutionary Biology , 11 ( 1 ): 125 , https://doi.org/10.1186/1471-2148-11-125 https://doi.org/10.1186/1471-2148-11-125 .

Alverson A J , Jansen R K , Theriot E C . 2007 . Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms . Molecular Phylogenetics and Evolution , 45 ( 1 ): 193 - 210 , https://doi.org/10.1016/j.ympev.2007.03.024 https://doi.org/10.1016/j.ympev.2007.03.024 .

Armbrust E V . 2009 . The life of diatoms in the world’s oceans . Nature , 459 ( 7244 ): 185 - 192 , https://doi.org/10.1038/nature08057 https://doi.org/10.1038/nature08057 .

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 .

Barinova S , Gabyshev V , Genkal S et al . 2023 . Diatoms of small water bodies as bioindicators in the assessment of climatic and anthropogenic impacts on the coast of Tiksi Bay, Russian Arctic . Water , 15 ( 8 ): 1533 , https://doi.org/10.3390/w15081533 https://doi.org/10.3390/w15081533 .

Beier S , Thiel T , Münch T et al . 2017 . MISA-web: a web server for microsatellite prediction . Bioinformatics , 33 ( 16 ): 2583 - 2585 , https://doi.org/10.1093/bioinformatics/btx198 https://doi.org/10.1093/bioinformatics/btx198 .

Belshaw R , Bensasson D . 2006 . The rise and falls of introns . Heredity , 96 ( 3 ): 208 - 213 , https://doi.org/10.1038/sj.hdy.6800791 https://doi.org/10.1038/sj.hdy.6800791 .

Beszteri B , John U , Medlin L K . 2007 . An assessment of cryptic genetic diversity within the Cyclotella meneghiniana species complex (Bacillariophyta) based on nuclear and plastid genes, and amplified fragment length polymorphisms . European Journal of Phycology , 42 ( 1 ): 47 - 60 , https://doi.org/10.1080/09670260601044068 https://doi.org/10.1080/09670260601044068 .

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 .

Bradbury J P . 1988 . A climatic-limnologic model of diatom succession for paleolimnological interpretation of varved sediments at Elk Lake, Minnesota . Journal of Paleolimnology , 1 ( 2 ): 115 - 131 , https://doi.org/10.1007/BF00196068 https://doi.org/10.1007/BF00196068 .

Chan P P , Lin B Y , Mak A J et al . 2021 . tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes . Nucleic Acids Research , 49 ( 16 ): 9077 - 9096 , https://doi.org/10.1093/nar/gkab688 https://doi.org/10.1093/nar/gkab688 .

Chang T P , Chang-Schneider H . 2008 . Zentrische kieselalgen in kemptener seen . Berichte der Bayerischen Botanischen Gesellschaft , 78 : 5 - 15 .

Chang T P , Steinberg C . 1989 . Identifizierung von nanoplanktischen Kieselalgen (Centrales, Bacillariophyceae) in der Rott und im Rott-Stausee (Bayern, Bundesrepublik Deutschland) . Archiv für Protistenkunde , 137 ( 2 ): 111 - 129 , https://doi.org/10.1016/S0003-9365(89)80003-X https://doi.org/10.1016/S0003-9365(89)80003-X .

Chen L , Liu T F , Yang D Y et al . 2013 . Analysis of codon usage patterns in Taenia pisiformis through annotated transcriptome data . Biochemical and Biophysical Research Communications , 430 ( 4 ): 1344 - 1348 , https://doi.org/10.1016/j.bbrc.2012.12.078 https://doi.org/10.1016/j.bbrc.2012.12.078 .

Chen S F , Zhou Y Q , Chen Y R et al . 2018 . Fastp: an ultra-fast all-in-one FASTQ preprocessor . Bioinformatics , 34 ( 17 ): i884 - i890 , https://doi.org/10.1093/bioinformatics/bty560 https://doi.org/10.1093/bioinformatics/bty560 .

Cvijović I , Good B H , Desai M M . 2018 . The effect of strong purifying selection on genetic diversity . Genetics , 209 ( 4 ): 1235 - 1278 , https://doi.org/10.1534/genetics.118.301058 https://doi.org/10.1534/genetics.118.301058 .

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 .

Downey K M , Julius M L , Theriot E C et al . 2021 . Phylogenetic analysis places Spicaticribra within Cyclotella . Diatom Research , 36 ( 2 ): 93 - 99 , https://doi.org/10.1080/0269249X.2021.1926332 https://doi.org/10.1080/0269249X.2021.1926332 .

Ellegren H . 2004 . Microsatellites: simple sequences with complex evolution . Nature Reviews Genetics , 5 ( 6 ): 435 - 445 , https://doi.org/10.1038/nrg1348 https://doi.org/10.1038/nrg1348 .

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 .

Gao Y , Lu Y , Song Y et al . 2022 . Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus . BMC Genomic Data , 23 ( 1 ): 46 , https://doi.org/10.1186/s12863-022-01064-8 https://doi.org/10.1186/s12863-022-01064-8 .

Glezer Z I , Makarova I V . 1986 . News order and family of diatoms (Bacillariophyta) . Botanicheskii Zhurnal , 71 ( 5 ): 673 - 676 .

Greiner S , Lehwark P , Bock R . 2019 . OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes . Nucleic Acids Research , 47 ( W1 ): W59 - W64 , https://doi.org/10.1093/nar/gkz238 https://doi.org/10.1093/nar/gkz238 .

Gui J , Tan X F . 1998 . The molecular taxonomy and identification of plant . Life Science Research , 2 ( 4 ): 253 - 257 , 277 , https://doi.org/10.16605/j.cnki.1007-7847.1998.04.003. https://doi.org/10.16605/j.cnki.1007-7847.1998.04.003. (in Chinese with English abstract)

Guiry M D , Guiry G M . 2024 . AlgaeBase . World-wide electronic publication, National University of Ireland, Galway . https://www.algaebase.org. Accessed on 2024-10-25 https://www.algaebase.org.Accessedon2024-10-25 .

Guiry M D . 2024 . How many species of algae are there? A reprise. Four Kingdoms, 14 phyla, 63 classes and still growing . Journal of Phycology , 60 ( 2 ): 214 - 228 , https://doi.org/10.1111/jpy.13431 https://doi.org/10.1111/jpy.13431 .

Guo H J , Liu J S , Luo L et al . 2017 . Complete chloroplast genome sequences of Schisandra chinensis : genome structure, comparative analysis, and phylogenetic relationship of basal angiosperms . Science China Life Sciences , 60 ( 11 ): 1286 - 1290 , https://doi.org/10.1007/s11427-017-9098-5 https://doi.org/10.1007/s11427-017-9098-5 .

Hamedi C , Gastineau R , Lemieux C et al . 2019 . Complete chloroplast genome of the diatom Skeletonema pseudocostatum from the Western Mediterranean coast of Algeria . Mitochondrial DNA Part B , 4 ( 1 ): 1091 - 1092 , https://doi.org/10.1080/23802359.2019.1586481 https://doi.org/10.1080/23802359.2019.1586481 .

Hasle G R , Heimdal B R . 1970 . Some species of the centric diatom genus Thalassiosira studied in the light and electron microscopes . Beihefte zur Nova Hedwigia , 31 : 543 - 581 , https://doi.org/10.1127/nova.beihefte/31/1970/543 https://doi.org/10.1127/nova.beihefte/31/1970/543 .

He P M , Zhang R X . 2000 . DNA and gene map of alga chloroplast genome . Journal of Shanghai Fisheries University , 9 ( 1 ): 51 - 58 , https://doi.org/10.3969/j.issn.1004-7271.2000.01.010 https://doi.org/10.3969/j.issn.1004-7271.2000.01.010 . (in Chinese)

He Y , Xiao H T , Deng C et al . 2016 . The complete chloroplast genome sequences of the medicinal plant Pogostemon cablin . International Journal of Molecular Sciences , 17 ( 6 ): 820 , https://doi.org/10.3390/ijms17060820 https://doi.org/10.3390/ijms17060820 .

Huang J , Chen R H , Li X G . 2017 . Comparative analysis of the comp lete chloroplast genome of four known Ziziphus species . Genes , 8 ( 12 ): 340 , https://doi.org/10.3390/genes8120340 https://doi.org/10.3390/genes8120340 .

Huang Y , Ma Q , Sun J et al . 2023 . Comparative analysis of Diospyros (Ebenaceae) plastomes: insights into genomic features, mutational hotspots, and adaptive evolution . Ecology and Evolution , 13 ( 7 ): e 10301 , https://doi.org/10.1002/ece3.10301 https://doi.org/10.1002/ece3.10301 .

Hustedt F . 1957 . Die diatomeenflora des Flußsystems der weser im gebiet der hansestadt bremen . Abhandlungen des Naturwissenschaftlichen Verein zu Bremen , 34 ( 3 ): 181 - 440 .

Jansen R K , Ruhlman T A . 2012 . Plastid genomes of seed plants . In: Bock R, Knoop V eds. Genomics of Chloroplasts and Mitochondria . Springer, Dordrecht . p. 103 - 126 , https://doi.org/10.1007/978-94-007-2920-9_5 https://doi.org/10.1007/978-94-007-2920-9_5 .

Jeffares D C , Mourier T , Penny D . 2006 . The biology of intron gain and loss . Trends in Genetics , 22 ( 1 ): 16 - 22 , https://doi.org/10.1016/j.tig.2005.10.006 https://doi.org/10.1016/j.tig.2005.10.006 .

Jiao Y , Jia H M , Li X W et al . 2012 . Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry ( Myrica rubra ) . BMC Genomics , 13 ( 1 ): 201 , https://doi.org/10.1186/1471-2164-13-201 https://doi.org/10.1186/1471-2164-13-201 .

Jung S W , Han M S , Ki J S . 2010 . Molecular genetic divergence of the centric diatom Cyclotella and Discostella (Bacillariophyceae) revealed by nuclear ribosomal DNA comparisons . Journal of Applied Phycology , 22 ( 3 ): 319 - 329 , https://doi.org/10.1007/s10811-009-9462-5 https://doi.org/10.1007/s10811-009-9462-5 .

Kaczmarska I , Beaton M , Benoit A C et al . 2006 . Molecular phylogeny of selected members of the order Thalassiosirales (Bacillariophyta) and evolution of the fultoportula . Journal of Phycology , 42 ( 1 ): 121 - 138 , https://doi.org/10.1111/j.1529-8817.2006.00161.x https://doi.org/10.1111/j.1529-8817.2006.00161.x .

Keck F , Rimet F , Franc A et al . 2016 . Phylogenetic signal in diatom ecology: perspectives for aquatic ecosystems biomonitoring . Ecological Applications , 26 ( 3 ): 861 - 872 , https://doi.org/10.1890/14-1966 https://doi.org/10.1890/14-1966 .

Khursevich G K , Kociolek J P . 2012 . A preliminary , worldwide inventory of the extinct , freshwater fossil diatoms from the orders Thalassiosirales, Stephanodiscales, Paraliales, Aulacoseirales, Melosirales, Coscindiscales, and Biddulphiales. In: Witkowski A, Kociolek J P, Compère P eds. Diatom Taxonomy and Ecology : from Local Discoveries to Global Impacts. Gebruder Borntraeger Press, Germany. p . 315 - 364 .

Khursevich G K . 2008 . Descriptions of new taxa, established after 1992 . In: Strelnikova N I, Tsoy I B eds. The Diatoms of Russia and Adjacent Countries: fossil and Recent . Saint Petersburg University Press, Saint Petersburg. p. 92 - 116 .

Ki J S . 2009 . Comparative molecular analysis of freshwater centric diatoms with particular emphasis on the nuclear ribosomal DNA of Stephanodiscus (Bacillariophyceae) . Algae , 24 ( 3 ): 129 - 138 , https://doi.org/10.4490/ALGAE.2009.24.3.129 https://doi.org/10.4490/ALGAE.2009.24.3.129 .

Kociolek J P , You Q M , Liu Q et al . 2020 . Continental diatom biodiversity discovery and description in China: 1848 through 2019 . PhytoKeys , 160 : 45 - 97 , https://doi.org/10.3897/phytokeys.160.54193 https://doi.org/10.3897/phytokeys.160.54193 .

Krebs W N , Bradbury J P , Theriot E . 1987 . Neogene and Quaternary lacustrine diatom biochronology, western USA . Palaios , 2 ( 5 ): 505 - 513 , https://doi.org/10.2307/3514621 https://doi.org/10.2307/3514621 .

Kulikovskiy M , Genkal S , Maltsev Y et al . 2022 . Resurrection of the diatom Genus Stephanocyclus (Coscinodiscophyceae: Stephanodiscaceae) on the basis of an integrated molecular and morphological approach . Fottea , 22 ( 2 ): 181 - 191 , https://doi.org/10.5507/fot.2021.025 https://doi.org/10.5507/fot.2021.025 .

Kurtz S , Choudhuri J V , Ohlebusch E et al . 2001 . REPuter: the manifold applications of repeat analysis on a genomic scale . Nucleic Acids Research , 29 ( 22 ): 4633 - 4642 , https://doi.org/10.1093/nar/29.22.4633 https://doi.org/10.1093/nar/29.22.4633 .

Kützing F T . 1834 . Synopsis diatomearum oder Versuch einer systematischen Zusammenstellung der Diatomeen . Linnaea , 8 ( 5 ): 529 - 620 .

Liu K Y , Chen Y , Cui Z M et al . 2021a . Comparative analysis of chloroplast genomes of Thalassiosira species. Frontiers in Marine Science , 8 : 788307 , https://doi.org/10.3389/fmars.2021.788307 https://doi.org/10.3389/fmars.2021.788307 .

Liu Q P , Xue Q Z . 2005 . Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species . Journal of Genetics , 84 ( 1 ): 55 - 62 , https://doi.org/10.1007/BF02715890 https://doi.org/10.1007/BF02715890 .

Liu S Y , Xu Q , Liu K Y et al . 2021b . Chloroplast genomes for five Skeletonema species: comparative and phylogenetic analysis. Frontiers in Plant Science , 12 : 774617 , https://doi.org/10.3389/fpls.2021.774617 https://doi.org/10.3389/fpls.2021.774617 .

Medlin L K , Kaczmarska I . 2004 . Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision . Phycologia , 43 ( 3 ): 245 - 270 , https://doi.org/10.2216/i0031-8884-43-3-245.1 https://doi.org/10.2216/i0031-8884-43-3-245.1 .

Medlin L K , Williams D M , Sims P A . 1993 . The evolution of the diatoms (Bacillariophyta). I. origin of the group and assessment of the monophyly of its major divisions . European Journal of Phycology , 28 ( 4 ): 261 - 275 , https://doi.org/10.1080/09670269300650381 https://doi.org/10.1080/09670269300650381 .

Moniz Morton B R . 2003 . The role of context-dependent mutations in generating compositional and codon usage bias in grass chloroplast DNA . Journal of Molecular Evolution , 56 ( 5 ): 616 - 629 , https://doi.org/10.1007/s00239-002-2430-1 https://doi.org/10.1007/s00239-002-2430-1 .

Nakov T , Guillory W X , Julius M L et al . 2015 . Towards a phylogenetic classification of species belonging to the diatom genus Cyclotella (Bacillariophyceae): transfer of species formerly placed in Puncticulata , Handmannia , Pliocaenicus and Cyclotella to the genus Lindavia . Phytotaxa , 217 ( 3 ): 249 - 264 , https://doi.org/10.11646/phytotaxa.217.3.2 https://doi.org/10.11646/phytotaxa.217.3.2 .

Nikolaev V A , Harwood D M . 2001 . Diversity and classification of centric diatoms . In: Economou-Amillie A ed. Proceedings of the 16 th International Diatom Symposium . University Athens, Greece. p. 127 - 152 .

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 .

Oliveira E J , Pádua J G , Zucchi M I et al . 2006 . Origin, evolution and genome distribution of microsatellites . Genetics and Molecular Biology , 29 ( 2 ): 294 - 307 , https://doi.org/10.1590/S1415-47572006000200018 https://doi.org/10.1590/S1415-47572006000200018 .

Oudot-Le Secq M P , Grimwood J , Shapiro H et al . 2007 . Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana : comparison with other plastid genomes of the red lineage . Molecular Genetics and Genomics , 277 ( 4 ): 427 - 439 , https://doi.org/10.1007/s00438-006-0199-4 https://doi.org/10.1007/s00438-006-0199-4 .

Plotkin J B , Kudla G . 2011 . Synonymous but not the same: the causes and consequences of codon bias . Nature Reviews Genetics , 12 ( 1 ): 32 - 42 , https://doi.org/10.1038/nrg2899 https://doi.org/10.1038/nrg2899 .

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 .

Qi Y Z . 1995 . Flora Algarum Sinicarum Aquae Dulcis. Tomus IV. Bacillariophyta. Centricae . Science Press , Beijing . 104 p. (in Chinese)

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 .

Round F E , Crawford R M , Mann D G . 1990 . The Diatoms: Biology and Morphology of the Genera . Cambridge University Press , Cambridge . 747 p. https://do 10.2307/1222958 http://dx.doi.org/10.2307/1222958

Sabir J S M , Yu M J , Ashworth M P et al . 2014 . Conserved gene order and expanded inverted repeats characterize plastid genomes of Thalassiosirales . PLoS One , 9 ( 9 ): e 107854 , https://doi.org/10.1371/journal.pone.0107854 https://doi.org/10.1371/journal.pone.0107854 .

Schultz K , Dreßler M , Jacques O et al . 2024 . Morphological and taxonomic implications of the formation of colonies in Cyclostephanos and Stephanodiscus (Bacillariophyta) . European Journal of Phycology , 59 ( 1 ): 71 - 81 , https://doi.org/10.1080/09670262.2023.2222297 https://doi.org/10.1080/09670262.2023.2222297 .

Schultz K , Hübener T , Dreßler M et al . 2021 . Disentangling the taxonomic history of the widespread and overlooked centric diatom Stephanodiscus makarovae and its transfer to Cyclostephanos . Taxonomy , 1 ( 4 ): 425 - 437 , https://doi.org/10.3390/taxonomy1040030 https://doi.org/10.3390/taxonomy1040030 .

Sharp P M , Li W H . 1987 . The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications . Nucleic Acids Research , 15 ( 3 ): 1281 - 1295 , https://doi.org/10.1093/nar/15.3.1281 https://doi.org/10.1093/nar/15.3.1281 .

Shields D C , Sharp P M . 1987 . Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases . Nucleic Acids Research , 15 ( 19 ): 8023 - 8040 , https://doi.org/10.1093/nar/15.19.8023 https://doi.org/10.1093/nar/15.19.8023 .

Smol J P . 1990 . Paleolimnology—recent advances and future challenges . In: De Bernardi R, Giussani G, Barbanti L eds. Scientific Perspectives in Theoretical and Applied Limnology . Memorie dell’Istituto Italiano di Idrobiologia. p. 253 - 276 .

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 .

Stoermer E F , Julius M L . 2003 . Centric diatoms . In: Wehr J D, Sheath R G eds. Freshwater Algae of North America . Academic Press , San Diego . p. 559 - 594 . https://do 10.1016/b978-012741550-5/50016-7 http://dx.doi.org/10.1016/b978-012741550-5/50016-7

Stoermer E F , Smol J P . 1999 . The Diatoms: Applications for the Environmental and Earth Sciences . Cambridge University Press , Cambridge . 469 p. http s://do 10.1017/cbo9780511613005 http://dx.doi.org/10.1017/cbo9780511613005

Tamura K , Stecher G , Peterson D et al . 2013 . MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 . Molecular Biology and Evolution , 30 ( 12 ): 2725 - 2729 , https://doi.org/10.1093/molbev/mst197 https://doi.org/10.1093/molbev/mst197 .

Thiel T , Michalek W , Varshney R et al . 2003 . Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley ( Hordeum vulgare L.) . Theoretical and Applied Genetics , 106 ( 3 ): 411 - 422 , https://doi.org/10.1007/s00122-002-1031-0 https://doi.org/10.1007/s00122-002-1031-0 .

Timme R E , Kuehl J V , Boore J L et al . 2007 . A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats . American Journal of Botany , 94 ( 3 ): 302 - 312 , https://doi.org/10.3732/ajb.94.3.302 https://doi.org/10.3732/ajb.94.3.302 .

Tuji A , Mohri Y , Ki J S et al . 2014 . Phylogeny of Praestephanos gen. nov. (Thalassiosirales, Bacillariophyceae) based on Stephanodiscus suzukii , and related freshwater Thalassiosiroid diatoms . Plankton and Benthos Research , 9 ( 2 ): 132 - 140 , https://doi.org/10.3800/pbr.9.132 https://doi.org/10.3800/pbr.9.132 .

Urbaniak L , Wojnicka-Półtorak A , Celinski K et al . 2019 . Genetic resources of relict populations of Pinus sylvestris (L.) in Western Carpathians assessed by chloroplast microsatellites . Biologia , 74 ( 9 ): 1077 - 1086 , https://doi.org/10.2478/s11756-019-00255-6 https://doi.org/10.2478/s11756-019-00255-6 .

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 .

Wolf M , Scheffler W , Nicklisch A . 2002 . Stephanodiscus neoastraea and Stephanodiscus heterostylus (Bacillariophyta) are one and the same species . Diatom Research , 17 ( 2 ): 445 - 451 , https://doi.org/10.1080/0269249X.2002.9705561 https://doi.org/10.1080/0269249X.2002.9705561 .

Wright F . 1990 . The ‘effective number of codons’ used in a gene . Gene , 87 ( 1 ): 23 - 29 , https://doi.org/10.1016/0378-1119(90)90491-9 https://doi.org/10.1016/0378-1119(90)90491-9 .

Wu M L , Chen S P , Chen H . 2019 . Condon preference of chloroplast genome of Bambusoideae . Journal of Forest and Environment , 39 ( 1 ): 9 - 14 , https://doi.org/10.13324/j.cnki.Jfcf.2019.01.002. https://doi.org/10.13324/j.cnki.Jfcf.2019.01.002. (in Chinese with English abstract)

Wu X M , Wu S F , Ren D M et al . 2007 . The analysis method and progress in the study of codon bias . Hereditas (Beijing) , 29 ( 4 ): 420 - 426 , https://doi.org/10.1360/yc-007-0420. https://doi.org/10.1360/yc-007-0420. (in Chinese with English abstract)

Xiang Y D , Nan F R , Liu X D et al . 2024 . A new species of Discostella guiyangensis sp. nov. (Bacillariophyta, Stephanodiscales) from Guiyang, China: morphology and phylogeny . Journal of Oceanology and Limnology , 42 ( 4 ): 1312 - 1324 , https://doi.org/10.1007/s00343-023-3123-4 https://doi.org/10.1007/s00343-023-3123-4 .

Yin D C , Huang W , Wu X H et al . 2012 . Preliminary study on biological characteristics of spring diatom bloom in the Hanjiang River . Journal of Yangtze River Scientific Research Institute , 29 ( 2 ): 6 - 10 . (in Chinese with English abstract)

Yu M J , Ashworth M P , Hajrah N H et al . 2018 . Evolution of the plastid genomes in diatoms . Advances in Botanical Research , 85 : 129 - 155 , https://doi.org/10.1016/bs.abr.2017.11.009 https://doi.org/10.1016/bs.abr.2017.11.009 .

Yu P , Yang L , You Q M et al . 2024 . Lineaperpetua gen. nov.: a new diatom genus in the Thalassiosirales supported by morphology and molecular data . Journal of Oceanology and Limnology , 42 ( 1 ): 277 - 290 , https://doi.org/10.1007/s00343-023-2312-5 https://doi.org/10.1007/s00343-023-2312-5 .

Zechman F W , Zimmer E A , Theriot E C . 1994 . Use of ribosomal DNA internal transcribed spacers for phylogenetic studies in diatoms . Journal of Phycology , 30 ( 3 ): 507 - 512 , https://doi.org/10.1111/j.0022-3646.1994.00507.x https://doi.org/10.1111/j.0022-3646.1994.00507.x .

Zhang F J , Wang T , Shu X C et al . 2020 . Complete chloroplast genomes and comparative analyses of L . chinensis , L . anhuiensis , and L . aurea (Amaryllidaceae) . International Journal of Molecular Sciences , 21 ( 16 ): 5729 , https://doi.org/10.3390/ijms21165729 https://doi.org/10.3390/ijms21165729 .

浏览量

Downloads

CSCD

文章被引用时，请邮件提醒。

Submit

工具集

关联资源

Phylogenetic study on Scenedesmacae with the description of a new genus Coccoidesmus gen. nov. (Chlorophyceae, Chlorophyta) and chloroplast genome analyses

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

Comparative chloroplast genomes of Ulva prolifera and U. linza (Ulvophyceae) provide genetic resources for the development of interspecific markers

Complete genome of Cobetia marina JCM 21022^T and phylogenomic analysis of the family Halomonadaceae