All Issue

2023 Vol.3, Issue 2 Preview Page
Characterization of the Complete Plastid Genome of Campylaephora boydenii (Ceramiaceae, Florideophyceae)
Su Yeon Kim1
,
Eun Chan Yang23*
1Korea Inter-University Institute of Ocean Science, Pukyong National University, Busan 48513, Korea
2Marine Ecosystem Research Center, Korea Institute of Ocean Science & Technology, Busan 49111, Korea
3Department of Ocean Science, University of Science and Technology, Daejeon 34113, Korea
*Corresponding Author
31 December 2023. pp. 113-121
PDF XML Citation
Abstract

The complete plastid genome of Campylaephora boydenii was sequenced and characterized. The new circular genome (OQ731916) is 171,790 bp in length with 27.7% GC content. The genome included 233 genes; 200 protein-coding sequences (CDS), 28 transfer RNA (tRNA), three ribosomal RNA (rRNA), one intron, and one transfer-messenger RNA (tmRNA) gene. The gene content and synteny of C. boydenii were highly congruent with those of other ceramiacean species, such as C. sungminbooi and Ceramothamnion japonicum. In 200 CDSs, four CDS showed significant differences (± 5%) in length, i.e., cpcG, petP, rpl33, and thiS. The trnM was a unique tRNA included group II intron with intronic-ORF. Additional complete plastid genomes of ceramiacean algae will provide significant information for the ecology, genetic diversity and phylogeny of ceramialean red algae.

Keywords
Campylaephora boydenii
Ceramiales, phylogeny
plastid genome
Rhodophyta
References
1
Barros-Barreto MB, Jaramillo MA, Hommersand MH, Ferreira PCG and Maggs CA. 2023. Phylogenetic analysis of the red algal tribe Ceramieae reveals multiple morphological homoplasies but defines new genera. Cryptogam Algol 44, 13-58. DOI: https://doi.org/10.5252/cryptogamie-algologie2023v44a2. 10.5252/cryptogamie-algologie2023v44a2
2
Boo SM and Lee IK. 1994. Ceramium and Campylaephora (Ceramiaceae, Rhodophyta). In: (Akatsuka I ed.) Biology of economic algae. SPB Academic Publishers, The Hague. pp 1-33.
3
Bruce MR and Saunders GW. 2015. Population genetic analyses are consistent with the introduction of Ceramium secundatum (Ceramiaceae, Rhodophyta) to Narragansett Bay, Rhode Island, USA. Ecol. Evol. 5, 5088-5095. https://doi.org/10.1002/ece3.1754. 10.1002/ece3.175426640684PMC4662316
4
Cho TO, Boo SM and Hansen GI. 2001. Structure and reproduction of the genus Ceramium (Ceramiales, Rhodophyta) from Oregon, USA. Phycologia 40, 547-571. https://doi.org/10.2216/i0031-8884-40-6-547.1. 10.2216/i0031-8884-40-6-547.1
5
Cho TO, Boo SM, Hommersand MH, Maggs CA, McIvor L and Fredericq S. 2008a. Gayliella gen. nov. in the tribe Ceramieae (Ceramiaceae, Rhodophyta) based on molecular and morphological evidence. J. Phycol. 44, 721-738. https://doi.org/10.1111/j.1529-8817.2008.00505.x. 10.1111/j.1529-8817.2008.00505.x27041431
6
Cho TO, Fredericq S and Boo SM. 2003a. Ceramium inkyuii sp. nov. (Ceramiaceae, Rhodophyta) from Korea: A new species based on morphological and molecular evidence. J. Phycol. 39, 236-247. https://doi.org/10.1046/j.1529-8817.2003.02018.x. 10.1046/j.1529-8817.2003.02018.x
7
Cho TO, Fredericq S, Murray SN and Boo SM. 2003b. New insights in the taxonomy of the Ceramiium sinicoloa complex: resurrection of Ceramium interruptum (Ceramiaceae, Rhodophyta). J. Phycol. 39, 775-788. https://doi.org/10.1046/j.1529-8817.2003.02161.x. 10.1046/j.1529-8817.2003.02161.x
8
Cho TO, Hommersand MH, Won BY and Fredericq S. 2008b. Generic boundaries and phylogeny of Campylaephora (Ceramiaceae, Rhodophyta), including Campylaephora californica (Farlow) comb. nov. Phycologia 47, 321-333. https://doi.org/10.2216/PH07-75.1. 10.2216/PH07-75.1
9
Cho TO and Riosmena-Rodriguez R. 2008. Ceramium periconicum sp. nov. (Ceramiaceae, Rhodophyta): a new subtidal species from Baja California Sur, Mexico. Bot. Mar. 51, 307-312. https://doi.org/10.1515/BOT.2008.039. 10.1515/BOT.2008.039
10
De Barros-Barreto MB, McIvor L, Maggs CA and Ferreira PCG. 2006. Molecular systematics of Ceramium and Centroceras (Ceramiaceae, Rhodophyta) from Brazil. J. Phycol. 42, 905-921. https://doi.org/10.1111/j.1529-8817.2006.00237.x. 10.1111/j.1529-8817.2006.00237.x
11
Díaz-Tapia P, Maggs CA, West JA and Verbruggen H. 2017. Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta). J. Phycol. 53, 920-937. https://doi.org/10.1111/jpy.12553. 10.1111/jpy.1255328561261
12
Díaz-Tapia P, Pasella MM, Verbruggen H and Maggs CA. 2019. Morphological evolution and classification of the red algal order Ceramiales inferred using plastid phylogenomics. Mol. Phylogenet. Evol. 137, 76-85. https://doi.org/10.1016/j.ympev.2019.04.022. 10.1016/j.ympev.2019.04.02231029748
13
Dierckxsens N, Mardulyn P and Smits G. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucl. Acids Res. 45, e18. https://doi.org/10.1093/nar/gkw955. 10.1093/nar/gkw95528204566PMC5389512
14
Greiner S, Lehwark P and Bock R. 2019. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucl. Acids Res. 47, W59-W64. https://doi.org/10.1093/nar/gkz238. 10.1093/nar/gkz23830949694PMC6602502
15
Guiry MD and Guiry GM. 2023. AlgaeBase. World-wide electronic publication, National University of Ireland, Galway. https://www. algaebase.org. Searched on 02 April 2023.
16
Hughey JR and Boo GH. 2016. Genomic and phylogenetic analysis of Ceramium cimbricum (Ceramiales, Rhodophyta) from the Atlantic and Pacific Oceans supports the naming of a new invasive Pacific entity Ceramium sungminbooi sp. nov. Bot. Mar. 59, 211-222. https://doi.org/10.1515/bot-2016-0036. 10.1515/bot-2016-0036
17
Lee J, Cho CH, Park SI, Choi JW, Song HS, West JA, Debashish B and Yoon HS. 2016. Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants. BMC Biology 14, 75. https://doi.org/10.1186/s12915-016-0299-5. 10.1186/s12915-016-0299-527589960PMC5010701
18
Liu S, Ni Y, Li J, Zhang X, Yang H, Chen H and Liu C. 2023. CPGView: A package for visualizing detailed chloroplast genome structures. Mol. Ecol. Resour. 23, 694-704. https://doi.org/10.1111/1755-0998.13729. 10.1111/1755-0998.1372936587992
19
Lin S-M, Fredericq S and Hommersand MH. 2001. Systematics of the Delesseriaceae (Ceramiales, Rhodophyta) based on large subunit rDNA and rbcL sequences, including the Phycodryoideae, subfam. nov. J. Phycol. 37, 881-899. https://doi.org/10.1046/j.1529-8817.2001.01012.x. 10.1046/j.1529-8817.2001.01012.x
20
Lowe TM and Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 44, W54-W57. https://doi.org/10.1093/nar/gkw413. 10.1093/nar/gkw41327174935PMC4987944
21
Maggs C A, Ward BA, McIvor LM, Evans CM, Rueness J and Stanhope MJ. 2002. Molecular analyses elucidate the taxonomy of fully corticated, nonspiny species of Ceramium (Ceramiaceae, Rhodophyta) in the British Isles. Phycologia 41, 409-420. https://doi.org/10.2216/i0031-8884-41-4-409.1. 10.2216/i0031-8884-41-4-409.1
22
Ni Y, Li J, Zhang C and Liu C. 2023. Generating Sequencing Depth and Coverage Map for Organelle Genomes. protocols.io https://dx.doi.org/10.17504/protocols.io.4r3l27jkxg1y/v1. 10.17504/protocols.io.4r3l27jkxg1y/v1
23
Stamatakis A. 2014. RaxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313. https://doi.org/10.1093/bioinformatics/btu033. 10.1093/bioinformatics/btu03324451623PMC3998144
24
Wolf MA, Sciuto K, Maggs CA, De Barros-Barreto MBB, Andreoli C and Moro I. 2011. Ceramium Roth (Ceramiales, Rhodophyta) from Venice lagoon (Adriatic Sea, Italy): comparative studies of Mediterranean and Atlantic taxa. Taxon 60, 1584-1595. https://doi.org/10.1002/tax.606004. 10.1002/tax.606004
25
Won BY and Cho TO.2011. Ceramium riosmenae sp. nov. (Ceramiaceae, Rhodophyta): a new complete corticated species on Gracilaria from Baja California Sur, Mexico. Algae 26, 289-297. https://doi.org/10.4490/algae.2011.26.4.289. 10.4490/algae.2011.26.4.289
26
Yang EC and Boo SM. 2004. Evidence for two independent lineages of Griffithsia (Ceramiaceae, Rhodophyta) based on plastid protein-coding psaA, psbA, and rbcL gene sequences. Mol. Phylogenet. Evol. 31, 680-688. https://doi.org/10.1016/j.ympev.2003.08.014. 10.1016/j.ympev.2003.08.01415062802
27
Yang EC, Cho GY, Kogame K, Carlile AL and Boo SM. 2008. RuBisCO cistron sequence variation and phylogeography of Ceramium kondoi (Ceramiaceae, Rhodophyta). Bot. Mar. 51, 370-377. https://doi.org/10.1515/BOT.2008.051. 10.1515/BOT.2008.051
28
Yang EC, Kim KM, Kim SY, Lee J, Bo GH, Lee J-H, Nelson WA, Yi G, Schmidt WE, Fredericq S, Boo SM, Bhattacharya D and Yoon HS. 2015. Highly conserved mitochondrial genomes among multicellular red algae of the Florideophyceae. Genome Biol. Evol. 8, 2394-2406. https://doi.org/10.1093/gbe/evv147. 10.1093/gbe/evv14726245677PMC4558864
29
Yang EC, Lee SY, Lee WJ and Boo SM. 2009. Molecular evidence for recolonization of Ceramium japonicum (Ceramiaceae, Rhodophyta) on the west coast of Korea after the last glacial maximum. Bot. Mar. 52, 307-315. https://doi.org/10.1515/BOT.2009.00510.1515/BOT.2009.005
30
Zuccarello GC, Sandercock B and West JA. 2002. Diversity within red algal species: variation in world-wide samples of Spyridia filamentosa (Ceramiaceae) and Murrayella periclados (Rhodomelaceae) using DNA markers and breeding studies. Eur. J. Phycol. 37, 403-417. https://doi.org/10.1017/S0967026202003827. 10.1017/S0967026202003827
Information
  • Publisher :The Korean Society of Phycology
  • Publisher(Ko) :한국조류학회
  • Journal Title :Aquatic Nature
  • Journal Title(Ko) :수생생물
  • Volume : 3
  • No :2
  • Pages :113-121
  • Received Date : 2023-12-08
  • Revised Date : 2023-12-22
  • Accepted Date : 2023-12-26
  • DOI :https://doi.org/10.23135/an.2023.3.2.5
Journal Informaiton Aquatic Nature Aquatic Nature
Online Submission
  • KISTI Current Status
  • KISTI Cited-by
  • open access
  • ccl
Journal Informaiton Journal Informaiton - close