Ceramium sungminbooi J.R. Hughey et G.H. Boo, 2016

Hughey, Jeffery R. & Boo, Ga Hun, 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., Botanica Marina (Warsaw, Poland) 59 (4), pp. 211-222 : 215-218

Ceramium sungminbooi J.R. Hughey et G.H. Boo sp. nov. ( Figures 1–5 )

Description

Thalli rose-pink to red in color, bushy and fan-shaped, globose when submerged, erect, 3–8 cm high and wide, pseudo-dichotomously branched, corticated only at the nodes ( Figure 1 ); apices slightly incurved ( Figure 2 ); the periaxial cells are five in number and the cortical bands consist of two to three layers of small cortical cells; cystocarps 300 µm in diameter, axial or lateral, and are naked or surrounded by two involucral branches ( Figure 3 ); tetrasporangia 30–40 µm in diameter, arising adaxially from periaxial cells, strongly emergent ( Figures 4 and 5 ); antheridia not observed. Female gametophytes mixed-phase containing cystocarps with tetrasporangia occurring on lower parts of the same thallus.

Etymology

The species epithet honors Professor Sung Min Boo, a student of Ceramium throughout his career, a dedicated teacher and mentor, and lifelong learner of the algae.

Holotype

S. M. Boo, G. Y. Cho et E. C. Yang s.n., CNU065811 in CNUK, 28.ii.2002, attached to pebbles on the mudflat at Hoedong , Jindo, Korea, 34°25′20.6″N, 126°20′50.5″E, tetrasporophyte ( Figure 1 ); isotypes: CNU065809 , CNU065810 .

Representative specimens

Heukeodo , Seosan , Korea, 24.viii.2006 ( CNU036904 - CNU036905 ); Hoedong, Jindo, Korea, 28.ii.2002 ( CNU034423 , CNU065806 - CNU065808 , CNU065812 ); Jangpyeongri, Tongyeong, Korea, 5.ii.2015 ( CNU066082 ) ; Sausalito , San Francisco Bay, California, USA, 27.xi.2014 ( UC2050596 ) , 23.xii.2014 ( UC2050597 ) , and 28.iii.2015 ( UC2050598 ) .

Representative organellar genomes

Mitochondrial – KU 145004, KU 145005 and plastid – KR 814486 and KR 025491.

Additional illustrations

Cho et al. (2002), figures 35–56; Kim (2012), figures 33–38.

Molecular analysis

ML and BI phylogenetic analyses using rbc L sequences from Ceramium including the complete sequence from the lectotype specimen of Ceramium cimbricum from Egerslev RØn, Limfjorden, Denmark, Ceramium sungminbooi from Hirsholmene, Denmark, C. sungminbooi from Oslofjord, Norway, and 10 specimens of C. sungminbooi from the north Pacific, generated congruent evolutionary hypotheses ( Figure 6 , only ML shown here). Ceramium cimbricum formed a moderately supported clade with the Atlantic species (68% bootstrap/0.92 BPP). Ceramium sungminbooi was situated in a strongly supported clade with Ceramium boydenii E.S. Gepp , Ceramium californicum J. Agardh , Ceramium gardneri Kylin , Ceramium sp. from Alaska, and four species of Campylaephora J. Agardh (96% bootstrap/1.0 BPP). Intraspecific sequence variation in C. sungminbooi ranged from 0 to 1 bp for the rbc L sequences. The two specimens of C. sungminbooi from Seosan, Korea differed by 1 bp from the specimens from Denmark, Norway, California, Oregon, and the other collections in Korea. The partial rbc L and rbc L- rbc S intergenic spacer sequence (GenBank AY 255473) of C. “ cimbricum ” from Akershus, Snaroya, Norway ( Skage et al. 2005) was identical to C. sungminbooi from California and Denmark. Interspecific sequence variation for this clade found that C. sungminbooi differed by 2.4–2.5% from C. californicum , 3.2–3.3% from C. boydenii , 4.8–4.9% from Ceramium sp. from Alaska, and 6.3–6.4% from C. gardneri . The lectotype sequence of C. cimbricum differed by 8.5% from C. sungminbooi .

The organellar genomes of the lectotype of C. cimbricum were not assembled due to low coverage and a preponderance of reads from epiphytic larvae of Mytilus trossulus ( Mytilidae , Bivalvia). However, the complete plastid genomes of C. sungminbooi from Hirsholmene, Denmark and California, USA were deciphered, and were similar in length (171,914 and 171,923 bp, respectively). The plastomes are AT rich (72.4%), and include 224 genes ( Table 2). Both contain three ribosomal RNA genes (5 S, 16 S, 23 S), 27 transfer RNAs, 46 ribosomal proteins (19 rps, 27 rpl), 27 ymfs (hypothetical chloroplast proteins), 16 open reading frames, 11 photosystem I, 19 photosystem II, 16 ATP synthase and cytochrome b/f complex, and 11 phycobiliprotein genes. Alignment of the two Ceramium plastomes showed that they differed by only 67 SNPs and nine gaps. The 67 SNPs account for 18 amino acid residue changes in 16 of the 194 coding genes characterized. Ten of the 18 substitutions represented conservative substitutions (amino acid substitutions that are not too dissimilar in their R group chemistry) and eight represented radical substitutions (amino acid substitutions that are dissimilar in their R group chemistry) ( Table 3).

Two mitochondrial genomes were assembled, but are partial due to an inverted repeat of approximately 700 bp in the mitogenomes of C. sungminbooi specimens from Hirsholmene, Denmark and California, USA. Comparison of the two indicates they are similar in length (24,508 bp for Denmark and 24,494 bp for California). The mitogenomes are AT rich (70.9%), and include 43 genes ( Table 4). Both mitogenomes contain two ribosomal RNA genes, 20 transfer RNAs, three ribosomal proteins, ymf39, orf140, and 16 genes involved in electron transport and oxidative phosphorylation. Alignment of the Ceramium mitogenomes identified 100 SNPs and 32 gaps. The 100 SNPs account for 11 amino acid residue changes over five (rpl16, cox3, cob, nad2, orf140) of the 21 coding genes

Gene groups Genes

Photosystem I psaA, psaB, psaC, psaD, psaE, psaF, psaI, psaJ, psaK, psaL, psaM

Photosystem II psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbN, psbT, psbV, psbW, psbX, psbY, psbZ, psb30

Protochlorophyllide reductase chlI

Phycobiliproteins apcA, apcB, apcD, apcE, apcF, cpeA, cpeB, cpcA, cpcB, cpcG

Cytochrome b/f complex petA, petB, petD, petF, petG, petJ, petM, petN

ATP synthase atpA, atpB, atpD, atpE, atpF, atpG, atpH, atpI

RNA polymerase rpoA, rpoB, rpoC1, rpoC2

Ribosomal proteins ( SSU) rps1, rps2, rps3, rps4, rps5, rps6, rps7, rps8, rps9, rps10, rps11, rps12, rps13, rps14, rps16, rps17, rps18, rps19, rps20

Ribosomal proteins ( LSU) rpl1, rpl2, rpl3, rpl4, rpl5, rpl6, rpl9, rpl11, rpl12, rpl13, rpl14, rpl16, rpl18, rpl19, rpl20, rpl21, rpl22, rpl23, rpl24, rpl27, rpl28, rpl31, rpl32, rpl33, rpl34, rpl35, rpl36

Transfer RNAs trnA-ACG, trnA-TGC, trnC-GCA, trnD-GTC, trnE-TTC, trnF-GAA, trnG-GCC, trnG-TCC, trnG-TTG, trnH-GTG, trnI-GAT, trnK-TTT, trnL-CAA, trnL-TAA, trnL-TAG, trnM-CAT (2X), trnN-GTT, trnP-TGG, trnR-CCG, trnR-TCT, trnS-TGA, trnS-GCT, trnT-TGT, trnV-TAC, trnW-CCA, trnY-GTA

Ribosomal RNAs 5 S, 23 S, 16 S

Hypothetical chloroplast orfs ycf3, ycf4, ycf16, ycf19, ycf20, ycf21, ycf22, ycf23, ycf24, ycf26, ycf29, ycf33, ycf34, ycf35, ycf36, ycf37, ycf38, ycf39, ycf40, ycf45, ycf46, ycf52, ycf54, ycf59, ycf60, ycf61, ycf65

Open reading frames orf7, orf13, orf58, orf68, orf121, orf198, orf199, orf238, orf240, orf263(2X), orf320, orf327, orf382, orf450, orf621

Other genes accA, accB, accD, acpP, argB, carA, cbbx, ccs1, ccsA, cemA, clpC, dnaB, dnaK, fabH, ftrB, ftsH, gltB, groEL, ilvB, ilvH, infB, infC, nblA, ntcA, odpA, odpB, ompR, pbsA, pgmA, preA, rbcL, rbcR, rbcS, rne, secA, secY, syfB, syh, tatC, thiG, trpA, trpG, trxA, tsf, tufA characterized. Three of the 11 substitutions represented conservative substitutions, and eight represented radical substitutions ( Table 3). Comparison of the C. cimbricum ( Denmark) mitogenome with the C. japonicum mitogenome found 5098 SNPs and 2280 gaps. Alignment of the genes for these two species found 631 amino acid substitutions, of which 245 are conservative substitutions and 386 are radical substitutions. Comparison of cox 1 sequences of C. sungminbooi found that those from Denmark and California were identical, but they differed by 2 bp (0.1%) from the Jindo, Korea specimens and by 13–16 bp (0.9–1.1%) from the Tongyeong and Seosan, Korea specimens.

Figures

Figure 6: Maximum likelihood phylogram of the genus Ceramium based on rbcL sequences. Bootstrap supports and Bayesian posterior probabilities (BPP) occur at the nodes. A dash (-) indicates values <50% for bootstrap and <0.90 for BPP.

Figures 1–5: Ceramium sungminbooi sp. nov. (1) Holotype of Ceramium sungminbooi from Jindo, Korea, CNU065811. Scale bar=2 cm. (2–5) Sample from boat docks at Sausalito, San Francisco Bay, CA, USA, UC2050593; (2) apices showing slightly incurved tips. Scale bar=100 µm. (3) Laterally positioned cystocarp. Scale bar=100 µm. (4) Emergent tetrasporangium. Scale bar=50 µm. (5) Adaxially arranged tetrasporangia. Scale bar=100 µm.