Morphology and Molecular Phylogeny of Hypnea flexicaulis(Gigartinales, Rhodophyta) from Korea

양은찬,부성민,Geraldino, Paul John L.,Yang, Eun-Chan,Bu, Sung-Min 한국조류학회(藻類) 2006 ALGAE Vol.21 No.4

Erythrolobus australicus sp. nov. (Porphyridiophyceae, Rhodophyta): a description based on several approaches

양은찬,John A. West,Joe Scott,윤환수,Akiko Yokoyama,Ulf Karsten,Susan Loiseaux de Goër,Evguenia Orlova 한국조류학회I 2011 ALGAE Vol.26 No.2

The unicellular marine red alga Erythrolobus australicus sp. nov. (Porphyridiophyceae) was isolated into laboratory culture from mangroves in Queensland and New South Wales, Australia. The single multi-lobed red to rose-red plastid has more than one pyrenoid and lacks a peripheral thylakoid. Arrays of small electron dense globules occur along the thylakoids. The nucleus is peripheral with a central to eccentric nucleolus. Each Golgi body is associated with a mitochondrion. The spherical cells are positively phototactic with slow gliding movement. The psaA + psbA phylogeny clearly showed that E. australicus is a distinct species, which is closely related to E. coxiae. The chemotaxonomically relevant and most abundant low molecular weight carbohydrate in E. australicus is floridoside with concentrations between 209and 231 μmol g^(-1) dry weight. Traces of digeneaside were also detected. These various approaches help to understand the taxonomic diversity of unicellular red algae.

Morphology and molecular phylogeny of Psilothalia dentata(Ceramiaceae, Rhodophyta)

양은찬,부성민,Kyung Mi Kim,Jan Runess 한국조류학회I 2004 ALGAE Vol.19 No.4

Psilothallia is a ceramiaceous red algal genus that includes three species worldwide: P. dentata, P. siliculosa, and P. striata. The latter two species are limited to Australian waters, and P. dentata occurs in Japan. We here report the detailed morphology of P. dentata, and also determined plastid protein-coding psbA in P. dentata and putative relatives. Psilothallia dentata is distinguished by compressed thalli with alternate-distichous determinate branchlets, six periaxial cells, rhizoidal filaments in axes, cystocarps with 7-8 involucral filaments, spermatangia on branched filaments, and tetrahedrally divided tetrasporangia on branched filaments. Psilothallia dentata is also unusual in that cystocarps, spermatangial clusters, and tetrasporangial tufts are formed on short adventitious indeterminate branches arising on axils of determinate branchlets. The phylogenetic trees of psbA sequences show that P. dentate was nested in a monophyletic clade comprising Ptilota, Neoptilota, and Plumaria. This result suggests that the taxonomic position of P. dentata may be transferred from the tribe Rhodocallideae to the Ptiloteae.

Reinstatement of Gracilariopsis chorda (Gracilariaceae, Rhodophyta) Based on Plastid rbcL and Mitochondrial cox1 Sequences

김명숙,양은찬,김수연,황일기,부성민 한국조류학회I 2008 ALGAE Vol.23 No.3

Two different molecular markers, the plastid rbcL and mitochondrial cox1 genes, were used to define the taxonomic position of the northwest Pacific Ocean species currently named Gracilaria chorda. We analyzed both genes (1,222 bp for rbcL and 1,245 bp for cox1) from 18 specimens collected in Korea, Japan, and China. Phylogenetic reconstruction revealed that this organism should be classified in the genus Gracilariopsis, rather than in the Gracilaria. Thus, Gracilariopsis chorda (Holmes) Ohmi is the legitimate name for Gracilaria chorda Holmes. Within the species, the sequences differed by 8 bp (0.7%) in rbcL and 5 bp (0.4%) in cox1. Six haplotypes of cox1 tended to be geographically organized. Gp. chorda is characterized by coarse, elongate terete axes, short filiform branchlets usually at irregular intervals, an abrupt transition in cell size from medulla to cortex, cystocarps without tubular nutritive cells connecting the gonimoblast to the upper pericarp, and relatively large gonimoblast cells of the cystocarp in the specimens collected from Wando in southern Korea. Two different molecular markers, the plastid rbcL and mitochondrial cox1 genes, were used to define the taxonomic position of the northwest Pacific Ocean species currently named Gracilaria chorda. We analyzed both genes (1,222 bp for rbcL and 1,245 bp for cox1) from 18 specimens collected in Korea, Japan, and China. Phylogenetic reconstruction revealed that this organism should be classified in the genus Gracilariopsis, rather than in the Gracilaria. Thus, Gracilariopsis chorda (Holmes) Ohmi is the legitimate name for Gracilaria chorda Holmes. Within the species, the sequences differed by 8 bp (0.7%) in rbcL and 5 bp (0.4%) in cox1. Six haplotypes of cox1 tended to be geographically organized. Gp. chorda is characterized by coarse, elongate terete axes, short filiform branchlets usually at irregular intervals, an abrupt transition in cell size from medulla to cortex, cystocarps without tubular nutritive cells connecting the gonimoblast to the upper pericarp, and relatively large gonimoblast cells of the cystocarp in the specimens collected from Wando in southern Korea.

The Occurrence of Griffithsia okiensis (Ceramiaceae, Rhodophyta) from Koreaon the Basis of Morphology and Molecular Data

김형섭,양은찬,부성민 한국조류학회I 2006 ALGAE Vol.21 No.1

Despite continued studies on red algal flora in Korea, the taxonomy of the tiny ceramiaceous algae has received little attention. We report for the first time Griffithsia okiensis from Korea on the basis of morphology and molecular data. The species is small in thalli height (0.3-1.5 cm), and in diameter of vegetative cells (50-500 μm), and the ratio of cell length/breadth is 2-3 times. It has two carpogonial branches from the supporting cell of procarp. We generated psbA and rbcL sequences from ten specimens of G. okiensis isolated from Korea and Japan and from one G. japonica species isolated Japan. Eight specimens of G. okiensis from Korea were almost identical in both psbA and rbcL regions, nevertheless they differed from Japanese specimens by 4 nucleotides in psbA and 7 in rbcL. In all analyses of psbA, rbcL, and psbA + rbcL data sets, G. okiensis was determined to be a different species from G. japonica isolated from Japan, although both species showed a sister relationship. For all that extensive collection trips, we found no evidence for the occurrence of G. japonica in Korea.

Characterization of the Complete Plastid Genome of Campylaephora boydenii (Ceramiaceae, Florideophyceae)

김수연,양은찬 한국조류학회I 2023 수생생물 Vol.3 No.2

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.

First Description of Petalonia zosterifolia and Scytosiphon gracilis (Scytosiphonaceae, Phaeophyceae) from Korea with Special Reference to nrDNA ITS Sequence Comparisons

GaYounCho,양은찬,SangHeeLee,SungMinBoo 한국조류학회I 2002 ALGAE Vol.17 No.3

Scytosiphonaceae is an ectocarpalean brown algal family, that is a recent focus of systematics and marine biodiversity. We describe Petalonia zosterifolia and Scytosiphon gracilis from Korea for the first time. P. zosterifolia occurred on the East coast, and had flat, linear and solid thalli. S. gracilis was found in Jeju, and had cylindrical to flat and hollow thalli. However, these two species are so similar that it is difficult to identify by morphology alone. In order to determine if the nuclear DNA reveals the distinctness of both species and to know their phylogenies, the ITS region sequences were newly determined in 22 samples of P. zosterifolia, Scytosiphon gracilis, and other three members of the genera from Korea. We found 0.12% variation among samples of P. zosterifolia from different locations, and no variation between S. gracilis samples from different years, but extensive interspecific divergences (13.62-22.83%) of each species to other members in Petalonia and Scytosiphon. The ITS sequence data consistently showed a close relationship between P. zosterifolia and S. gracilis. This result is congruent with morphology and with the published data of plastid rbc and partial nrDNA large subunit gene sequences, and suggests that P. zosterifolia and S. gracilis might have diverged from the most recent common ancestor.

한국산 꼬시래기의 세포소기관 유전체 정보 및 계통관계

김수연,유영채,양은찬 한국조류학회I 2022 수생생물 Vol.2 No.2

꼬시래기과는 다세포성 진정홍조류로 유용성 종을 다수 포함하고 있다. 전세계적으로 4속(Curdiea속, Gracilaria속, Gracilariopsis속 및 Melanthalia속) 239종이 보고되었으며, 우리나라에는 2속 10종이 알려져 있다. 이 중 꼬시래기(Gracilaria vermiculophylla)는 우리나라를 포함한 북서태평양 고유종으로, 지난 30-40년간 전세계 곳곳으로 이동한 침입종으로 유명하다. 본 연구에서는 우리나라 꼬시래기의 세포소기관 유전체 자료를 확보하고 계통유연관계를 파악하고자 하였다. 전남 고흥에서 채집한 꼬시래기의 색소체 유전체(OP978508) 180,269 bp (29.5% GC, 238개 유전자) 및 미토콘드리아 유전체(OP978509) 26,090 bp (28.4% GC, 52개 유전자)를 확보하여 이전의 자료와 비교분석하고 계통수를 구축하였다. 고흥 꼬시래기의 색소체 유전체는 미국 및 중국 개체의 색소체 유전체와 99.93% 이상 유사하였다. 반면, 미토콘드리아 유전체의 경우 중국 개체(94.16%)보다 미국 개체(99.52%)와 더욱 유사하였다. 꼬시래기 4개체(고흥 1, 미국 1, 중국 2)의 미토콘드리아 유전체 정렬 결과, 15개의 삽입 및 결실 부위가 존재하였으며, nad3-nad1-nad2-sdh4-nad4 부위에서 가장 높은 변이를 보였다. 미토콘드리아 24개 CDS의 아미노산서열을 이용하여 구축한 유합계통수는 고흥 꼬시래기가 미국 Hog Island 꼬시래기와 가장 유사함을 지지한다. 꼬시래기의 새로운 색소체 유전체 및 미토콘드리아 유전체는 유용성 꼬시래기과 홍조류의 다양성 및 계통연구에 중요한 기초자료가 될 것이다. The Gracilariacea is a representative red algal group including many economic species. The four genera (Curdiea, Gracilaria, Gracilariopsis and Melanthalia) and 239 species were reported in the world, and two genera (Gracilaria and Gracilariopsis) and 10 species were recorded in Korea. Among them, Gracilaria vermiculophylla has been an endemic species in the northwest Pacific region, however, it also known as global invasive species since last couples of decades. This study was conducted to secure organelles genomes of Gracilaria vermiculophylla from the Goheung, Korea and to use the data for phylogenetic analysis of the species. In present study, we sequenced, assembled and annotated the plastid (ptDNA: OP978508, 180,269 bp, 29.5% GC, 238 genes) and mitochondria (mtDNA: OP978509, 26,090 bp, 28.4% GC, 52 genes) genomes of G. vermiculophylla. The ptDNA of Goheung individual showed (> 99.93% identity) similar to those of the USA and China. However, the mtDNA of Goheung was more similar to the USA (99.52% identity) than that of the China (94.16%). Total 15 distinct indels were found in mtDNAs alignment of four G. vermiculophylla (Korea 1, USA 1, China 2) individuals, and nad3-nad1-nad2-sdh4-nad4 was identified as the highly variable region in the mtDNA. The combined amino acid (AA) phylogeny based on 24 CDS (coding sequence) of mtDNA supported the close relationship of individuals between Goheung, Korea and Hog Island, USA. Newly determined ptDNA and mtDNA of G. vermiculophylla maybe useful for the diversity and phylogeny of economic red algae such as Gracilaraceae.

Characterization of cetacean Numt and its application into cetacean phylogeny

이정현,고영준,양은찬,이재학,이경원,정재연,박기정,정옥성,박종화,임형순 한국유전학회 2015 Genes & Genomics Vol.37 No.12

The translocations of mitochondrial DNA into chromosomal DNA (nuclear mitochondrial DNA, Numt) are ubiquitous in eukaryotes including yeasts, plants, and animals. The features of Numt and the recent sequencing technology can facilitate an expanded application of Numt into a valuable phylogenetic marker for unresolved taxa. To date, the phylogeny of extant cetaceans has been studied by a variety of morphological and molecular data and still has long attracted attention. Here, the Numts of cattle, two baleen whale and four toothed whales were detected by BLAST-search of the mitochondrial sequences of each species against its corresponding nuclear genome and we investigated the characteristics of cetacean Numt and revisited the phylogeny and evolution of cetartiodactyl using Numts. The content and distribution of Numt length showed similar patterns among six cetacean genomes. Under-representation of D-loop region-derived Numts and different abundance of Numt across D-loop sub-domains were observed in cetacean Numts except sperm whale. Examination of Numt location in cetacean nuclear genomes showed that some of orthologous Numts were integrated into exons, introns, and pseudogenes, suggesting that cetacean Numts may contribute to cetacean biology and evolution. Our phylogenetic study with cetacean Numt based on the maximum likelihood method corresponded to the study from other phylogenetic markers.

Taxonomic note of Polysiphonia pacifica (Ceramiales, Rhodophyta) complex with focus on Pacific isolates

Myung Sook Kim,양은찬 한국조류학회I 2005 ALGAE Vol.20 No.1

Polysiphonia pacifica is rhodomelaceous red algal species that includes five varieties in Pacific Ocean: P. pacifica var. delicatula, P. pacifica var. distans, P. pacifica var. determinata, P. pacifica var. disticha, and P. pacifica var. gracilis. We here report morphology and phylogeny of P. pacifica to confirm the relationships among previously described varieties as a loan of type specimens from US and to assess phylogenetic relationships of closely related species using plastid protein-coding rbcL gene. Polysiphonia pacifica is distinguished by having creeping filaments attached by unicellular rhizoids not cut off by cross walls, four pericentral cells, ecorticate, trichoblasts rare, ultimate branchlets attenuate at the tip but not pungent, and tetrasporangia in long straight series in the ultimate branchlets. The protein-coding plastid rbcL gene sequence data show that P. pacifica is distinctly different from the superficially similar species, P. morrowii and P. stricta. However, the rbcL sequences of P. pacifica var. pacifica and var. disticha are identical though they have morphological variation.