Cyanobacterial Taxonomy: Current Problems and Prospects for the Integration of Traditional and Molecular Approaches

Komarek, Jiri The Korean Society of Phycology 2006 ALGAE Vol.21 No.4

The application of modern ecological, ultrastructural and molecular methods, aided by the cultivation of numerous cyanobacterial morphotypes, has substantially changed our knowledge of these organisms. It has led to major advances in cyanobacterial taxonomy and criteria for their phylogenetic classification. Molecular data provide basic criteria for cyanobacterial taxonomy; however, a correct phylogenetic system cannot be constructed without combining genetic data with knowledge from the previous 150 years research of cyanobacterial diversity. Thus, studies of morphological variation in nature, and modern morphological, ultrastructural, ecophysiological and biochemical characters need to be combined in a “polyphasic” approach. Taxonomic concepts for generic and infrageneric ranks are re-evaluated in light of combined phenotypic and molecular criteria. Despite their usefulness in experimental studies, the limitations of using strains from culture collections for systematic and nomenclatural purposes is highlighted. The need for a continual revision of strain identification and proper nomenclatural practice associated with either the bacteriological or botanical codes is emphasized. Recent advances in taxonomy are highlighted in the context of prospects for understanding cyanobacterial diversity from natural habitats, and the evolutionary and adaptational processes that cyanobacteria undergo.

Cyanobacterial Taxonomy: Current Problems and Prospects for the Integration of Traditional and Molecular Approaches [Review]

Jirˇí Komárek 한국조류학회I 2006 ALGAE Vol.21 No.4

The application of modern ecological, ultrastructural and molecular methods, aided by the cultivation of numerous cyanobacterial morphotypes, has substantially changed our knowledge of these organisms. It has led to major advances in cyanobacterial taxonomy and criteria for their phylogenetic classification. Molecular data provide basic criteria for cyanobacterial taxonomy; however, a correct phylogenetic system cannot be constructed without combining genetic data with knowledge from the previous 150 years research of cyanobacterial diversity. Thus, studies of morphological variation in nature, and modern morphological, ultrastructural, ecophysiological and biochemical characters need to be combined in a “polyphasic” approach. Taxonomic concepts for generic and infrageneric ranks are re-evaluated in light of combined phenotypic and molecular criteria. Despite their usefulness in experimental studies, the limitations of using strains from culture collections for systematic and omenclatural purposes is highlighted. The need for a continual revision of strain identification and proper nomenclatural practice associated with either the bacteriological or botanical codes is emphasized. Recent advances in taxonomy are highlighted in the context of prospects for understanding cyanobacterial diversity from natural habitats, and the evolutionary and adaptational processes that cyanobacteria undergo.

Algal genomics perspective: the pangenome concept beyond traditional molecular phylogeny and taxonomy

이준모 국립생물자원관 2021 Journal of species research Vol.10 No.2

Algal genomics approaches provide a massive number of genome/transcriptome sequences and reveal the evolutionary history vis-à-vis primary and serial endosymbiosis events that contributed to the biodiversity of photosynthetic eukaryotes in the eukaryote tree of life. In particular, phylogenomic methods using several hundred or thousands of genes have provided new insights into algal taxonomy and systematics. Using this method, many novel insights into algal species diversity and systematics occurred, leading to taxonomic revisions. In addition, horizontal gene transfers (HGTs) of functional genes have been identified in algal genomes that played essential roles in environmental adaptation and genomic diversification. Finally, algal genomics data can be used to address the pangenome, including core genes shared among all isolates and partially shared strain-specific genes. However, some aspects of the pangenome concept (genome variability of intraspecies level) conflict with population genomics concepts, and the issue is closely related to defining species boundaries using genome variability. This review suggests a desirable future direction to merge algal pangenomics and population genomics beyond traditional molecular phylogeny and taxonomy.

DNA 바코드 동정을 위한 염기서열 간 Kimura 2-모수 거리의 임계값

김명숙,이정형 한국자료분석학회 2014 Journal of the Korean Data Analysis Society Vol.16 No.5

DNA barcoding arose as a new tool for taxonomy. However, their validities still need to be empirically evaluated. It is that species identification performs by calculation and comparison of distances using DNA barcoding which is extracted from COI (cytochrome c oxidase I). There is the threshold between DNA barcoding for each specific taxa which can be used species identification. It is possible to reduce the probability of misidentification. In this paper, we discussed that the threshold of distance between DNA barcodings requires for identification and delimitation of species in the evaluation of biodiversity. We propose the threshold selection method to reduce probability of misidentification using the Kimura 2-parameter (K2P) distance between DNA barcodings which have unstable or difficult species identification. The result showed that our proposed threshold selection method of K2P distance is effective. DNA 바코드는 분류학 분야의 새로운 도구로 제안되었으나, DNA 바코드의 유효성은 여전히 경험적으로 평가될 필요성이 있다. DNA 바코드를 이용한 생물종의 동정은 미토콘드리아 COI(cytochrome c oxidase I) 유전자를 대상으로 추출된 DNA 염기서열들 간 거리의 계산과 비교를 통해 이루어진다. 이 때 연구대상의 특정 분류군들마다 종을 동정하는데 사용할 수 있는 DNA 바코드 거리간의 임계값이 존재하며, 이를 이용하여 오동정(misidentification)의 가능성을 줄일 수 있다. 본 논문에서는 생물다양성의 평가에서 반드시 필요한 정확한 종의 동정을 위한 종의 경계를 설정하기 위하여 DNA 바코드 염기서열간 거리의 임계값(threshold)에 대해 논의하였다. 즉, 동정이 불안정한 것으로 간주되거나 동정이 어려운 경우 DNA 바코드들 간의 Kimura 2-모수 거리를 이용하여 오동정의 확률을 줄이기 위한 임계값 선택법을 제안하고, 이를 8종 24개체의 Neosiphonia와 3종 12개체의 Polysiphonia 바코드 자료에 적용하여 Kimura 2-모수 거리의 임계값 선택에 의한 분류가 효율적임을 확인하였다.

Molecular analyses and reproductive structure to verify the generic relationships of Hypnea and Calliblepharis (Cystocloniaceae, Gigartinales), with proposal of C. saidana comb. nov.

Yang, Mi Yeon,Kim, Myung Sook The Korean Society of Phycology 2017 ALGAE Vol.32 No.2

The genera Hypnea and Calliblepharis of the family Cystocloniaceae are discriminated by their female reproductive structure, especially in the formation of carposporangia and gonimoblasts. Hypnea saidana, once classified based on obsolete evidence, has not been studied phylogenetically using molecular analysis and detailed reproductive structure though it shares many morphologic features with the genus Calliblepharis. To provide better understanding of generic relationship of H. saidana with Hypnea and Calliblepharis, we carried out molecular analyses using the nuclear-encoded small subunit ribosomal DNA (SSU) and chloroplast-encoded large subunit of the RuBisCO (rbcL), and exact morphological observations focusing on the reproductive structures of wild specimens. Our molecular phylogeny showed that H. saidana is closely related to Calliblepharis, but distinct from the clade of Hypnea. Female reproductive structure of H. saidana characterized by upwardly developing chains of carposporangia, central reticulum of cell, and gonimoblast filaments not connected to the pericarp provides definite evidence to assign the taxonomic position of this species to Calliblepharis. Based on our combined molecular and morphological analyses, we have proposed Calliblepharis saidana comb. nov., expanding the distribution of Calliblepharis habitat from the eastern Atlantic South Africa, the northern Indian Ocean, Australasia, and Brazil to the western Pacific Ocean.

Evaluation of nuclear ribosomal RNA and chloroplast gene markers for the DNA taxonomy of centric diatoms

Lee, M.A.,Faria, D.G.,Han, M.S.,Lee, J.,Ki, J.S. Pergamon Press ; Elsevier Science Ltd 2013 Biochemical systematics and ecology Vol.50 No.-

Diatoms are highly diversified microeukaryotes with a taxonomy that has been under perpetual revision, particularly by means of molecular analyses. In this study, we evaluated typical genes to find the best molecular marker for the DNA taxonomy of centric diatoms, including Chaetoceros Ehrenberg, Cyclotella Kutzing ex de Brebisson, Discostella Houk & Klee, Stephanodiscus Ehrenberg, and Thalassiosira Cleve. Our test genes included nuclear ribosomal RNA (e.g. small subunit, 5.8S, and large subunit [LSU]), and chloroplast genes (e.g. ribulose-1, 5-biphoshate carboxylase oxygenase and D1 protein of the photosystem II reaction centre core complex [psbA]). Calculated genetic divergence was highest for LSU ribosomal RNA D1-D5 (p-distance of 12.3), followed by 5.8S (7.7), ribulose-1, 5-biphoshate carboxylase oxygenase (7.4), small subunit (6.6), and psbA (3.7). The phylogenetic trees for individual genes effectively separated taxonomically tested centric diatoms with different phylogenetic resolutions; however, psbA was incongruent with others. These taxonomic resolving powers were in agreement with genetic divergences. Parsimony analysis showed that LSU evolved 1.97 times more rapidly than psbA and 1.07 times more rapidly than 5.8S. These results suggest that all of the tested genes except psbA can be used as taxonomic markers for centric diatoms and that LSU is the best molecular marker.

New Record of a Sea Urchin Echinometra mathaei (Echinoidea: Camarodonta: Echinometridae) from Jeju Island, Korea and Its Molecular Analysis

이택준,신숙 한국동물분류학회 2012 Animal Systematics, Evolution and Diversity Vol.28 No.3

Echinoids were collected at depths of 5-10 m in Munseom, Jeju Island by SCUBA diving on November 23,2008 and September 15, 2009. Two specimens were identified as Echinometra mathaei (Blainville, 1825)based on morphological characteristics and molecular analyses of mitochondrial cytochrome c oxidase subunit I partial sequences. Echinometra mathaei collected from Korea was redescribed with photographs and was compared with other species from GenBank based on molecular data. Phylogenetic analyses showed that no significant differences were between base sequences of E. mathaei from Korea and that from GenBank. To date, 13 echinoids including this species have been reported from Jeju Island, and 32 echinoids have been recorded in Korea.

New Record of a Sea Urchin Echinometra mathaei (Echinoidea: Camarodonta: Echinometridae) from Jeju Island, Korea and Its Molecular Analysis

Lee, Taek-Jun,Shin, Sook The Korean Society of Systematic Zoology 2012 Animal Systematics, Evolution and Diversity Vol.28 No.3

Echinoids were collected at depths of 5-10 m in Munseom, Jeju Island by SCUBA diving on November 23, 2008 and September 15, 2009. Two specimens were identified as Echinometra mathaei (Blainville, 1825) based on morphological characteristics and molecular analyses of mitochondrial cytochrome c oxidase subunit I partial sequences. Echinometra mathaei collected from Korea was redescribed with photographs and was compared with other species from GenBank based on molecular data. Phylogenetic analyses showed that no significant differences were between base sequences of E. mathaei from Korea and that from GenBank. To date, 13 echinoids including this species have been reported from Jeju Island, and 32 echinoids have been recorded in Korea.

New Record of a Sea Urchin Echinometra mathaei (Echinoidea: Camarodonta: Echinometridae) from Jeju Island, Korea and Its Molecular Analysis

Taekjun Lee,Sook Shin 한국동물분류학회 2012 Animal Systematics, Evolution and Diversity Vol.28 No.3

Echinoids were collected at depths of 5-10 m in Munseom, Jeju Island by SCUBA diving on November 23, 2008 and September 15, 2009. Two specimens were identified as Echinometra mathaei (Blainville, 1825) based on morphological characteristics and molecular analyses of mitochondrial cytochrome c oxidase subunit I partial sequences. Echinometra mathaei collected from Korea was redescribed with photographs and was compared with other species from GenBank based on molecular data. Phylogenetic analyses showed that no significant differences were between base sequences of E. mathaei from Korea and that from GenBank. To date, 13 echinoids including this species have been reported from Jeju Island, and 32 echinoids have been recorded in Korea.

Molecular Phylogeny of the Subfamily Sciarinae Billberg (Diptera: Sciaridae)

Seunggwan Shin,Sunghoon Jung,Heungsik Lee,Seunghwan Lee 한국응용곤충학회 2012 한국응용곤충학회 학술대회논문집 Vol.2012 No.10

The phylogeny of the subfamily Sciarinae is reconstructed by the result of maximum likelihood, maximum parsimony, and Bayesian inference of 4,809 bp from two mitochondrial (COI and 16S) and two nuclear (18S and 28S) genes. The current subfamily Sciarinae is polyphyletic, since the genera Chaetosciara, Mouffetina, Schwenckfeldina, and Scythropochroa are grouped separately as the sister clade of other subfamilies. The monophyly of the genera Chaetosciara, Sciara, Scythropochroa, and Trichosia s. str. is strongly supported; however, the genus Leptosciarella s. l. is polyphyletic due to the separation of subgenus Leptosciarella (Leptospina) as a sister taxa of remaining Sciarinae (Leptosciarella s. str., Sciara, and Trichosia s. str.). The classification of the Sciarinae is revised and discussed on the basis of molecular phylogenetic hypotheses.