• ALGAE
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• v.37 no.2
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• pp.123-133
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• 2022

Genetic diversity and distribution patterns of marine macroalgae are increasingly being documented in Southeast Asia. These studies show that there can be significant levels of genetic diversity and isolation between populations on either side of the Thai-Malay Peninsula. Bostrychia tenellla is a common filamentous red seaweed in the region and the entity is represented by at least two cryptic species. Despite being highly diverse and widespread, genetic variation and population structure of this species complex remains understudied, especially around the Thai-Malay Peninsula. We analyzed genetic diversity and inferred the phylogeographic pattern of specimens identified as B. tenella using the plastid RuBisCo spacer from samples from the Andaman Sea and the Gulf of Thailand. Our genetic analysis confirmed the occurrence of the two cryptic B. tenella species (B and C) along both coasts. Cryptic species B was more common in the area and displayed higher genetic diversity than species C. Historical demographic analyses indicated a stable population for species B, but more recent population expansion for species C. Our analyses also revealed that both cryptic species from the Andaman Sea possessed higher genetic diversity than those of the Gulf of Thailand. We also detected moderate to high levels of gene flow and weak phylogeographic structure of cryptic species B between the two coasts. In contrast, phylogeographic analysis showed genetic differences between populations of both cryptic species within the Andaman Sea. Overall, these results suggest that cryptic B. tenella species around Thai-Malay Peninsula may have undergone different demography histories, and their patterns of genetic diversity and phylogeography were likely caused by geological history and regional sea surface current circulation in the area.

• Journal of Microbiology and Biotechnology
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• v.27 no.4
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• pp.834-837
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• 2017

A distinct double-stranded RNA (dsRNA) cryptic virus, named spinach cryptic virus 1 (SpCV1), was identified from spinach transcriptome datasets. The SpCV1 genome has two dsRNA genome segments. The larger dsRNA1 has an open reading frame for a conserved RNA-dependent RNA polymerase (RdRp). The smaller dsRNA2 encodes a putative coat protein (CP). The sequence identity of SpCV1 RdRp and CP to the closest cryptic virus is 81% and 60%, respectively. Phylogenetic analysis indicates that SpCV1 is a novel member of the genus Alphapartitivirus (family Partitiviridae).

• ALGAE
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• v.33 no.3
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• pp.205-214
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• 2018

Red algae in the genus Portieria produce secondary halogenated monoterpenes, which are effective deterrents against herbivores, as secondary metabolites. Portieria hornemannii samples from various sites contain different concentrations of these metabolites, suggesting the existence of genetic diversity and cryptic species. To evaluate the genetic diversity and species distribution of Portieria in the northwest Pacific, we analyzed rbcL sequences of samples collected from Korea, Japan, and Taiwan. The phylogenetic analysis revealed five distinct lineages at the species level. One was recognized as Portieria japonica and the others were cryptic lineages in P. hornemannii. The rbcL haplotypes of P. japonica were genetically fragmented into two subgroups of geographic origin; Korean and Japanese. The four cryptic lineages within P. hornemannii were also geographically structured at a much finer scale. These results suggest that different genetic lineages in Portieria evolved from variable microhabitats, consequently influencing secondary metabolites. Further study is required to resolve the relationships between genetic and secondary metabolite variations in Portieria.

• Microbiology and Biotechnology Letters
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• v.32 no.3
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• pp.282-285
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• 2004

The polyene antibiotics including nystatin, pimaricin, amphotericin and candicidin are a family of most promising antifungal polyketide compounds, typically produced by rare actinomycetes species. The biosynthetic gene clusters for these polyenes have been previously investigated, revealing the presence of highly homologous biosynthetic genes among polyene-producers such as polyketide synthase (PKS) and cytochrome P450 hydroxylase (CYP) genes. Based on amino acid sequence alignment among actinomycetes CYP genes, the highly-conserved regions specific for only polyene CYP genes were identified and chosen for degenerate PCR primers, followed by the PCR-screening with various actinomycetes genomic DNAs. Among tested several polyene non-producing actinomycetes strains, Pseudonorcardia autotrophica strain was selected based on the presence of PCR product with polyene-specific CYP gene primers, and then confirmed to contain a cryptic novel polyene hydroxylase gene in the chromosome. These results suggest that the polyene-specific hydroxylase gene PCR should be an efficient way of screening and isolating potentially-valuable cryptic polyene antibiotic biosynthetic genes from various microorganisms including rare actinomycetes.

• Journal of Industrial Technology
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• v.28 no.B
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• pp.53-57
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• 2008

From the extensive screening for small cryptic plasmid among about 23 lactic acid bacteria (LAB), 2.4 kb of cryptic plasmid was isolated from Lactobacillus farciminis strain KCTC 3681 and named as pLF24. The plasmid pLF24 was a circular molecule of 2,396 base-pairs in length with a G+C content of 38%. Two protein-coding sequences could be predicted. ORF1 and ORF2 showed homologies to plasmids of gram-positive bacteria. The replication protein coded by ORF2 and the plus origin, were similar to replication regions of other gram-positive bacteria as shown in plasmids such as pLH2, pLS141-1 and pLC2. The nucleotide sequence of pLF24 was deposited into Genbank data base with an accession number of EU429343. The newly isolated plasmid can be used for construction of shuttle vector in Lactobacillus bacteria.

• Journal of Ecology and Environment
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• v.37 no.4
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• pp.395-410
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• 2014

The genus Callophyllis is recorded as six separate species with imprecise species delimitation in Korea. To elucidate the species boundaries of Korean Callophyllis, we performed morphological observations and molecular analyses, and included three Japanese Callophyllis species from the type locality. From the results of molecular analyses using plastid rbcL and mitochondrial COI-5P genes, we confirmed ten Callophyllis species, including five cryptic ones: C. adhaerens, C. adnata, C. crispata, and C. japonica from Korea and Japan; C. hayamensis as an unrecorded species from Korea; C. cartilaginea, C. mollitia, C. repens, C. serratifolia, and C. undulata as new species from Korea. There were no Korean specimens that matched C. adnata or C. crispata from Japan, except Korean C. japonica, which formed a genetic group with the Japanese species. We obtained the interspecific divergences among the five cryptic species as 0.6-4.5% in rbcL and 2.8-8.4% in COI-5P. We recognized that the species diversity of Callophyllis has been underestimated from the northwestern Pacific region. The species boundary of Callophyllis from Korea and Japan will be a cornerstone to revealing the phylogenetic affinity of the genus distributed in both hemispheres of the western Pacific.

• Genomics & Informatics
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• v.1 no.1
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• pp.55-60
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• 2003

The nucleotide sequence of pZMO1, a small cryptic plasmid of Zymomonas mobilis ATCC10988 was determined. Analysis of 1,680 bp of sequence revealed $69\%$ identity with Shigella sonnei plasmid, pKYM and $61\%$ identity with Nostoc sp. ss DNA replicating plasmid. Analysis of a deduced amino acid sequence of an orf of pZMO1 revealed $75\%$ identity and $90\%$ similarity with the repA gene of Synechocystis sp. plasmid pCA2.4. The upstream region of the repA gene of pZMO1 possesses six directed repeat sequences and two inverted repeat sequences at downstream of the IR consensus sequence of nick region of rolling circle replication (RCR) plasmid. A typical terminator hairpin structure was found at the downstream region of repA gene. Degradation of single-stranded plasmid DNA by S1 nuclease was detected by Southern hybridization. It suggests that pZMO1 replicates by a rolling circle mechanism in Z. mobilis ATCC10988 cells.

• Journal of Microbiology and Biotechnology
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• v.23 no.6
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• pp.837-842
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• 2013

A cryptic plasmid, pMBLR00, from Leuconostoc mesenteroides subsp. mesenteroides KCTC 3733 was isolated, characterized, and used for the construction of a cloning vector to engineer Leuconostoc species. pMBLR00 is a rolling circle replication plasmid, containing 3,370 base pairs. Sequence analysis revealed that pMBLR00 has 3 open reading frames: Cop (copy number control protein), Rep (replication protein), and Mob (mobilization protein). pMBLR00 replicates by rolling circle replication, which was confirmed by the presence of a conserved double-stranded origin and single-stranded DNA intermediates. An Escherichia coli-Leuconostoc shuttle vector, pMBLR02, was constructed and was able to replicate in Leuconostoc citreum 95. pMBLR02 could be a useful genetic tool for metabolic engineering and the genetic study of Leuconostoc species.

• Journal of Microbiology and Biotechnology
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• v.13 no.6
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• pp.1018-1020
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• 2003

The complete 1,486 nucleotide sequence of a cryptic plasmid separated from Lactobacillus bifermentans strain A02 isolated from Kimchi has been determined. The plasmid, designated as pA021, encodes a 33,488 Da putative Rep protein. Based on the sequence similarity, the protein shows homology with coding protein of pRS1, a previously reported plasmid of Oenococcus oeni and the replication initiation protein (Rep) of the Staphylococcal pT181 plasmid family.

• Journal of Microbiology and Biotechnology
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• v.19 no.4
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• pp.403-408
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• 2009

A number of bifidobacterial species of human origin were screened for the presence of cryptic plasmids. One strain, Bifidobacterium longum FI10564, harbored plasmids of approximately 2.2 kb, 3.6 kb, and 4.9 kb in size. The smallest plasmid, pFI2576(2,197 bp), was studied in detail and its complete nucleotide sequence was determined. Computer-assisted analysis of this novel plasmid(G+C content 62%) identified 9 putative open reading frames(orfs), 3 of which were shown to be probable genes. These putative genes are arranged in an operon-like structure, in which the overlapping orfs 1 and 2 encode putative Rep proteins and are highly homologous to the rep genes of the B. longum plasmid pMBI(1,847 bp). The mechanism of replication of pFI2576 was investigated using Southern blot analysis of whole cell lysates, with and without S1 nuclease treatment, and atomic force microscopy(AFM). The results indicate that pFI2576 is likely to use the theta mode of replication.