• Journal of Ecology and Environment
• /
• 제41권1호
• /
• pp.9-18
• /
• 2017

Background: Species in the heterokont genus Synura are colonial and have silica scales whose ultrastructural characteristics are used for classification. We examined the ultrastructure of silica scales and molecular data (nuclear SSU rDNA and LSU rDNA, and plastid rbcL sequences) to better understand the taxonomy and phylogeny within the section Petersenianae of genus Synura. In addition, we report the first finding of newly recorded Synura species from Korea. Results: We identified all species by examination of scale ultrastructure using scanning and transmission electron microscopy (SEM and TEM). Three newly recorded species from Korea, Synura americana, Synura conopea, and Synura truttae were described based on morphological characters, such as cell size, scale shape, scale size, keel shape, number of struts, distance between struts, degree of interconnections between struts, size of base plate pores, keel pores, base plate hole, and posterior rim. The scales of the newly recorded species, which belong to the section Petersenianae, have a well-developed keel and a characteristic number of struts on the base plate. We performed molecular phylogenetic analyses based on sequence data from three genes in 32 strains (including three outgroup species). The results provided strong statistical support that the section Petersenianae was monophyletic, and that all taxa within this section had well-developed keels and a defined number of struts on the base plate. Conclusions: The phylogenetic tree based on sequence data of three genes was congruent with the data on scale ultrastructure. The resulting phylogenetic tree strongly supported the existence of the section Petersenianae. In addition, we propose newly recorded Synura species from Korea based on phylogenetic analyses and morphological characters: S. americana, S. conopea, and S. truttae.

• ALGAE
• /
• 제35권3호
• /
• pp.293-301
• /
• 2020

The applications of DNA barcoding have a wide range of uses, such as in taxonomic studies to help elucidate cryptic species and phylogenetic relationships and analyzing environmental samples for biodiversity monitoring and conservation assessments of species. After obtaining the DNA barcode sequences, sequence similarity-based homology analysis is commonly used. This means that the obtained barcode sequences are compared to the DNA barcode reference databases. This bioinformatic analysis necessarily implies that the overall quantity and quality of the reference databases must be stringently monitored to not have an adverse impact on the accuracy of species identification. With the development of next-generation sequencing techniques, a noticeably large number of DNA barcode sequences have been produced and are stored in online databases, but their degree of validity, accuracy, and reliability have not been extensively investigated. In this study, we investigated the extent to which the amount and types of erroneous barcode sequences were deposited in publicly accessible databases. Over 4.1 million sequences were investigated in three largescale DNA barcode databases (NCBI GenBank, Barcode of Life Data System [BOLD], and Protist Ribosomal Reference database [PR2]) for four major DNA barcodes (cytochrome c oxidase subunit 1 [COI], internal transcribed spacer [ITS], ribulose bisphosphate carboxylase large chain [rbcL], and 18S ribosomal RNA [18S rRNA]); approximately 2% of erroneous barcode sequences were found and their taxonomic distributions were uneven. Consequently, our present findings provide compelling evidence of data quality problems along with insufficient and unreliable annotation of taxonomic data in DNA barcode databases. Therefore, we suggest that if ambiguous taxa are presented during barcoding analysis, further validation with other DNA barcode loci or morphological characters should be mandated.

• Journal of Plant Biotechnology
• /
• 제38권4호
• /
• pp.301-307
• /
• 2011

The medicinal herb Oldenlandia diffusa is known as a folk medicine for the treatment of hepatitis, sore throat, appendicitis, malignant tumors and urethral infection in Southern China and Korea. Another species O. corymbosa, is also used for the therapy of the similar conditions, however, only O. diffusa is referred to the medicinal herb by Chinese Pharmacopoeia. Due to their similar morphology, O. diffusa and O. corymbosa are often misidentified. To easily identify O. diffusa from O. corymbosa, the phylogenetic utility of nuclear ribosomal DNA (nrDNA) internal transcribed spacers (ITS) were investigated among different O. diffusa and O. corymbosa populations in Korea. The nrDNA ITS sequence of O. diffusa contained 791 bp, with GenBank accession number of JF837601-JF837602. The nrDNA ITS sequence of O. corymbosa was 785-786 bp, with GenBank accession number of JF837603-JF837611. The results showed that there are some certain divergences in the ITS region sequence between both species, even among different populations of the same species. Particularly, O. corymbosa ST-4 population showed the highest dissimilarity of the ITS region sequence with other nine populations of O. corymbosa and two populations of O. diffusa. This consequence makes us further understand the molecular diversification between O. corymbosa and O. diffusa, and help to promote the correct use and safety.

• 생태와환경
• /
• 제52권4호
• /
• pp.385-393
• /
• 2019

Chironomid communities are indicators of water pollution because of their ability to thrive under freshwater conditions. However, it is difficult to distinguish between chironomid larvae based on morphology. DNA barcoding, based on nucleotide sequences of marker genes, can be used to identify chironomid larvae. Samples of chironomid larvae were collected from Gwangju Stream and Pungyeongjeong Stream, tributaries of the Yeongsan River in South Korea. We identified 3 subfamilies, 13 genera, 16 species, and 1 cryptic species. There were 7 genera and 10 species from the subfamily Chironominae, 5 genera and 5 species from subfamily Orthocladiinae, 1 genus and 1 species from subfamily Tanipodinae, and the cryptic chironomid species of the family Chironomidae. There were 21 individuals from, 7 species and 1 cryptic species from the Gwangju Stream and 24 individuals, belonging to 10 species from the Pungyeongjeong Stream. The only species detected in both streams was Cricotopus bicinctus. The relationship between water quality and the species detected was difficult to explain, but the number of species showed a tendency to increase at sites where water quality was poor. Additional investigations and studies are needed to understand the relationship between water quality and the chironomid species occurring in these two streams.

• 식물조직배양학회지
• /
• 제24권4호
• /
• pp.225-231
• /
• 1997

For genetic engineering to be commercially viable, an efficient transformation system is needed to produce transgenic plane from diverse genotypes ("generalized protocol"). Development of such a system requires optimization of a number of components such as gene transfer agent, plant tissues competent for both regeneration and transformation, and control of transgene expression. Although several novel gene transfer methods have been developed for plane, a majority of stably transformed plane express the introduced genes at low levels. Moreover, silencing of selectable marker genes shortly after their incorporation into plant chromosomes may result in low recovery of transgenic tissues from selection. Matrix attachment regions (MARs) are DNA sequences that bind to the cell's proteinaceous nuclear matrix to form DNA loop domains. MARs have been shown to increase transgene expression in tobacco cells, and reduce position in mature transgenic plants. Flanking an antibiotic resistance transgene with MARs should therefore lead to improved rates of transformation in a diversity of species, and may permit recalcitrant species and genotypes to be successfully transformed. Literature review and recent data from my laboratory suggest that MARs can serve as a transformation booster in recalcitrant plant species.

• 한국약용작물학회지
• /
• 제12권3호
• /
• pp.214-218
• /
• 2004

우리 나라 전역에서 수집한 7종의 자생 둥굴레로부터 genomic DNA을 추출한 후 Operon random primer(10-mer)를 이용하여 PCR을 수행하여 재현성이 있으면서 polymorphism을 보이는 19개의 primer를 선발하였다. 선발한 primer로부터 PCR에 의해 증폭된 DNA의 크기는 $3000{\sim}300\;bp$이었고, 19개의 random primer에서 복제된 전체 band의 수는 114개에서 157개로 공시종간에 많은 차이를 보였으며, band의 유무에 근거한 유연관계 분석에서 7개의 공시종은 각시둥굴레와 층층둥굴레가 1개군으로, 여타 종들을 1개군으로 크게 2개군으로 분리되어 유전적으로 상당한 차이가 있는 것으로 나타났다.

• 한국동물학회지
• /
• 제13권4호
• /
• pp.112-126
• /
• 1970

This paper deals with cytogenetical and cytochemical studies of the carp (Cyprinus carpio), the funa (Carassius carassius) and their hybrids. When kept under a confined condition, the carp and the funa mate andcan produce hybrids. Reciprocal crosses are also possible with similar results. The hybrids grow regularly with no observed abnormalities in the course of their development. They rank intermediate between the parent species in several characters. The hybrid males are completely sterile, while a hybrid female laid eggs in backcrossing. The spermatogenetic activity in hybrid testes is greatly disturbed. The chromosomes as observed in spermatogonial devision of hybrids are 100 in number, being the total sum of the haploid numbers of the parents, 50 for the carp and 50 for the funa. Meiosis in the hybrid testes is highly disturbed being arrested at early stages of the meiotic prophase. Most of the germ-cells undergo pycnotic degeneration during the period from late leptotene, and no spermatozoa are produced. In some hybrid specimens, the gonads show mosaic structures composed of testicular and ovarian elements, anevidence suggesting that sterility is associated with intersexuality caused by genetic unbalance between the parent species. The DNA amount in spermatogonial nuclei of thehybrids is approximately the same as that of liver nuclei, showing the 2n value. The DNA amount in the pachytene nuclei of the hybrids is less than the 4n value, while the parent species have the reduced amount of DNA in their pachytene nuclei. A consideration was made that the reduced amount of DNA in the hybrid cells may cause the disturbance of cellular activity leading to the subsequent degeneration of cells. Some aspects of enzymatic pattern in the carp, funa and their hybrids are. going on.

• 한국자원식물학회지
• /
• 제27권3호
• /
• pp.249-255
• /
• 2014

The rice belonging to Oryza sativa is not only has significant economic importance, for it is the major source of nutrition for about 3 billion all around the world. But also plays a vital role as a model organism, because it has a number of advantages to be a model plant, such as efficient transformation system and small genome size. Many methods and techniques have been conducted to attempt to distinguish different Oryza sativa species, such as amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and so on. However, studies using sequence analysis of internal transcribed spacer (ITS), a region of ribosomal RNA has not been reported until now. This study was undertaken with an aim to understand the phylogenetic relationships among sixteen isolates of Oryza sativa collected from abroad and fifteen isolates collected from Korea, using ribosomal RNA (rRNA) internal transcribed spacer (ITS) sequences to compare the phylogeny relationships among different Oryza sativa species. The size variation obtained among sequenced nuclear ribosomal DNA (nrDNA) ITS region ranged from 515bp to 1000bp. The highest interspecific genetic distance (GD) was found between Sfejare 45 (FR12) and Anapuruna (FR15). Taebong isolate showed the least dissimilarity of the ITS region sequence with other thirty isolates. This consequence will help us further understanding molecular diversification in intra-species population and their phylogenetic analysis.

• Fisheries and Aquatic Sciences
• /
• 제10권1호
• /
• pp.24-29
• /
• 2007

Our objective was to clarify the cytogenetic characteristics, including karyotypes, cellular DNA content, and nuclear size of erythrocytes, of black plaice Pleuronectes obscurus, dotted gizzard shad Konosirus punctatus, and perch sculpin Pseudoblennius percoides, collected from the coastal areas of Jo Island, Busan, Korea. Karyotypes of P. obscurus and K. punctatus both had a diploid number of 48 and a fundamental number (FN) of 48, with a chromosome formula of 48T. The karyotype of p. percoides had a diploid number of 46 and FN of 56, with a chromosome formula of 10SM +36T. No sex-associated heteromorphic pairs were detected for any species. The variation in DNA values (P. obscurus=1.15 pg/nucleus, K. punctatus=1.56pg/nucleus, P. percoides=1.11 pg/nucleus) was positively related to variation in chromosome FN.

• 한국수산과학회지
• /
• 제33권6호
• /
• pp.489-495
• /
• 2000

The 185 ribosomal RNA gene (185 rDNA) of the marine alga Porphyra sp. 723 (Bangiales, Rhodophyta) was amplified using the polymerase chain reaction and its sequence was analysed. The Porphyra species was a summer strain collected on rocks in upper intertidal zone at Ikidae, Pusan on 23rd July 1999. The fronds were $1{\~}5 cm$ long, monostromatic, and orbicular or ovate shaped, They had spinulate processes at margin of the frond, Comparison of this 185 rDNA sequence with the other Forphyra species indicates that Porphyra sp. 723 has the same 185 rDNA sequence derived from Porphyra suborbiculata (NCBI access number; AB 013180) except one base pair substitution in 2327 base pairs.