National Institute of Biological Resources

Incheon, South Korea

National Institute of Biological Resources

Incheon, South Korea

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Repinski S.L.,University of California at Davis | Kwak M.,University of California at Davis | Kwak M.,National Institute of Biological Resources | Gepts P.,University of California at Davis
Theoretical and Applied Genetics | Year: 2012

In a common bean plant exhibiting determinate growth, the terminal shoot meristem switches from a vegetative to reproductive state, resulting in a terminal inflorescence. Contrary to this, indeterminate growth habit results in a terminal meristem that remains vegetative where it further regulates the production of lateral vegetative and reproductive growth. In the last century, breeders have selected determinate growth habit, in combination with photoperiod insensitivity, to obtain varieties with a shorter flowering period, earlier maturation and ease of mechanized harvest. Previous work has identified TFL1 as a gene controlling determinate growth habit in Arabidopsis thaliana. In this work, we have validated that the Phaseolus vulgaris candidate gene, PvTFL1y, is the functional homolog of TFL1 using three independent lines of evidence. First, in a population of ~1,500 plants, PvTFL1y was found to co-segregate with the phenotypic locus for determinate growth habit (fin) on chromosome 01. Second, using quantitative PCR, we found that two unique haplotypes associated with determinacy at the PvTFL1y locus, a 4. 1-kb retrotransposon and a splice-site mutation, cause mRNA abundance to decrease 20-133 fold, consistent with the recessive nature of fin. Finally, using a functional complementation approach, through Agrobacterium-mediated transformation of determinate Arabidopsis, we rescued tfl1-1 mutants with the wild-type PvTFL1y gene. Together, these three lines of evidence lead to the conclusion that PvTFL1y is the functional homolog of the Arabidopsis gene, TFL1, and is the gene responsible for naturally occurring variation for determinacy in common bean. Further work exploring the different haplotypes at the PvTFL1y locus may lead to improved plant architecture and phenology of common bean cultivars. © 2012 Springer-Verlag.


News Article | November 2, 2016
Site: www.eurekalert.org

The first whole genome sequence of the Far Eastern Amur leopard is published in the open access journal Genome Biology, providing new insight into carnivory and how it impacts on genetic diversity and population size. Mr. Yunsung Cho, lead author from Ulsan National Institute of Science and Technology, said: "Using the Amur leopard genome and comparing it to that of other mammalian genomes we found that carnivory seems to be a strong selection force for genes involved in dietary adaptation - something not as apparent in mammals that are omnivores or herbivores. For example, cows could eat meat without it having a major impact on their health, but leopards eating grass would quickly die as they have evolved to survive on meat." Specialized diets result in physiological, biochemical and morphological adaptations and carnivory is considered to be an evolutionary instable diet. Current research shows that animals in the cat family, Felidae, have relatively low genetic diversity and small population sizes. This could be due to the inflexible nature of their strict diet and explains their vulnerability and critical conservation status. Mr. Cho explained: "Carnivory related genetic adaptations such as extreme agility, muscle power and specialized diet make leopards such successful predators, but these lifestyle traits also make them genetically vulnerable." An international team of researchers sequenced the Amur leopard genome using a muscle sample of a female from Korea. They then analyzed a further 18 mammalian genomes including eight carnivores (domestic cat, tiger, cheetah, lion, leopard, polar bear, killer whale and Tasmanian devil), five omnivores (human, mouse, dog, pig, and opossum) and five herbivores (giant panda, cow, horse, rabbit, and elephant). Comparing the genomes they found that carnivores share two genes that are not present in other genomes that play an important role in bone development and repair, which could drive selection for a diet specialized towards meat. Professor Steve O'Brien, who has been researching rare endangered cat species for decades emphasizes that "Leopards are the most widespread species of the big cats, found in Africa to the Russian Far East, and thrive in a variety of environments. However, populations are fast declining, especially the Amur leopard, which is now critically endangered and perhaps the most endangered animal species on Earth." This is the first de novo genome assembly and the second leopard genome to be sequenced following the snow leopard published in 2013. The researchers hope that this Amur leopard reference genome will serve as a useful tool for understanding Felidae evolution and aid conservation. Dr. Soonok Kim, who initiated and led the project as the PI of National Institute of Biological Resources of Korea adds: "Cats are also a good model for studying health issues, such as human diabetes, and this new leopard genome reference is an environmental treasure that could help us understand these conditions further." 1. Images are available. Please contact Alanna Orpen. 2. Comparison of three dietary groups in mammals: carnivore, omnivore, and herbivore genome analyses with a new leopard assembly Soonok Kim, Yun Sung Cho, Hak-Min Kim et al. Genome Biology 2016 During the embargo period, please contact Alanna Orpen for a copy of the article. After the embargo lifts, the article will be available at the journal website here: https:/ Please name the journal in any story you write. If you are writing for the web, please link to the article. All articles are available free of charge, according to BioMed Central's open access policy. 3. Genome Biology covers all areas of biology and biomedicine studied from a genomic and post-genomic perspective. Content includes research, new methods and software tools, and reviews, opinions and commentaries. Areas covered include, but are not limited to: sequence analysis; bioinformatics; insights into molecular, cellular and organismal biology; functional genomics; epigenomics; population genomics; proteomics; comparative biology and evolution; systems and network biology; genomics of disease; and clinical genomics. All content is open access immediately on publication. 4. BioMed Central is an STM (Science, Technology and Medicine) publisher which has pioneered the open access publishing model. All peer-reviewed research articles published by BioMed Central are made immediately and freely accessible online, and are licensed to allow redistribution and reuse. BioMed Central is part of Springer Nature, a major new force in scientific, scholarly, professional and educational publishing, created in May 2015 through the combination of Nature Publishing Group, Palgrave Macmillan, Macmillan Education and Springer Science+Business Media. http://www.


Kim M.J.,Chonnam National University | Kang A.R.,Chonnam National University | Jeong H.C.,Insect Research Institute of Hampyeong | Kim K.-G.,National Institute of Biological Resources | Kim I.,Chonnam National University
Molecular Phylogenetics and Evolution | Year: 2011

Lepidoptera is one of the largest insect orders, but the phylogenetic relationships within this order, have yet to be adequately described. Among these unresolved relationships include those regarding the monophyly of the Macrolepidoptera and interfamilial relationships of the true butterflies superfamily Papilionoidea. We present two new mitochondrial genomes (mitogenomes) belonging to the butterfly family Lycaenidae to explore the phylogenetic relationships existing among lepidopteran superfamilies and true butterfly families from a mitogenome perspective, and to evaluate the characteristics of the lepidopteran mitogenomes. Our consensus phylogeny of the Lepidoptera largely supported the superfamilial relationships (((((Bombycoidea + Geometroidea) + Noctuoidea) + Pyraloidea) + Papilionoidea) + Tortricoidea), signifying a lack of support for a traditionally defined Macrolepidoptera. The familial relationships of the true butterflies concordantly recovered the previously proposed phylogenetic hypothesis (((Lycaenidae + Nymphalidae) + Pieridae) + Papilionidae). The test for the effect of optimization schemes (exclusion and inclusion of third codon position of PCGs and two rRNA genes, with and without partitions) on the resolution and relationships within the Lepidoptera have demonstrated that the majority of analyses did not substantially alter the relevant topology and node support, possibly as the result of relatively strong signal in mitogenomes for intraordinal relationships in Lepidoptera. © 2011 Elsevier Inc.


Mr. Yunsung Cho, lead author from Ulsan National Institute of Science and Technology, said: "Using the Amur leopard genome and comparing it to that of other mammalian genomes we found that carnivory seems to be a strong selection force for genes involved in dietary adaptation - something not as apparent in mammals that are omnivores or herbivores. For example, cows could eat meat without it having a major impact on their health, but leopards eating grass would quickly die as they have evolved to survive on meat." Specialized diets result in physiological, biochemical and morphological adaptations and carnivory is considered to be an evolutionary instable diet. Current research shows that animals in the cat family, Felidae, have relatively low genetic diversity and small population sizes. This could be due to the inflexible nature of their strict diet and explains their vulnerability and critical conservation status. Mr. Cho explained: "Carnivory related genetic adaptations such as extreme agility, muscle power and specialized diet make leopards such successful predators, but these lifestyle traits also make them genetically vulnerable." An international team of researchers sequenced the Amur leopard genome using a muscle sample of a female from Korea. They then analyzed a further 18 mammalian genomes including eight carnivores (domestic cat, tiger, cheetah, lion, leopard, polar bear, killer whale and Tasmanian devil), five omnivores (human, mouse, dog, pig, and opossum) and five herbivores (giant panda, cow, horse, rabbit, and elephant). Comparing the genomes they found that carnivores share two genes that are not present in other genomes that play an important role in bone development and repair, which could drive selection for a diet specialized towards meat. Professor Steve O'Brien, who has been researching rare endangered cat species for decades emphasizes that "Leopards are the most widespread species of the big cats, found in Africa to the Russian Far East, and thrive in a variety of environments. However, populations are fast declining, especially the Amur leopard, which is now critically endangered and perhaps the most endangered animal species on Earth." This is the first de novo genome assembly and the second leopard genome to be sequenced following the snow leopard published in 2013. The researchers hope that this Amur leopard reference genome will serve as a useful tool for understanding Felidae evolution and aid conservation. Dr. Soonok Kim, who initiated and led the project as the PI of National Institute of Biological Resources of Korea adds: "Cats are also a good model for studying health issues, such as human diabetes, and this new leopard genome reference is an environmental treasure that could help us understand these conditions further." More information: Soonok Kim et al. Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly, Genome Biology (2016). DOI: 10.1186/s13059-016-1071-4


Ahn K.-J.,Chungnam National University | Jeon M.-J.,National Institute of Biological Resources | Branham M.A.,University of Florida
Cladistics | Year: 2010

A phylogenetic analysis of the tribe Liparocephalini Fenyes is presented based on morphological and molecular characters. The data set comprised 50 adult morphological characters, partial COI (907 bp), COII (366 bp) and 12S rDNA (325-355 bp), and nearly complete sequences of 18S rDNA (1768-1902 bp) for 21 species. Eighteen species of liparocephaline beetles from all eight genera and three outgroups, are included. The sequences were analysed separately and simultaneously with morphological characters by direct optimization in the program POY4 and by partitioned Bayesian analysis for the combined data. The direct optimization (DO) tree for the combined data under equal weighting, which also shows a minimum incongruence length difference value, resulted in a monophyletic Liparocephalini with the following patterns of phylogenetic relationships (outgroup ((Baeostethus, Ianmoorea) (Paramblopusa ((Amblopusa, Halorhadinus) (Liparocephalus, Diaulota))))). A sensitivity analysis using 16 different parameter sets for the combined data shows the monophyly of the liparocephalines and all its genera under all parameter sets. Bayesian analysis resulted in topological differences in comparison with the DO tree under equal weighting only in the position of the genus Paramblopusa and clade (Amblopusa + Halorhadinus), which were reversed. Historical biogeography and the stepwise evolutionary colonization of intertidal habitat in the Liparocephalini are discussed. Based on the biogeographical analyses, we hypothesize that the ancestor of the Liparocephalini occurred along the Panthallassan Ocean, the direct antecedent of the Pacific Ocean, followed by repeated dispersals to the Nearctic from the Palearctic. We also hypothesize that ancestors of the Liparocephalini appear to have arisen in the littoral zone of beaches and then colonized rocky reef areas in the low tidal zone later through high- to mid-tide zones. © The Willi Hennig Society 2009. © The Willi Hennig Society 2009.


Park J.-G.,Daegu University | Cho J.-L.,National Institute of Biological Resources
Journal of Crustacean Biology | Year: 2013

We erect Hangangbathynella n. gen. to accomodate two new parabathynellid species, H. taechooni and H. eunokae, collected from subterranean water in South Korea. The new genus is characterized by: the 7-segmented antennules and antennae, absence of a medial seta on the second maxillary segment, a 2-segmented exopod of thoracopods I-VII, oval form of the male thoracopod VIII with penial organ displaying a smooth surface and gourd-shaped epipod, absence of pleopods, uropodal protopod with homonomous spines, pleotelson with one lateral seta near the base of the furcal rami and protruding anal operculum with sharp triangular process. The two new species differ in body size, in the number of spines of the uropodal protopod, in setae on the third maxillary segment, in the number of the spines on the mandibular spine row, as well as in the form of female thoracopod VIII. © The Crustacean Society, 2013.


Bae K.H.,National Institute of Biological Resources
Turkish Journal of Biology | Year: 2015

Bupleurum latissimum Nakai is a critically important endangered plant belonging to the family Apiaceae. Seed germination was promoted by soaking in the dormancy breaker gibberellic acid (GA3) (50% germination as compared with 4% of the control). An optimal temperature for germination of seed previously soaked in GA3 solution was determined by incubation at various temperatures. Seed germination of 31.8% was observed at 25 °C. These results indicate that the seeds of B. latissimum are difficult to germinate, even when treated with GA3. The greatest callus induction (94.8%) was observed in root explants of seedlings grown on MS medium containing a specific concentration of 2,4-dichlorophenoxyacetic acid (2,4-D) (1.0 mg L–1) and N6-benzyladenine (BA) (3.0 mg L–1). Induction of somatic embryo was observed in 78.5% of the root segment cultured on MS medium containing 3.0 mg L–1 2,4-D alone. The highest shoot induction rate was obtained in MS medium containing 30 g L–1 sucrose (number of shoots, 6.8; average length of shoot, 8.8 cm). After acclimation in artificial soil (1:1:1 mixture of peat moss, perlite, and sand) and transfer to the greenhouse, 98% of plantlets survived over 2 months. This in vitro propagation protocol will be very useful for the conservation of this critically endangered plant. © TÜBİTAK.


Moon K.H.,National Institute of Biological Resources
Journal of Japanese Botany | Year: 2011

As a result of taxonomic studies of the genus Menegazzia (Parmeliaceae, Lecanorales) in Korea, four species are recognized; M. anteforata Aptroot, M. J. Lai & Sparrius, M. nipponica K. H. Moon, Kurok. & Kashiw., M. primaria Aptroot, M. J. Lai & Sparrius and M. terebrata (Hoffm.) A. Massal. Among them M. anteforata is a new addition to the present area. Menegazzia asahinae (Yasuda ex Asahina) R. Sant. is excluded from the lichen flora of Korea.


An analytical procedure is proposed for the direct simultaneous determination in a single scan of Co, Cu, Fe, Ni and V in sediment pore waters by means of adsorptive cathodic stripping voltammetry (ACSV) with mixed ligands (DMG and catechol). Optimum conditions for the determination of these five elements were studied. Detection limits of the technique depended upon the reproducibility of the procedure blank, and were found to be 0.04 nM Co, 0.09 nM Cu, 1.29 nM Fe, 0.46 nM Ni and 2,52 nM V making the method suitable for the direct simultaneous determination of these five metals in pore waters, estuarine waters and probably coastal waters. © 2011 Elsevier B.V. All rights reserved.


News Article | November 10, 2016
Site: www.nature.com

Carnivores have experienced stronger natural selection than plant-eating animals, perhaps because of their limited diet. Joo-Hong Yeo at the National Institute of Biological Resources in the Republic of Korea and his colleagues compared the genomes of 18 mammals, including carnivores such as leopards, omnivores such as humans, and herbivores such as giant pandas. They found that carnivore genomes have lost many genes for carbohydrate digestion, and share changes to genes involved in muscle strength and agility, making them good hunters. By contrast, omnivore and herbivore genomes shared fewer adaptations with others in their groups, suggesting that their diets have imposed weaker selection compared with that of carnivores. Many big cats showed recent losses in genetic diversity, suggesting that population declines may be linked to their strict diet.

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