An Analysis of The Transaction Sector of the Philippine Economy

Nomar Jethro Y. Mata,Agham C. Cuevas 한국무역연구원 2012 The International Academy of Global Business and T Vol.8 No.1

As a follow-up to the pioneering work of Wallis and North (1986), this study attempts to measure the level of transaction sector output in the Philippine economy by dividing the industries between transaction industries and transformation industries. The transaction sector output, the sum of the outputs of the transaction industries, was computed by using the national income accounts. This paper also measures the changes in the relative sizes of the transformation and transaction sector output by using the theoretical concept constructed by Datta et al. (2004) called the support ratio. The support ratio shows how much of the transformation sector output is supported by one peso spent in the transaction sector. The results show that the transaction sector has been increasing over time but the support ratio has been generally declining. The possible reasons for the increase of transaction sector output are increases in specialization brought by market expansion, development in technology, and government privatization and deregulation policies. Other reasons for the declining support ratio, such as shifts of non-market goods in the market, negative role of institutions, changes in the consumers’ preferences, and market imperfections, are all highly possible in the Philippine context.

Karyotypic Analyses of Six Horticultural Species by DAPI Staining and Fluorescence in Situ Hybridization Methods

Nomar Espinosa Waminal,Shin Jae Kang,Jee Hee Lee,Seong Han Sohn,Do Sun Kim,Jang-Ho Hahn,Dong Hern Kim,Yoon Jung Hwang,Hyun Hee Kim 한국원예학회 2014 한국원예학회 학술발표요지 Vol.2014 No.10

FISH Karyotype Analyses of Four Cucurbitaceae Species Using 5S and 45S rDNA Probes

Nomar Espinosa Waminal,Bo Reum Park,Hadassah Roa Belandres,Yoon Jung Hwang,Hyun Hee Kim 한국원예학회 2014 한국원예학회 학술발표요지 Vol.2014 No.10

FISH Karyotype Analysis of Four Wild Cucurbitaceae Species Using 5S and 45S rDNA Probes and the Emergence of New Polyploids in Trichosanthes kirilowii Maxim.

Nomar Espinosa Waminal,Hyun Hee Kim 한국원예학회 2015 원예과학기술지 Vol.33 No.6

Wild relative species of domesticated crops are useful genetic resources for improving agronomic traits. Cytogenetic investigations based on chromosome composition provide insight into basic genetic and genomic characteristics of a species that can be exploited in a breeding program. Here, we used FISH analysis to characterize the ploidy level, chromosome constitution, and genomic distribution o f 5S and 4 5S r ibosomal DNA ( rDNA) in f our wild C ucurbitaceae s pecies, namely, Citrullus lanatus (Thunb.) Mansf. var. citroides L. H. Bailey (2n = 22), Melothria japonica Maxim. (2n = 22), Sicyos angulatus L. (2n = 24), and Trichosanthes kirilowii Maxim. (2n = 66, 88, 110 cytotypes), collected in different areas of Korea. All species were diploids, except for T. kirilowii, which included hexa-, octa-, and decaploid cytotypes (2n = 6x = 66, 8x = 88, and 10x = 110). All species have small metaphase chromosomes in the range of 2–5 μm. The 45S rDNA signals were localized distally compared to the 5S rDNA. C. lanatus var. citroides and M. japonica showed one and two loci of 45S and 5S rDNA, respectively, with co-localization of rDNA signals in one M. japonica chromosome. S. angulatus showed two co-localized signals of 5S and 45S rDNA loci. The hexaploid T. kirilowii cytotype showed five signals each for 45S and 5S rDNA, with three being co-localized. This is the first report of hexaploid and decaploid cytotypes in T. kirilowii. These results will be useful in future Cucurbitaceae breeding programs.

Repeat Evolution in Brassica rapa (AA), B. oleracea (CC), and B. napus (AACC) Genomes

( Nomar Espinosa Waminal ),( Sampath Perumal ),( Jonghoon Lee ),( Hyun Hee Kim ),( Tae Jin Yang ) 한국육종학회 2016 Plant Breeding and Biotechnology Vol.4 No.2

The genus Brassica is an important resource for major agricultural products such as oils, vegetable and fodder. The Brassiceae tribe-specific whole-genome triplication that occurred ~15.9 million years ago influenced the speciation and morphological diversification that has been exploited in agriculture, making Brassica an excellent model system for studying polyploidization- mediated evolution. Genome sequencing and comparative genome analysis have revealed conserved structures and uncovered the genome evolution of Brassica species. While chromosome shuffling and asymmetric subgenome gene retention are widely reported in Brassica species, limited information is available about the dynamics of repetitive elements (REs), which are central to epigenetic mechanisms and thus play a pivotal role in plant genome adaptation and evolution. The assembled reference genome sequences of B. rapa (AA) and B. oleracea (CC), and their derived allotetraploid, B. napus (AACC), cover 58%, 86%, and 75% of their respective estimated genome sizes. The remaining non-assembled genome portions vary between these three genome sequences, and the major components remain hidden in each genome. Here, we review the dynamics of the major Brassica repeats that have played roles in speciation of the AA, CC, and AACC genomes. We show that 10 major Brassica repeats appear to occupy more than 50% of each respective unassembled genome sequence, yet represent less than 1% of assembled reference genome sequences. We have estimated their genome proportions using whole-genome Illumina reads and cytogenetic analyses in an attempt to understand the role of these repeats in genome evolution.

Dual‐color FISH karyotype analyses using rDNAs in three Cucurbitaceae species

Nomar Espinosa Waminal,김남수,김현희 한국유전학회 2011 Genes & Genomics Vol.33 No.5

Dual-color fluorescence in situ hybridization (FISH) analysis of three Cucurbitaceae species from different genera was conducted using 5S and 45S rDNA probes. In Benincasa hispida (Thunb.) Cogn. (2n=24), the 45S rDNA probe hybridized on two chromosomes, one in the short arm of a medium-sized metacentric chromosome and another at the satellite of a chromosome. The 5S rDNA hybridized at a site proximal to the centromere of the same short arm of the 45S rRNA gene locus that occupied almost the entire short arm. For Citrullus lanatus (Thunb.) Matsum & Nakai (2n=22), the 45S rDNA probe hybridized at sites in the short arms of two chromosomes and the 5S rDNA probe was co-localized with the 45S rRNA locus at the region proximal to the centromere in one chromosome. The 45S rRNA loci occupied almost all of the short arms in both chromosomes. In Cucurbita moschata Duch. (2n=40), the 45S rDNA probe hybridized in five chromosomes in which the 45S rRNA genes occupied almost two-thirds of the chromosomes in two large chromosomes and the entire short arm of a medium-sized chromosome. Two other loci were present in two medium-sized chromosomes, one in the proximal region in the short arm of a chromosome and another at the tip of the long arm of a chromosome. Chromosomes of B. hispida were relatively larger than those of the other two species. The karyotype of B. hispida is composed of two metacentrics and 10 submetacentrics, while that of C. lanatus is composed of seven metacentrics and four submetacentrics and that of C. moschata is composed of 18 metacentrics and two submetacentrics. Comparative chromosome evolution among the three Cucurbitaceae species was attempted using the karyotypes and the chromosomal distribution patterns of the 5S and 45S rDNAs. The results presented herein will be useful in elucidating the phylogenetic relationships among Cucurbitaceae species, and will provide basic data for their breeding programs.

Dual-color FISH Karyotype and rDNA Distribution Analyses on Four Cucurbitaceae Species

Nomar Espinosa Waminal,김현희 한국원예학회 2012 Horticulture, Environment, and Biotechnology Vol.53 No.1

Karyotype and ribosomal DNA distribution on four Cucurbitaceae species was analyzed through dual-color fluorescence in situ hybridization (FISH) using 5S and 45S rDNA probes. Chromosome sizes varied slightly among the species with Cucumis sativus relatively the largest (~2.5 μm) and Momordica charantia the smallest (~1 μm). In Cucumis sativus L. (2n = 14), the 45S rDNA hybridized on the pericentromeric area of five chromosomes (metacentric a, b, c, g, and submetacentric d) and the 5S rDNA on the region proximal to the centromere of the short arm of chromosome e. In Luffa cylindrica (L.) Roem. (2n = 26), the 45S rDNA hybridized on the distal regions of the short arms of five chromosomes (metacentric a, b, c, f, and submetacentric d) and the 5S rDNA on the region proximal to the centromere of the short arm of chromosome e. In Lagenaria siceraria (Molina) Standl. (2n = 22), the 45S rDNA hybridized on the distal regions of the short arms of two chromosomes (submetacentric b and metacentric e)and the 5S rDNA juxtaposed with the 45S rDNA signal in a region proximal to the centromere on chromosome e. In Momordica charantia L. (2n = 22), the 45S rDNA hybridized on the majority of the short arms of two metacentric chromosomes (d and k) and the 5S rDNA on the proximal region of the short arm of chromosome e. The interphase and metaphase rDNA distribution and FISH karyotype analyses of the four species showed the possible fate of rDNAs through the process that lead to the interspecific variations among the cucurbits. These results will be useful in elucidating the phylogenetic relationships among Cucurbitaceae species.

Characterization of Chromosome-Specific Microsatellite Repeats and Telomere Repeats Based on Low Coverage Whole Genome Sequence Reads in Panax ginseng

( Nomar Espinosa Waminal ),( Remnyl Joyce Pellerin ),( Woojong Jang ),( Hyun Hee Kim ),( Tae-jin Yang ) 한국육종학회 2018 Plant Breeding and Biotechnology Vol.6 No.1

Repetitive DNA elements are ubiquitous in plant genomes. Although repeats provide relevant information for cytogenetic, evolutionary, and genomic studies, identifying and characterizing their sequence and chromosomal distribution are not always easily achieved through conventional methods. However, a high-throughput identification of genomic repeats can be obtained with short reads from next-generation sequencing data. Here, we identified the telomeric and two chromosome-specific repeats in Panax ginseng using low-coverage whole genome sequence data. The telomeric repeat sequence is same with the canonical angiosperm sequence, (TTTAGGG)n, and localized mostly in every chromosome termini, except for an additional interstitial location in chromosome 10. A dinucleotide (GA) microsatellite, PgGA15, with total genome representation (GR) of more than 33 kb localized in the long arm of chromosome 20. An 11-bp minisatellite, Pgms1, with more than 58 kb of GR localized in the long arm of chromosome 1. This study provides chromosome-specific markers for cytogenetic studies in P. ginseng.

Cytogenetic mapping of Panax ginseng major DNA repeats: Evidence for allotetraploidy and utility for chromosome identification

Nomar Espinosa Waminal,Hong-Il Choi,Hyun Hee Kim,Tae-Jin Yang 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07

There is a growing number of plant genomes that are being sequenced, but most of these available assemblies do not cover the entire genome mainly due to the highly repetitive sequences found in most plant genomes. Nevertheless, these repeats, although a challenge in assembly algorithms, provide relevant information about a genome’s history that could help explain its structure and complexity. Here, we cytogenetically mapped previously and presently characterized major repeats of Panax ginseng genome, including several LTR retrotransposons (PgDel2, PgDel3, PgTat1, PgTat2, PgTork) and one tandem repeat, PgTR Fluorescence in situ hybridization (FISH) results showed differential accumulation of Ty3/gypsy LTR retrotransposons into different chromosomal regions or subgenomes, suggesting a non-random preferential amplification of retrotransposons in these regions and an allopolyploid origin of P. ginseng. In silico analysis based on 1x whole genome sequence reads suggests that PgTR is the most abundant tandem repeat in ginseng, which was further corroborated by FISH analysis. More importantly, its unique distribution pattern among the 24 ginseng chromosomes, coupled with the non-random distribution of LTR retrotransposons and rDNA arrays, allowed us to discriminate and characterize each individual ginseng chromosome. These different newly characterized cytogenetic markers allowed reorganization of previously reported ginseng karyotype with better resolution, demonstrating the irutility in ginseng chromosome identification. These information give us insight about the genomic structure of P. ginseng, and should be useful for future comparative cytogenetics studies among closely related species to unravel its genomic history. This work was supported by the Next-Generation BioGreen21 Program (No. PJ008202), Rural Development Administration, Republic of Korea.

Five-color fl uorescence in situ hybridization system for karyotyping of Panax ginseng

Nomar Espinosa Waminal,Tae-Jin Yang,인준교,HyunHeeKim 한국원예학회 2020 Horticulture, Environment, and Biotechnology Vol.61 No.5

Chromosomal mapping of repetitive elements is invaluable in understanding genome structure and evolution. Repetitive elementsconstitute ~ 80% of the allotetraploid ginseng ( Panax ginseng ) genome. Preparing sporophytic metaphase chromosomesof ginseng is laborious; therefore, it would be advantageous to maximize the information obtained from a single slide. Here,we investigated the suitability of simultaneous fi ve-color fl uorescence in situ hybridization using major ginseng repeats,namely PgDel1 , PgDel2 , PgTel, and Pg167TR. For Pg167TR, we generated two degenerate probe libraries (Pg167TRa andPg167TRb) based on the chromosomal target coverage. We labeled the probes with dark-red, blue, red, orange, and greenfl uorochromes and used excitation/emission fi lter sets specifi c to each fl uorochrome to detect fl uorescence in situ hybridizationsignals. PgDel1 was distributed across all 24 chromosome pairs, except for the secondary constriction region of chromosome16, whereas PgDel2 was distributed over 12 of the 24 pairs. PgTel was localized in the termini of chromosomesand in an intercalary region in chromosome 13. Pg167TRa and Pg167TRb were distributed among 22 chromosome pairswith loci polymorphisms. These results showed the utility of fi ve-color fl uorescence in situ hybridization for chromosomalmapping of fi ve repeats to expedite karyotyping and facilitate genome evolution studies in ginseng and other plant species.