Karyotypes of Three Exotic Cucurbit Species Based on Triple-Color FISH Analysis

Remnyl Joyce Pellerin,Nomar Espinosa Waminal,Hadassah Roa Belandres,Hyun Hee Kim 한국원예학회 2018 원예과학기술지 Vol.36 No.3

Cytogenetic investigations based on chromosome composition provide insight into basic genetic and genomic characteristics of a species that in turn facilitate species identification and breeding programs. Tandem repeats (TRs) like the 45S rDNA, 5S rDNA and telomeric repeats are ubiquitous in nuclear genomes and are good cytogenetic markers for karyotyping. In this study, we analyzed the karyotypes of three exotic cucurbit species, namely Cucumis melo var. flexuosus (L.) Naudin (2n = 24), Melothria pendula L. (2n = 24) and Trichosanthes anguina L. (2n = 22), based on the cytogenetic distribution of the 45S, 5S and Arabidopsis-type telomeric TRs through triple-color fluorescence in situ hybridization. T. anguina had larger chromosomes (3.2-5.4 μm) compared to C. melo var. flexuosus and M. pendula (1.5-2.2 μm and 1.8-2.5 μm). One and two pairs of 5S and 45S rDNA signals were observed in C. melo var. flexuosus, respectively; while M. pendula and T. anguina had four and three pairs of 45S rDNA, respectively, and two pairs of 5S rDNA. Co-localized signals of 5S and 45S rDNA were observed in M. pendula and T. anguina, but not in C. melo var. flexuosus. Telomeric repeats were observed at chromosome ends of all chromosomes. This information will be useful in future cytogenomic and phylogenetic studies facilitating cucurbit breeding programs.

Triple-color FISH Karyotype Analysis of Four Korean Wild Cucurbitaceae Species

Remnyl Joyce Pellerin,Nomar Espinosa Waminal,Hyun Hee Kim 한국원예학회 2018 원예과학기술지 Vol.36 No.1

Cytogenetic mapping of DNA markers provides insights into a species’ basic genomic structure and facilitates the deduction of phylogenetic relationships between related species. The family Cucurbitaceae has numerous economically and medicinally important crop species. In addition, wild Cucurbitaceae species can provide important genetic resources for crop improvement. However, cytogenetic information for many species is still insufficient. Here, triple-color fluorescence in situ hybridization (FISH) was performed on four Korean wild Cucurbitaceae species of Actinostemma tenerum Grift, Thladiantha dubia Bunge, Sechium edule (Jacq.) Swartz, and Gynostemma pentaphyllum (Thunb.) Makino using 5S rDNA, 45S rDNA, and telomeric-repeat probes. The chromosome numbers of the four species were 2n = 2x = 16, 18, 28, and 2n = 6x = 66, respectively. The four species have relatively small chromosomes, ranging from 2.16 to 5.38 ㎛. One 5S and three 45S rDNA signals were observed in T. dubia, with one colocalization on a satellite chromosome (1:3:1), while signal patterns were 1:1:0, 1:3:0, and 4:5:0 for A. tenerum, S. edule, and G. pentaphyllum, respectively. Compared with that of 5S rDNA, 45S rDNA localization was more distal, except on chromosome 8 of A. tenerum and chromosomes 2 and 3 of S. edule. The species exhibited telomeric signals on the chromosomal terminal region, while additional signals hybridized on the pericentromeric region in A. tenerum chromosomes 1, 2, 4, and 5. These results will contribute to elucidating phylogenetic relationships among Cucurbitaceae species and improve on-going Cucurbitaceae breeding programs.

FISH mapping of rDNA and telomeric repeats in 10 Senna species

Remnyl Joyce Pellerin,Nomar Espinosa Waminal,김현희 한국원예학회 2019 Horticulture, Environment, and Biotechnology Vol.60 No.2

Plants of the genus Senna (Fabaceae) are valued for industrial and medicinal properties that have spurred crop improvementthrough breeding programs. However, there is very little chromosomal data for this genus, limiting the potential for cytogeneticsand genomics research. Here, we used fl uorescence in situ hybridization (FISH) to perform a comparative analysis of10 Senna spp. karyotypes (2n = 28 except S. tora with 2n = 26). We detected diff erences in the distributions of rDNA geneclusters and Arabidopsis -type telomeric repeats (TTT AGG G) n . Only one 5S rDNA pair was detected in all species, but weobserved more interspecies variation for 45S rDNA: four pairs in S. didymobotrya, S. spectabilis, and S. viarum ; two pairsin S. candolleana ; and one pair in S. bauhinioides, S. multiglandulosa, S. occidentalis , and S. tora . In both S. leandrii andS. sulfurea , 45S rDNA distribution was hemizygous. While all chromosomes possessed telomeric signals in the terminalregion, this signal was also present in the interstitial regions of all S. tora chromosomes and, less obviously (fewer chromosomes,weaker signals), in S. occidentalis . These preliminary data demonstrate interspecifi c karyotype variation that revealsSenna genome dynamics. Our results facilitate cytogenetic mapping of other major repeats, thus contributing to an improvedunderstanding of Senna genome structure and evolutionary history.

Fluorescence in situ Hybridization Karyotype Analysis of Seven Platycodon grandiflorum (Jacq.) A. DC. Cultivars

Remnyl Joyce Pellerin,Nomar Espinosa Waminal,Ji Young Kim,Yurry Um,Hyun Hee Kim 한국원예학회 2017 원예과학기술지 Vol.35 No.6

Platycodon grandiflorum has long been cultivated for its medicinal properties and economic value, prompting crop improvement programs that have spurred the development of new cultivars. However, limited cytogenetic information is available for this species, especially for different P. grandiflorum cultivars. Karyotype analysis via fluorescence in situ hybridization (FISH) provides essential information about chromosome count and the localization of DNA sequences, thus providing a chromosome-level understanding of genome structure. Here, we carried out triple-color FISH karyotype analysis of various P. grandiflorum (Jacq.) A. DC. cultivars using 5S and 45S ribosomal DNA (rDNA) and telomeric repeat probes. The karyotype is composed of 2n = 18 chromosomes consisting of seven pairs of metacentric chromosomes, one pair of submetacentric chromosomes, and one pair of subtelocentric chromosomes. The chromosome length ranges from 1.92 to 4.98 μm. One pair of 5S rDNA loci was observed on either the intercalary or pericentromeric regions of chromosome 3. All cultivars showed 45S rDNA signals on chromosome 9, and in two closely related cultivars, one additional pair of 5S rDNAs co-localized with these 45S rDNAs. Arabidopsis -type telomeric repeats were observed in most telomeric regions of the chromosomes in all seven cultivars. Our data lay the foundation for future cytogenetic studies of P. grandiflorum focusing on breeding and the elucidation of its genome structure.

Pre-labelled oligo probe-FISH karyotype analyses of four Araliaceae species using rDNA and telomeric repeat

Hui Chao Zhou,Remnyl Joyce Pellerin,Nomar Espinosa Waminal,양태진,김현희 한국유전학회 2019 Genes & Genomics Vol.41 No.7

Background The family Araliaceae contains many medicinal species including ginseng of which the whole genome sequencing analyses have been going on these days. Objective To characterize the chromosomal distribution of 5S and 45S rDNAs and telomeric repeat in four ginseng related species of Aralia elata (Miq.) Seem., Dendropanax morbiferus H. Lév., Eleutherococcus sessiliflorus (Rupr. Et Maxim.) Seem., Kalopanax septemlobus (Thunb. ex A.Murr.) Koidz. Method Pre-labelled oligoprobe (PLOP)-fluorescence in situ hybridization (FISH) was carried out. Results The chromosome number of A. elata was 2n = 24, whereas that of the other three species of D. morbiferus, E. sessiliflorus, and K. septemlobus was 2n = 48, corresponding to diploid and tetraploid, respectively, based on the basic chromosome number x = 12 in Araliaceae. In all four species, one pair of 5S signals were detected in the proximal regions of the short arms of chromosome 3, whereas in K. septemlobus, the 5S rDNA signals localized in the subtelomeric region of short arm of chromosome 3, while all the 45S rDNA signals localized at the paracentromeric region of the short arm of chromosome 1. And the telomeric repeat signals were detected at the telomeric region of both short and long arms of most chromosomes. Conclusion The PLOP-FISH was very effective compared with conventional FISH method. These results provide useful comparative cytogenetic information to better understand the genome structure of each species and will be useful to trace the history of ginseng genomic constitution.

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.

Amniotic constriction band: a report of two cases with unique clinical presentations

Sunil Richardson,Rakshit Vijay Khandeparker,Philippe Pellerin 대한구강악안면외과학회 2017 대한구강악안면외과학회지 Vol.43 No.3

Amniotic constriction band is a rare clinical entity with varied manifestations that range from a combination of congenital malformations to isolated malformations that are unique to each patient. The etiology of this entity remains unknown. Herein, we highlight two cases of amniotic constriction band that presented to our unit with unique clinical characteristics. To the best of our knowledge, an isolated circumferential band of scarring on the face with ocular involvement, as demonstrated by the first case, and a combination of bilateral complete cleft lip and palate with bilateral microphthalmia, auto-amputation of the right thumb, and a constriction band on the left thumb, as demonstrated by the second case, are extremely rare presentations of amniotic constriction band that were not previously reported in the literature and therefore necessitate a special mention. We discuss potential etiologies for these cases and review the existing literature on this entity.

Conservation of Biodiversity and Its Ecological Importance of Korean Paddy Field

조영손,이동규,Zhin-Ryong Choe,Min-Soo Han,Kristie Pellerin 한국작물학회 2006 Korean journal of crop science Vol.51 No.7

Biodiversity is closely related to the conservation of ecosystems. Ecosystems provide more subtle, but equally essential, services. Microorganisms decompose human’s waste and renew the soils that produce our food crops. Biodiversity in Korean paddies encompass 54 families and 107 species of freshwater invertebrates. In terms of the number of aquatic insects affected by different sources, the order starting with the highest population was swine slurry > chemical fertilizer > fresh straw with reduced fertilizers > control. The number of freshwater invertebrate and aquatic macro- invertebrate in surface water of the plots without insecticidal application were 2 and 2.1 times greater than in fields receiving insecticide applications, respectively. The soil microfungal flora of the 85 isolates paddy fields in Korea was 30 species in 13 genera and 11 isolates were unidentified yet. Agricultural policy should be changed to assist the conservation of bio-diversity because until now the agricultural ecosystems have been negatively affected from the development of high-yield varieties to enhance food production, and the expansion of fertilizer and chemical use. For the conservation of agricultural ecosystems, agricultural practices with less investment and more resource saving, as well as enhancing the safety of agricultural and livestock products are essential. Finally, this paper was written for the contribution for the development of environmentally friendly farming systems with neighboring or whole ecosystems. Biodiversity is closely related to the conservation of ecosystems. Ecosystems provide more subtle, but equally essential, services. Microorganisms decompose human’s waste and renew the soils that produce our food crops. Biodiversity in Korean paddies encompass 54 families and 107 species of freshwater invertebrates. In terms of the number of aquatic insects affected by different sources, the order starting with the highest population was swine slurry > chemical fertilizer > fresh straw with reduced fertilizers > control. The number of freshwater invertebrate and aquatic macro- invertebrate in surface water of the plots without insecticidal application were 2 and 2.1 times greater than in fields receiving insecticide applications, respectively. The soil microfungal flora of the 85 isolates paddy fields in Korea was 30 species in 13 genera and 11 isolates were unidentified yet. Agricultural policy should be changed to assist the conservation of bio-diversity because until now the agricultural ecosystems have been negatively affected from the development of high-yield varieties to enhance food production, and the expansion of fertilizer and chemical use. For the conservation of agricultural ecosystems, agricultural practices with less investment and more resource saving, as well as enhancing the safety of agricultural and livestock products are essential. Finally, this paper was written for the contribution for the development of environmentally friendly farming systems with neighboring or whole ecosystems.

Conservation of Biodiversity and Its Ecological Importance of Korean Paddy Field

Cho, Young-Son,Lee, Dong-Kyu,Choe, Zhin-Ryong,Han, Min-Soo,Pellerin, Kristie The Korean Society of Crop Science 2006 Korean journal of crop science Vol.51 No.6

Biodiversity is closely related to the conservation of ecosystems. Ecosystems provide more subtle, but equally essential, services. Microorganisms decompose human's waste and renew the soils that produce our food crops. Biodiversity in Korean paddies encompass 54 families and 107 species of freshwater invertebrates. In terms of the number of aquatic insects affected by different sources, the order starting with the highest population was swine slurry > chemical fertilizer > fresh straw with reduced fertilizers > control. The number of freshwater invertebrate and aquatic macro-invertebrate in surface water of the plots without insecticidal application were 2 and 2.1 times greater than in fields receiving insecticide applications, respectively. The soil microfungal flora of the 85 isolates paddy fields in Korea was 30 species in 13 genera and 11 isolates were unidentified yet. Agricultural policy should be changed to assist the conservation of biodiversity because until now the agricultural ecosystems have been negatively affected from the development of high-yield varieties to enhance food production, and the expansion of fertilizer and chemical use. For the conservation of agricultural ecosystems, agricultural practices with less investment and more resource saving, as well as enhancing the safety of agricultural and livestock products are essential. Finally, this paper was written for the contribution for the development of environmentally friendly farming systems with neighboring or whole ecosystems.

Comparative triple-color FISH mapping in eleven Senna species using rDNA and telomeric repeat probes

Thi Hong Nguyen,Nomar Espinosa Waminal,이도신,Remnyl Joyce Pellerin,Thanh Dat Ta,Nicole Bon Campomayor,Byung Yong Kang,김현희 한국원예학회 2021 Horticulture, Environment, and Biotechnology Vol.62 No.6

Senna is a diverse and paraphyletic genus in the subfamily Caesalpinioideae (Fabaceae Lindl.) comprising various speciesof industrial and medicinal value. To date, the genome-based taxonomic relationship among several Senna species remainsenigmatic. Cytogenetic information is invaluable in deciphering phylogenetic relationships and evolutionary history. However,insuffi cient chromosomal research for many Senna species impedes comparative cytotaxonomic analyses aimed at understandingtheir genomic evolution. To provide additional Senna -related molecular cytogenetic information, we karyotyped11 Senna species by employing triple-color fl uorescence in situ hybridization using 5S rDNA, 45S rDNA, and Arabidopsisthaliana -type telomeric pre-labeled oligonucleotide probes. Chromosome numbers were predominantly 2 n = 28, but 2 n = 22( S. marilandica ) and 2 n = 24 ( S. unifl ora ) were also observed. While most species revealed only one interstitial 5S rDNAlocus, except for S. unifl ora which has two loci, a range of one to three 45S rDNA loci were detected at distal chromosomalregions. Additionally, we observed a hemizygous 45S rDNA locus in S. auriculata . In addition to chromosome termini,weak signals for telomeric repeats were found in interstitial regions in S. hirsuta, S. corymbosa , and S. alexandrina . Thesecytogenetic data can be integrated with molecular phylogenetic data for more comprehensive Senna cytotaxonomic analyses.