1
|
Thongnetr W, Aiumsumang S, Kongkaew R, Tanomtong A, Suwannapoom C, Phimphan S. Cytogenetic characterisation and chromosomal mapping of microsatellite and telomeric repeats in two gecko species (Reptilia, Gekkonidae) from Thailand. COMPARATIVE CYTOGENETICS 2021; 15:41-52. [PMID: 33603980 PMCID: PMC7873012 DOI: 10.3897/compcytogen.v15i1.58208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Studies of chromosomes of Cyrtodactylus jarujini Ulber, 1993 and C. doisuthep Kunya et al., 2014 to compare microsatellite and TTAGGG sequences by classical and molecular techniques were conducted in Thailand. Karyological typing from a conventional staining technique of C. jarujini and C. doisuthep showed diploid chromosome numbers of 40 and 34 while the Fundamental Numbers (NF) were 56 in both species. In addition, we created the chromosome formula of the chromosomes of C. jarujini showing that 2n (40) = Lsm 1 + Lsm 2 + Lt 3 + Mm 1 + Mt 4 + Sm 2 + Sa 2 + St 5 while that of C. doisuthep was 2n (34) = Lsm 3 + Lm 2 + Lt 3 + Mm 1 + Mt 2 + Sm 4 + Sa 1 + St 1. Ag-NOR staining revealed NOR-bearing chromosomes in chromosome pairs 13 and 14 in C. jarujini, and in chromosome pairs 9 and 13 in C. doisuthep. This molecular study used the FISH technique, as well as microsatellite probes including (A)20, (TA)15, (CGG)10, (CGG)10, (GAA)10, (TA)15 and TTAGGG repeats. The signals showed that the different patterns in each chromosome of the Gekkonids depended on probe types. TTAGGG repeats showed high distribution on centromere and telomere regions, while (A)20, (TA)15, (CGG)10, (CGG)10, (GAA)10 and (TA)15 bearing dispersed over the whole genomes including chromosomes and some had strong signals on only a pair of homologous chromosomes. These results suggest that the genetic linkages have been highly differentiated between the two species.
Collapse
Affiliation(s)
- Weera Thongnetr
- Walai Rukhavej Botanical Research institute, Mahasarakham University, Kantharawichai, Maha Sarakham, ThailandMahasarakham UniversityMaha SarakhamThailand
| | - Surachest Aiumsumang
- Biology program, Faculty of Science and Technology, Phetchabun Rajabhat University, Phetchabun, 67000, ThailandPhetchabun Rajabhat UniversityPhetchabunThailand
| | - Rodjarin Kongkaew
- Program of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen, 40002, ThailandKhon Kaen UniversityKhon KaenThailand
| | - Alongklod Tanomtong
- Program of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen, 40002, ThailandKhon Kaen UniversityKhon KaenThailand
| | - Chatmongkon Suwannapoom
- Department of Fishery, School of Agriculture and Natural Resources, University of Phayao, Muang, Phayao, 56000, ThailandUniversity of PhayaoPhayaoThailand
| | - Sumalee Phimphan
- Biology program, Faculty of Science and Technology, Phetchabun Rajabhat University, Phetchabun, 67000, ThailandPhetchabun Rajabhat UniversityPhetchabunThailand
| |
Collapse
|
2
|
Koomgun T, Laopichienpong N, Singchat W, Panthum T, Phatcharakullawarawat R, Kraichak E, Sillapaprayoon S, Ahmad SF, Muangmai N, Peyachoknagul S, Duengkae P, Ezaz T, Srikulnath K. Genome Complexity Reduction High-Throughput Genome Sequencing of Green Iguana ( Iguana iguana) Reveal a Paradigm Shift in Understanding Sex-Chromosomal Linkages on Homomorphic X and Y Sex Chromosomes. Front Genet 2020; 11:556267. [PMID: 33193634 PMCID: PMC7606854 DOI: 10.3389/fgene.2020.556267] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/24/2020] [Indexed: 12/27/2022] Open
Abstract
The majority of lizards classified in the superfamily Iguanoidea have an XX/XY sex-determination system in which sex-chromosomal linkage shows homology with chicken (Gallus gallus) chromosome 15 (GGA15). However, the genomics of sex chromosomes remain largely unexplored owing to the presence of homomorphic sex chromosomes in majority of the species. Recent advances in high-throughput genome complexity reduction sequencing provide an effective approach to the identification of sex-specific loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA), and a better understanding of sex chromosome dynamics in Iguanoidea. In this study, we applied Diversity Arrays Technology (DArTseqTM) in 29 phenotypic sex assignments (14 males and 15 females) of green iguana (Iguana iguana). We confirmed a male heterogametic (XX/XY) sex determination mode in this species, identifying 29 perfectly sex-linked SNP/PA loci and 164 moderately sex-linked SNP/PA loci, providing evidence probably indicative of XY recombination. Three loci from among the perfectly sex-linked SNP/PA loci showed partial homology with several amniote sex chromosomal linkages. The results support the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex-chromosomal linkages. However, only one locus among the moderately sex-linked loci showed homology with GGA15, which suggests that the specific region homologous to GGA15 was located outside the non-recombination region but in close proximity to this region of the sex chromosome in green iguana. Therefore, the location of GGA15 might be further from the putative sex-determination locus in green iguana. This is a paradigm shift in understanding linkages on homomorphic X and Y sex chromosomes. The DArTseq platform provides an easy-to-use strategy for future research on the evolution of sex chromosomes in Iguanoidea, particularly for non-model species with homomorphic or highly cryptic sex chromosomes.
Collapse
Affiliation(s)
- Tassika Koomgun
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Nararat Laopichienpong
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | | | | | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand.,Center for Advanced Studies in Tropical Natural Resources, National Research University, Kasetsart University, Bangkok, Thailand.,Center of Excellence on Agricultural Biotechnology, Bangkok, Thailand.,Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University, Bangkok, Thailand
| |
Collapse
|
3
|
Jean A, Tardy F, Allatif O, Grosjean I, Blanquier B, Gerlier D. Assessing mycoplasma contamination of cell cultures by qPCR using a set of universal primer pairs targeting a 1.5 kb fragment of 16S rRNA genes. PLoS One 2017; 12:e0172358. [PMID: 28225826 PMCID: PMC5321415 DOI: 10.1371/journal.pone.0172358] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 02/04/2017] [Indexed: 11/24/2022] Open
Abstract
Mycoplasmas (a generic name for Mollicutes) are a predominant bacterial contaminant of cell culture and cell derived products including viruses. This prokaryote class is characterized by very small size and lack of a cell wall. Consequently, mycoplasmas escape ultrafiltration and visualization under routine microscopic examination, hence the ease with which cells in culture can be contaminated, with routinely more than 10% of cell lines being contaminated. Mycoplasma are a formidable threat both in fundamental research by perverting a whole range of cell properties and functions and in the pharmacological use of cells and cell derived products. Although many methods have been developed, there is still a need for a sensitive, universal assay. Here is reported the development and validation of a quantitative polymerase chain reaction (qPCR) based on the amplification of a 1.5 kb fragment covering the 16S rDNA of the Mollicute class by real-time PCR using universal U1 and U8 degenerate primers. The method includes the addition of a DNA loading probe to each sample to monitor DNA extraction and the absence of PCR inhibitors in the extracted DNA, a positive mycoplasma 16S rDNA traceable reference sample to exclude any accidental contamination of an unknown sample with this reference DNA, an analysis procedure based on the examination of the melting curve and the size of the PCR amplicon, followed by quantification of the number of 16S rDNA copies (with a lower limit of 19 copies) when relevant, and, if useful, the identification of the contaminating prokaryote by sequencing. The method was validated on a collection of mycoplasma strains and by testing over 100 samples of unknown contamination status including stocks of viruses requiring biosafety level 2, 3 or 4 containments. When compared to four established methods, the m16S_qPCR technique exhibits the highest sensitivity in detecting mycoplasma contamination.
Collapse
Affiliation(s)
- Audrey Jean
- Univ Lyon, SFR BioSciences, ENS de Lyon, Inserm US8, CNRS UMS344, UCBL, Lyon, France
| | - Florence Tardy
- ANSES, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, VetAgro Sup, Univ Lyon, UMR Mycoplasmoses des Ruminants, Marcy l'Etoile, France
| | - Omran Allatif
- CIRI, International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Isabelle Grosjean
- Univ Lyon, SFR BioSciences, ENS de Lyon, Inserm US8, CNRS UMS344, UCBL, Lyon, France
| | - Bariza Blanquier
- Univ Lyon, SFR BioSciences, ENS de Lyon, Inserm US8, CNRS UMS344, UCBL, Lyon, France
| | - Denis Gerlier
- Univ Lyon, SFR BioSciences, ENS de Lyon, Inserm US8, CNRS UMS344, UCBL, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| |
Collapse
|
4
|
Qin XM, Li HM, Zeng ZH, Zeng DL, Guan QX. Genetic variation and differentiation of Gekko gecko from different populations based on mitochondrial cytochrome b gene sequences and karyotypes. Zoolog Sci 2012; 29:384-9. [PMID: 22639809 DOI: 10.2108/zsj.29.384] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Black-spotted and red-spotted tokay geckos are distributed in different regions and have significant differences in morphological appearance, but have been regarded as the same species, Gekko gecko, in taxonomy. To determine whether black-spotted and red-spotted tokay geckos are genetically differentiated, we sequenced the entire mitochondrial cytochrome b gene (1147 bp) from 110 individuals of Gekko gecko collected in 11 areas including Guangxi China, Yunnan China, Vietnam, and Laos. In addition, we performed karyotypic analyses of black-spotted tokay geckos from Guangxi China and red-spotted tokay geckos from Laos. These phylogenetic analyses showed that black-spotted and red-spotted tokay geckos are divided into two branches in molecular phylogenetic trees. The average genetic distances are as follows: 0.12-0.47% among six haplotypes in the black-spotted tokay gecko group, 0.12-1.66% among five haplotypes in the red-spotted tokay gecko group, and 8.76-9.18% between the black-spotted and red-spotted tokay geckos, respectively. The karyotypic analyses showed that the karyotype formula is 2n = 38 = 8m + 2sm + 2st + 26t in red-spotted tokay geckos from Laos compared with 2n = 38 = 8m + 2sm + 28t in black-spotted tokay geckos from Guangxi China. The differences in these two kinds of karyotypes were detected on the 15th chromosome. The clear differences in genetic levels between black-spotted and red-spotted tokay geckos suggest a significant level of genetic differentiation between the two.
Collapse
Affiliation(s)
- Xin-Min Qin
- College of Life Science, Guangxi Normal University, Guilin, Guangxi 541004, China.
| | | | | | | | | |
Collapse
|
5
|
Chromosomal evolution in Gekkonidae. I. Chromosome painting between Gekko and Hemidactylus species reveals phylogenetic relationships within the group. Chromosome Res 2011; 19:843-55. [PMID: 21987185 DOI: 10.1007/s10577-011-9241-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 09/05/2011] [Accepted: 09/05/2011] [Indexed: 10/17/2022]
Abstract
Geckos are a large group of lizards characterized by a rich variety of species, different modes of sex determination and diverse karyotypes. In spite of many unresolved questions on lizards' phylogeny and taxonomy, the karyotypes of most geckos have been studied by conventional cytogenetic methods only. We used flow-sorted chromosome-specific painting probes of Japanese gecko (Gekko japonicus), Mediterranean house gecko (Hemidactylus turcicus) and flat-tailed house gecko (Hemidactylus platyurus) to reveal homologous regions and to study karyotype evolution in seven gecko species (Gekko gecko, G. japonicus, G. ulikovskii, G. vittatus, Hemidactylus frenatus, H. platyurus and H. turcicus). Generally, the karyotypes of geckos were found to be conserved, but we revealed some characteristic rearrangements including both fissions and fusions in Hemidactylus. The karyotype of H. platyurus contained a heteromorphic pair in all female individuals, where one of the homologues had a terminal DAPI-negative and C-positive heterochromatic block that might indicate a putative sex chromosome. Among two male individuals studied, only one carried such a polymorphism, and the second one had none, suggesting a possible ZZ/ZW sex determination in some populations of this species. We found that all Gekko species have retained the putative ancestral karyotype, whilst the fission of the largest ancestral chromosome occurred in the ancestor of modern Hemidactylus species. Three common fissions occurred in the ancestor of Mediterranean house and flat-tailed house geckos, suggesting their sister group relationships. PCR-assisted mapping on flow-sorted chromosome libraries with conserved DMRT1 gene primers in G. japonicus indicates the localization of DMRT1 gene on chromosome 6.
Collapse
|
6
|
Yu X, Peng Y, Aowphol A, Ding L, Brauth S, Tang YZ. Geographic variation in the advertisement calls ofGekko geckoin relation to variations in morphological features: implications for regional population differentiation. ETHOL ECOL EVOL 2011. [DOI: 10.1080/03949370.2011.566581] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
7
|
Gamble T. A review of sex determining mechanisms in geckos (Gekkota: Squamata). Sex Dev 2010; 4:88-103. [PMID: 20234154 PMCID: PMC2855288 DOI: 10.1159/000289578] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 07/27/2009] [Indexed: 11/19/2022] Open
Abstract
Geckos are a species-rich clade of reptiles possessing diverse sex determining mechanisms. Some species possess genetic sex determination, with both male and female heterogamety, while other species have temperature-dependent sex determination. I compiled information from the literature on the taxonomic distribution of these sex determining mechanisms in geckos. Using phylogenetic data from the literature, I reconstructed the minimum number of transitions among these sex determining mechanisms with parsimony-based ancestral state reconstruction. While only a small number of gecko species have been characterized, numerous changes among sex determining mechanisms were inferred. This diversity, coupled with the high frequency of transitions, makes geckos excellent candidates as a model clade for the study of vertebrate sex determination and evolution.
Collapse
Affiliation(s)
- T. Gamble
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minn., USA
| |
Collapse
|
8
|
TOKUNAGA SHOJI. Temperature-Dependent Sex Determination in Gekko japonicus (Gekkonidae, Reptilia). (temperature-dependent sex determination/Gekko japonicus/sex differentiation/Reptilia). Dev Growth Differ 1985. [DOI: 10.1111/j.1440-169x.1985.00117.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
9
|
Judd HL, Laughlin GA, Bacon JP, Benirschke K. Circulating androgen and estrogen concentrations in lizards (Iguana iguana). Gen Comp Endocrinol 1976; 30:391-5. [PMID: 992358 DOI: 10.1016/0016-6480(76)90091-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
10
|
Cohen MM, Clark HF, Jensen F. Effects of SV40 virus on the chromosomes of poikilothermic cells (Gekko gecko) cultivated at different temperatures. Int J Cancer 1972; 9:618-25. [PMID: 4350127 DOI: 10.1002/ijc.2910090319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|