Research Article |
Corresponding author: Kornsorn Srikulnath ( kornsorn.s@ku.ac.th ) Academic editor: Nina Bogutskaya
© 2017 Aorarat Suntronpong, Watcharaporn Thapana, Panupon Twilprawat, Ornjira Prakhongcheep, Suthasinee Somyong, Narongrit Muangmai, Surin Peyachoknagul, Kornsorn Srikulnath.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
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Among teleost fishes, Asian swamp eel (Monopterus albus Zuiew, 1793) possesses the lowest chromosome number, 2n = 24. To characterize the chromosome constitution and investigate the genome organization of repetitive sequences in M. albus, karyotyping and chromosome mapping were performed with the 18S – 28S rRNA gene, telomeric repeats, microsatellite repeat motifs, and Rex retroelements. The 18S – 28S rRNA genes were observed to the pericentromeric region of chromosome 4 at the same position with large propidium iodide and C-positive bands, suggesting that the molecular structure of the pericentromeric regions of chromosome 4 has evolved in a concerted manner with amplification of the 18S – 28S rRNA genes. (TTAGGG)n sequences were found at the telomeric ends of all chromosomes. Eight of 19 microsatellite repeat motifs were dispersedly mapped on different chromosomes suggesting the independent amplification of microsatellite repeat motifs in M. albus. Monopterus albus Rex1 (MALRex1) was observed at interstitial sites of all chromosomes and in the pericentromeric regions of most chromosomes whereas MALRex3 was scattered and localized to all chromosomes and MALRex6 to several chromosomes. This suggests that these retroelements were independently amplified or lost in M. albus. Among MALRexs (MALRex1, MALRex3, and MALRex6), MALRex6 showed higher interspecific sequence divergences from other teleost species in comparison. This suggests that the divergence of Rex6 sequences of M. albus might have occurred a relatively long time ago.
Asian swamp eel, C-band, dispersion, microsatellite repeat, retroelement
Teleost fishes possess high morphological and physiological variation with nearly 30,000 extant species (Nelson 2016). The Asian swamp eel (Monopterus albus Zuiew, 1793) is a commercially important, air-breathing fish (Synbranchidae, Synbranchiformes) which is a protogynous hermaphrodite native in freshwaters of East and Southeast Asia and invasive elsewhere in the world including North America (
Synbranchids are freshwater eel-like fishes which include four genera (Macrotrema Cantor, 1849, Monopterus Lacépède, 1800, Ophisternon McClelland, 1844, and Synbranchus Bloch, 1795) and Monopterus is phylogenetically located at the basal position except for the Macrotrema (
Vertebrate genomes are commonly characterized by a large copy number of repetitive sequences, belonging to two main classes: the site-specific type (such as satellite DNA, microsatellite repeats, ribosomal RNA genes and telomeric sequences), and the interspersed type (transposable elements, TEs) (
In this study, karyotyping was performed with conventional Giemsa staining, 4', 6-diamidino-2-phenylindole (DAPI) and propidium iodide (PI) fluorescent staining, C-banding, and fluorescence in situ hybridization (FISH) with four repetitive elements; namely, the 18S − 28S ribosomal RNA genes, telomeric (TTAGGG)n sequences, Rex retroelements and 19 microsatellite repeat motifs. Partial DNA fragments of Rex retroelements (Rex1, Rex3, and Rex6) were molecularly characterized and the evolutionary processes responsible for these retroelements in teleost genomes were discussed, together with the organization of synbranchid genomes.
Ten specimens of the Asian swamp eel were purchased from an animal pet shop in Bangkok, Thailand. Animal care and all experimental procedures were approved by the Animal Experiment Committee, Kasetsart University, Thailand (approval no. ACKU00958), and conducted according to the Regulations on Animal Experiments at Kasetsart University, Thailand. Mitotic chromosomes were obtained from gill and kidney cells using the air drying method. Briefly, after intraperitoneal injection of 0.01% colchicine (Sigma, St. Louis, Missouri, USA) in the proportion of 0.7 ml per 100 g of fish weight for 2 h, fishes were anesthetized in ice-cold water, and the anterior portion of the gill and kidney were removed and used for mitotic chromosome preparation. After hypotonic treatment of gill and kidney in 0.075 M KCl for 50 min at room temperature, the organs were minced and placed in the first fixative solution (3:1 methanol/acetic acid) for 5 min and in the second fixative solution (2:1 methanol/acetic acid) for 5 min on ice. The cells were collected by filtration using gauze, and then fixed with 3:1 methanol/acetic acid. The cells in suspension were dropped onto clean glass slides and air-dried. The slides were kept at -80°C until use. For karyotyping with conventional Giemsa staining, the chromosome slides were stained with 4% Giemsa solution (pH 7.2) for 10 min.
To examine the chromosomal distribution of constitutive heterochromatin, C-banding was performed using the standard barium hydroxide/saline/Giemsa method (
Genomic DNA was extracted from liver and muscle tissue following the standard salting-out protocol as described previously (
Multiple sequence alignments of the three data sets (Rex1, Rex3, and Rex6) were performed with those of other teleosts taken from the NCBI database (Suppl. material
Chromosomal locations of the 18S – 28S rRNA genes, Rex retroelements (Rex1, Rex3, and Rex6), telomeric (TTAGGG)n sequences, and 19 microsatellite repeat motifs: (CA)15, (GC)15, (GA)15, (AT)15, (CAA)10, (CAG)10, (CAT)10, (CGG)10, (GAG)10, (AAT)10, (AAGG)8, (AATC)8, (AGAT)8, (ACGC)8, (AAAT)8, (AAAC)8, (AATG)8, (AAATC)6, and (AAAAT)6 were determined using FISH, as described previously (
For dual-color FISH, two probes differentially labeled with either biotin-16-dUTP or digoxigenin-11-dUTP (Roche Diagnostics) were mixed in hybridization buffer and co-hybridized to one slide. After hybridization, digoxigenin- and biotin-labeled probes were stained with anti-digoxigenin-rhodamine Fab fragments (Roche Diagnostics) and avidin labeled with fluorescein isothiocyanate (avidin-FITC; Invitrogen), respectively.
Over 10 Giemsa-stained metaphase spreads were examined for each M. albus individual. Diploid chromosome number is 24 (FN = 24) comprising twelve pairs of acrocentric chromosomes (Fig.
Fluorescence hybridization signals for the 18S – 28S rRNA genes were also detected at the pericentromeric region of chromosome 4 co-localizing with both PI-positive bands and large C-positive heterochromatin blocks (Fig.
Chromosomal locations of the 18S – 28S rRNA genes and (TTAGGG)n sequences in Monopterus albus. Hybridization pattern of FITC-labeled 18S – 28S rRNA genes (green) (a) and rhodamine-labeled TTAGGG repeats (red) (b) on DAPI-stained chromosomes, and their co-hybridization pattern (c). Hybridization pattern of FITC-labeled 18S – 28S rRNA genes (green) (d) on PI-stained chromosomes. PI-stained patterns of the same metaphase spreads of (d) is shown in (e). Arrowheads indicate FISH signals of the 18S – 28S rRNA genes. Arrows indicate the large PI-stained region. Scale =10 μm.
Eight of the 19 microsatellite repeat motifs were dispersedly mapped onto most chromosomes (Fig.
M. albus Rex1 (MALRex1) obtained from a single M. albus individual was localized to the pericentromeric region and interstitial sites of all chromosomes, except for chromosomes 4 and 9 where MALRex1 was found only at interstitial sites (Fig.
Chromosomal locations of Rex1, Rex3, and Rex6 in Monopterus albus. Hybridization pattern of FITC-labeled Rex1 (green) (a) on PI-stained chromosomes, and rhodamine-labeled Rex3 (red) (b) and Rex6 (red) (c) on DAPI-stained chromosomes. Scale =10 μm.
Chromosomal locations of Rex3 and Rex6 in Monopterus albus. Hybridization pattern of FITC-labeled Rex3 (green) (b) and rhodamine-labeled Rex6 (red) (c) on DAPI-stained chromosomes, and their co-hybridization pattern (d). DAPI-stained patterns of the same metaphase spreads of (b, c, and d) is shown in (a). Scale =10 μm.
The nucleotide sequence of a 533 bp-fragment of MALRex1 was used in multiple sequence alignment with 28 other teleosts, evidencing 32 indel sites. Sequence divergence among species varied from 0 to 50.13% with an average of 29.56±1.13% (Suppl. material
Phylogenetic placements of partial nucleotide sequences of Rex1 from 28 teleosts. Support values at each node are Bayesian posterior probability.
Phylogenetic placements of partial nucleotide sequences of Rex3 from 24 teleosts. Support values at each node are Bayesian posterior probability.
Phylogenetic placements of partial nucleotide sequences of Rex6 from 17 teleosts. Support values at each node are Bayesian posterior probability.
Synonymous substitution site (Ks) per nonsynonymous substitution sites (Ka) of Rex1 retroelement among twenty eight teleosts.
AJA | PTI | HLE | HNI | OFL | CAL | OLA | FUN | GAF | PME | PAM | PGR | XMA | MAL | LCA | AOC | CMO | CLA | GPR | HBI | ONI | PSC | SDI | DMA | NCO | TNE | GAC | BBA | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Anguilla japonica (AJA) | ||||||||||||||||||||||||||||
Pseudotocinclus tietensis (PTI) | 2.09 | |||||||||||||||||||||||||||
Hisonotus leucofrenatus (HLE) | 1.97 | 2.97 | ||||||||||||||||||||||||||
Hypostomus nigromaculatus (HNI) | 2.71 | 3.07 | 3.14 | |||||||||||||||||||||||||
Otocinclus flexilis (OFL) | 2.18 | 2.82 | 2.69 | 3.43 | ||||||||||||||||||||||||
Coregonus albula (CAL) | 3.20 | 3.28 | 2.78 | 2.75 | 3.22 | |||||||||||||||||||||||
Oryzias latipes (OLA) | 1.93 | 2.37 | 2.14 | 2.67 | 2.19 | 2.62 | ||||||||||||||||||||||
Fundulus sp. (FUN) | 2.05 | 2.06 | 1.76 | 2.38 | 2.39 | 2.15 | 1.62 | |||||||||||||||||||||
Gambusia affinis (GAF) | 1.75 | 1.87 | 1.62 | 1.81 | 1.97 | 2.20 | 1.56 | 1.74 | ||||||||||||||||||||
Poecilia mexicana (PME) | 2.06 | 1.83 | 1.79 | 1.76 | 1.70 | 2.33 | 1.62 | 1.83 | 4.03 | |||||||||||||||||||
Phallichthys amates (PAM) | 1.82 | 1.52 | 1.51 | 1.80 | 1.79 | 2.01 | 1.53 | 1.71 | 2.22 | 3.31 | ||||||||||||||||||
Poeciliopsis gracilis (PGR) | 1.55 | 1.67 | 1.57 | 1.72 | 1.81 | 1.64 | 1.71 | 1.53 | 2.43 | 2.10 | 2.17 | |||||||||||||||||
Xiphophorus maculatus (XMA) | 1.85 | 1.72 | 1.54 | 1.86 | 1.99 | 2.16 | 1.66 | 1.78 | 3.23 | 3.20 | 2.11 | 2.26 | ||||||||||||||||
Monopterus albus (MAL) | 2.65 | 2.52 | 1.80 | 3.08 | 1.97 | 3.18 | 2.45 | 2.56 | 1.93 | 2.20 | 1.88 | 1.50 | 1.91 | |||||||||||||||
Lates calcarifer (LCA) | 1.34 | 2.05 | 1.44 | 3.01 | 2.60 | 2.45 | 2.21 | 1.65 | 1.62 | 1.84 | 1.64 | 1.44 | 1.75 | 1.75 | ||||||||||||||
Astronotus ocellatus (AOC) | 2.63 | 2.27 | 1.90 | 2.60 | 2.77 | 2.55 | 2.27 | 2.47 | 1.82 | 1.89 | 1.80 | 1.58 | 1.84 | 1.46 | 1.91 | |||||||||||||
Cichla monoculus (CMO) | 2.69 | 2.30 | 1.93 | 2.65 | 2.83 | 2.60 | 2.30 | 2.43 | 1.82 | 1.89 | 1.80 | 1.60 | 1.84 | 1.49 | 1.91 | 0.00 | ||||||||||||
Cichlasoma labridens (CLA) | 2.24 | 2.59 | 2.55 | 2.92 | 2.70 | 2.82 | 2.07 | 2.49 | 1.80 | 1.80 | 1.69 | 1.41 | 1.77 | 2.24 | 2.14 | 2.31 | 2.26 | |||||||||||
Geophagus proximus (GPR) | 2.63 | 2.27 | 1.90 | 2.60 | 2.77 | 2.55 | 2.27 | 2.47 | 1.82 | 1.89 | 1.80 | 1.58 | 1.84 | 1.46 | 1.91 | n/c | 0.00 | 2.31 | ||||||||||
Heterandria bimaculata (HBI) | 2.01 | 2.72 | 2.69 | 2.44 | 2.67 | 2.57 | 2.15 | 1.94 | 1.64 | 1.89 | 1.72 | 1.57 | 1.63 | 2.32 | 2.04 | 2.39 | 2.35 | 3.02 | 2.39 | |||||||||
Oreochromis niloticus (ONI) | 1.82 | 2.60 | 2.44 | 2.86 | 2.67 | 2.59 | 2.11 | 2.35 | 1.70 | 1.91 | 1.73 | 1.64 | 1.68 | 2.24 | 2.02 | 2.35 | 2.30 | 3.80 | 2.35 | 1.86 | ||||||||
Pterophyllum scalare (PSC) | 2.69 | 2.30 | 1.93 | 2.65 | 2.83 | 2.60 | 2.30 | 2.43 | 1.82 | 1.89 | 1.80 | 1.60 | 1.84 | 1.49 | 1.91 | 0.00 | n/c | 2.26 | 0.00 | 2.35 | 2.30 | |||||||
Symphysodon discus (SDI) | 2.13 | 2.55 | 2.47 | 2.74 | 2.57 | 2.63 | 2.08 | 2.43 | 1.72 | 1.89 | 1.74 | 1.58 | 1.68 | 2.02 | 2.02 | 2.06 | 2.02 | 1.35 | 2.06 | 2.37 | 3.56 | 2.02 | ||||||
Dissostichus mawsoni (DMA) | 2.86 | 2.58 | 1.99 | 2.83 | 2.23 | 3.34 | 2.16 | 2.05 | 1.64 | 1.96 | 1.67 | 1.52 | 1.70 | 1.89 | 1.90 | 2.20 | 2.24 | 2.40 | 2.20 | 2.00 | 2.22 | 2.24 | 2.23 | |||||
Notothenia coriiceps (NCO) | 3.22 | 3.14 | 2.26 | 3.02 | 2.41 | 3.70 | 2.28 | 2.30 | 1.84 | 2.19 | 1.74 | 1.53 | 1.88 | 2.59 | 2.32 | 2.47 | 2.52 | 2.74 | 2.47 | 2.27 | 2.53 | 2.52 | 2.65 | 3.78 | ||||
Trematomus newnesi (TNE) | 2.75 | 2.73 | 2.20 | 2.86 | 2.18 | 3.37 | 2.10 | 2.37 | 1.70 | 2.04 | 1.67 | 1.61 | 1.76 | 2.39 | 2.14 | 2.29 | 2.33 | 2.79 | 2.29 | 2.24 | 2.58 | 2.33 | 2.62 | 3.75 | 3.20 | |||
Gymnodraco acuticeps (GAC) | 2.71 | 2.67 | 2.00 | 2.84 | 2.09 | 3.18 | 2.10 | 2.04 | 1.71 | 1.98 | 1.63 | 1.54 | 1.75 | 2.06 | 2.16 | 2.16 | 2.20 | 2.41 | 2.16 | 2.03 | 2.25 | 2.20 | 2.27 | 1.76 | 1.79 | 1.45 | ||
Battrachocottus baikalensis (BBA) | 2.51 | 2.30 | 2.39 | 2.91 | 2.35 | 4.24 | 2.17 | 2.11 | 1.73 | 1.92 | 1.64 | 1.81 | 1.73 | 2.75 | 2.38 | 2.62 | 2.66 | 2.22 | 2.62 | 2.18 | 2.07 | 2.66 | 2.30 | 2.57 | 2.72 | 2.86 | 2.50 |
Synonymous substitution site (Ks) per nonsynonymous substitution sites (Ka) of Rex3 retroelement among twenty four teleosts.
AAN | CCA | DRE | AFA | CCU | PTI | ELU | OLA | FUN | GAF | HBI | PFO | PAM | XHE | MAL | SCH | AOC | CMO | CLA | GSU | ONI | PSC | SDI | BBA | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Anguilla anguilla (AAN) | ||||||||||||||||||||||||
Cyprinus carpio (CCA) | 1.40 | |||||||||||||||||||||||
Danio rerio (DRE) | 1.33 | 1.56 | ||||||||||||||||||||||
Astyanax fasciatus (AFA) | 1.02 | 1.07 | 0.90 | |||||||||||||||||||||
Corumbataia cuestae (CCU) | 0.94 | 1.16 | 0.97 | 1.62 | ||||||||||||||||||||
Pseudotocinclus tietensis (PTI) | 0.98 | 1.09 | 0.96 | 1.63 | 2.29 | |||||||||||||||||||
Esox lucius (ELU) | 1.05 | 1.52 | 1.80 | 0.98 | 1.08 | 0.91 | ||||||||||||||||||
Oryzias latipes (OLA) | 1.35 | 0.81 | 1.31 | 0.88 | 0.97 | 0.91 | 1.01 | |||||||||||||||||
Fundulus sp.(FUN) | 1.35 | 1.26 | 1.49 | 0.93 | 1.12 | 1.09 | 1.71 | 1.03 | ||||||||||||||||
Gambusia affinis (GAF) | 1.13 | 0.84 | 1.19 | 0.88 | 1.09 | 0.96 | 1.11 | 0.81 | 0.80 | |||||||||||||||
Heterandria bimaculata (HBI) | 1.35 | 1.47 | 1.53 | 0.87 | 1.06 | 1.02 | 1.59 | 0.87 | 0.94 | 0.87 | ||||||||||||||
Poecilia formosa (PFO) | 1.19 | 0.94 | 1.45 | 0.83 | 1.01 | 0.96 | 1.15 | 1.19 | 0.91 | 0.83 | 1.07 | |||||||||||||
Phallichthys amates (PAM) | 1.17 | 1.08 | 1.44 | 0.82 | 1.02 | 0.97 | 1.23 | 0.89 | 0.65 | 1.01 | 0.76 | 0.75 | ||||||||||||
Xiphophorus hellerii (XHE) | 1.30 | 1.14 | 1.48 | 0.82 | 1.04 | 0.99 | 1.36 | 0.84 | 0.72 | 0.94 | 0.97 | 1.55 | 1.03 | |||||||||||
Monopterus albus (MAL) | 1.06 | 1.25 | 1.66 | 0.94 | 0.90 | 0.85 | 1.48 | 0.81 | 1.24 | 0.93 | 1.27 | 1.07 | 1.00 | 1.01 | ||||||||||
Siniperca chuatsi (SCH) | 1.12 | 0.95 | 1.36 | 0.90 | 0.96 | 0.97 | 0.97 | 0.63 | 1.54 | 0.97 | 1.32 | 1.28 | 1.02 | 1.22 | 0.92 | |||||||||
Astronotus ocellatus (AOC) | 1.00 | 1.39 | 1.63 | 1.00 | 0.89 | 0.90 | 1.20 | 1.01 | 1.11 | 1.01 | 1.22 | 1.27 | 1.18 | 1.09 | 0.81 | 1.15 | ||||||||
Cichla monoculus (CMO) | 0.92 | 0.95 | 1.28 | 0.99 | 1.01 | 0.98 | 0.92 | 0.75 | 0.85 | 0.84 | 0.89 | 0.87 | 0.79 | 0.74 | 0.71 | 0.74 | 1.03 | |||||||
Cichlasoma labridens (CLA) | 0.97 | 1.20 | 1.63 | 1.04 | 1.04 | 1.01 | 0.96 | 0.64 | 0.93 | 0.89 | 0.96 | 0.96 | 0.82 | 0.76 | 0.78 | 0.90 | 1.22 | 0.15 | ||||||
Geophagus surinamensis (GSU) | 1.02 | 1.13 | 1.07 | 1.50 | 1.84 | 2.27 | 1.15 | 0.96 | 1.15 | 1.07 | 1.10 | 1.10 | 1.07 | 1.05 | 0.92 | 1.01 | 0.94 | 1.04 | 1.06 | |||||
Oreochromis niloticus (ONI) | 1.35 | 1.53 | 1.80 | 0.98 | 1.03 | 1.07 | 1.47 | 0.74 | 0.99 | 0.79 | 0.90 | 0.98 | 0.87 | 0.84 | 1.06 | 1.12 | 1.15 | 0.69 | 0.71 | 1.02 | ||||
Pterophyllum scalare (PSC) | 1.24 | 1.56 | 1.37 | 1.01 | 0.88 | 0.90 | 1.55 | 1.04 | 1.22 | 1.11 | 1.02 | 1.25 | 1.25 | 1.17 | 0.98 | 1.21 | 1.65 | 1.51 | 1.26 | 0.97 | 0.99 | |||
Symphysodon discus (SDI) | 0.97 | 1.11 | 1.51 | 1.03 | 1.01 | 1.01 | 0.93 | 0.60 | 0.94 | 0.80 | 0.92 | 0.94 | 0.77 | 0.75 | 0.73 | 0.85 | 1.05 | 0.16 | 0.00 | 1.03 | 0.74 | 1.17 | ||
Battrachocottus baikalensis (BBA) | 1.16 | 0.92 | 1.42 | 0.98 | 0.94 | 0.93 | 0.93 | 0.70 | 1.07 | 0.89 | 0.92 | 0.87 | 0.74 | 0.78 | 0.84 | 0.54 | 0.91 | 0.70 | 0.77 | 1.07 | 0.71 | 1.06 | 0.70 |
Synonymous substitution site (Ks) per nonsynonymous substitution sites (Ka) of Rex6 retroelement among seventeen teleosts.
OLA | GAF | PFO | PGR | XMA | MAL | AOC | CLA | CMO | CRE | GPR | HBI | MAU | ONI | PSC | SDI | RSO | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Oryzias latipes (OLA) | |||||||||||||||||
Gambusia affinis (GAF) | 0.34 | ||||||||||||||||
Poecilia formosa (PFO) | 0.28 | 0.71 | |||||||||||||||
Poeciliopsis gracilis (PGR) | 0.18 | 0.98 | 0.59 | ||||||||||||||
Xiphophorus maculatus (XMA) | 0.23 | 0.73 | 0.55 | 1.10 | |||||||||||||
Monopterus albus (MAL) | 0.94 | 1.02 | 0.96 | 0.99 | 1.03 | ||||||||||||
Astronotus ocellatus (AOC) | 0.71 | 0.68 | 0.64 | 0.60 | 0.62 | 0.88 | |||||||||||
Cichlasoma labridens (CLA) | 0.89 | 0.78 | 0.99 | 0.77 | 0.80 | 0.93 | 1.69 | ||||||||||
Cichla monoculus (CMO) | 0.55 | 0.42 | 0.54 | 0.41 | 0.33 | 0.86 | 0.90 | 1.35 | |||||||||
Crenicichla sp. (CRE) | 0.33 | 0.40 | 0.49 | 0.33 | 0.29 | 0.85 | 0.51 | 1.18 | 0.73 | ||||||||
Geophagus proximus (GPR) | 0.72 | 0.72 | 0.84 | 0.73 | 0.69 | 0.84 | 1.05 | 1.37 | 1.15 | 0.91 | |||||||
Hemichromis bimaculatus (HBI) | 0.27 | 1.16 | 0.00 | 0.85 | 0.82 | 0.95 | 0.74 | 1.02 | 0.59 | 0.57 | 0.90 | ||||||
Melanochromis auratus (MAU) | 0.64 | 0.58 | 0.68 | 0.67 | 0.59 | 0.81 | 0.83 | 1.20 | 1.32 | 0.66 | 1.14 | 0.79 | |||||
Oreochromis niloticus (ONI) | 0.61 | 0.57 | 0.68 | 0.64 | 0.57 | 0.85 | 0.86 | 1.36 | 1.07 | 0.54 | 1.08 | 0.77 | 0.89 | ||||
Pterophyllum scalare (PSC) | 0.75 | 0.73 | 0.91 | 0.73 | 0.69 | 0.90 | 1.03 | 1.83 | 1.54 | 1.20 | 1.33 | 1.00 | 1.27 | 1.01 | |||
Symphysodon discus (SDI) | 0.80 | 0.59 | 0.82 | 0.52 | 0.56 | 1.01 | 1.27 | 1.60 | 0.89 | 1.04 | 1.24 | 0.85 | 1.40 | 1.30 | 1.61 | ||
Rexea solandri (RSO) | 0.92 | 0.93 | 0.86 | 0.87 | 0.88 | 1.08 | 0.97 | 1.12 | 0.92 | 0.97 | 0.94 | 0.91 | 0.98 | 0.96 | 0.97 | 1.04 |
The karyotype of M. albus (2n = 24, FN = 24) composed of 12 acrocentric chromosome pairs was found to be similar to that reported by
In this study, eight microsatellite repeat motifs [(CAG)10, (CAA)10, (CGG)10, (GAG)10, (AGAT)8, (ACGC)8, (AAAT)8, and (AAATC)6] were dispersedly mapped on different chromosomes (Fig.
The diversity of chromosomal distribution for Rex retroelements (Rex1, Rex3, and Rex6) was found in teleosts (Table
Chromosomal distribution of Rex1, Rex3, and Rex6 in teleosts. “n.d.” means not described.
Order | Family | Species | Chrosmosomal distribution | Chromosome number | Reference | ||
---|---|---|---|---|---|---|---|
Rex1 | Rex3 | Rex6 | |||||
Characiformes | Characidae | Astyanax paranae | dispersion | telomeric region | n.d. | 2n = 50 |
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Astyanax fasciatus | n.d. | telomeric region | n.d. | 2n = 46 – 48 |
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Siluriformes | Loricariidae | Hisonotus leucofrenatus | dispersion | n.d. | n.d. | 2n = 54 |
|
Hypostomus nigromaculatus | dispersion | dispersion | dispersion | 2n = 76 |
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Pseudotocinclus tietensis | dispersion | dispersion | n.d. | 2n = 54 |
|
||
Salmoniformes | Salmonidae | Coregonus albula | pericentromeric region | n.d. | n.d. | 2n = 80 |
|
Coregonus fontanae | pericentromeric region | n.d. | n.d. | 2n = 80 |
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Synbranchiformes | Synbranchidae | Monopterus albus | pericentromeric region and insterstitial site | dispersion | dispersion | 2n = 24 | in this study |
Perciformes | Latidae | Lates calcarifer | telomeric region | centromeric region | n.d. | 2n = 48 |
|
Cichlidae | Astronotus ocellatus | centromeric region | telomeric region | telomeric region | 2n = 48 |
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Cichla kelberi | centromeric region | centromeric region | dispersion | 2n = 48 |
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Cichla monoculus | telomeric region | telomeric region | telomeric region | 2n = 48 |
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Geophagus proximus | telomeric region | telomeric region | telomeric region | 2n = 48 |
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Hemichromis bimaculatus | pericentromeric region | pericentromeric region | centromeric region | 2n = 44 |
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Melanochromis auratus | pericentromeric region | pericentromeric region | pericentromeric region | 2n = 44 |
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Oreochromis niloticus | pericentromeric region | pericentromeric region | pericentromeric region | 2n = 44 |
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Pterophyllum scalare | centromeric region | telomeric region | telomeric region | 2n = 48 |
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Oreochromis niloticus | pericentromeric region | pericentromeric region | pericentromeric region | 2n = 44 |
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Symphysodon discus | dispersion | telomeric region | telomeric region | 2n = 60 |
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Nototheniidae | Dissostichus mawsoni | dispersion | dispersion | n.d. | 2n = 48 |
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Notothenia coriiceps | dispersion | dispersion | n.d. | 2n = 22 |
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Trematomus newnesi | dispersion | dispersion | n.d. | 2n = 46 |
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Bathydraconidae | Gymnodraco acuticeps | dispersion | dispersion | n.d. | 2n = 48 |
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The differences in the copy number and chromosomal distribution of MALRex1, MALRex3, and MALRex6 suggest that these retroelements were independently amplified or lost in the lineage of M. albus, where MALRex3 is prone to retain a copy number higher than MALRex1 and MALRex6. A similar case of copy number variation in Rex retroelements was also found in several Antarctic nototheniid species (
Three Rex retroelements were identified in the genome of M. albus, and the degree of sequence divergence for the three retroelements was high (14–67%) from other species in comparison. MALRex1 and MALRex3 showed high interspecific sequence divergences from Cyprinodontiformes and Characiformes, respectively, but low interspecific sequence divergences from Perciformes fishes for Rex1 and Esociformes for Rex3 (Suppl. materials 3 and 4). This suggests that M. albus and Perciformes or Esociformes shared relatively recent activity of Rex1 or Rex3, respectively. The average Ks/Ka value of Rex1 was higher than 1 between all compared species and between M. albus and other species (Table
Only few data of Rex6 sequences were available because specific PCR primers were not feasibly effective to detect this element in the genome of teleosts (
The present results of chromosomal distribution and molecular diversity of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, and Rex retroelements) revealed the chromosome constitution and genome organization of Asian swamp eels. This enabled us to learn more about the chromosome constitution in synbranchid fishes and teleosts as a whole. Further work is required to investigate and compare synbranchid fishes, including M. cuchia, to better understand the process of karyotype and genome evolution in this lineage.
This study was financially supported by grants from the Thailand Research Fund, the Commission on Higher Education and Kasetsart University (TRF-CHE-KU grant number MRG5480224); Kasetsart University Research and Development Institute (KURDI) (No. 7.58), Kasetsart University; Fellowship of Capacity Building for Kasetsart University on Internationalization (No. 0513.10109/1757); Professor Motivation (PM) (No. PM4/2558) and Special Track Staff (STS) (No. STS1/2558) from the Faculty of Science, Kasetsart University; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU, Thailand) (No.6/2558); and Science Achievement Scholarship of Thailand (SAST) (No. 5717400071 and 5717400381) from the Office of the Higher Education Commission. We would like to thank Chayajit Deekrachang (Department of Fisheries, Thailand) for technical support for maintaining Asian swamp eels. We are also grateful to Amara Thongpan, Thiti Kanchanaketu, and Siwapech Sillapaprayoon (Kasetsart University, Thailand) for helpful discussions.
Supplementary Table
Data type: Table
Explanation note: Primers used molecular cloning in this study.
Supplementary Table
Data type: Table
Explanation note: Teleost species and nucleotide sequences of the Rex1, Rex3, and Rex6 genes used in this study. “–” means no data.
Supplementary Table
Data type: Table
Explanation note: Pairwise comparison of nucleotide sequence divergences of Rex1 among twenty eight teleosts.
Supplementary Table
Data type: Table
Explanation note: Pairwise comparison of nucleotide sequence divergences of Rex3 among twenty eight teleosts.
Supplementary Table 5
Data type: Table
Explanation note: Pairwise comparison of nucleotide sequence divergences of Rex6 among seventeen teleosts.
Supplementary Figure
Data type: Image
Explanation note: Phylogenetic placements of partial nucleotide sequences of Rex1 from 28 teleosts and from Physalaemus henselii, Peters 1872 (KU842414) as the outgroup. Support values at each node are Bayesian posterior probability.
Supplementary Figure
Data type: Image
Explanation note: Phylogenetic placements of partial nucleotide sequences of Rex6 from 17 teleosts and from Podocnemis unifilis, Troschel 1848 (KR336823) as the outgroup. Support values at each node are Bayesian posterior probability.