Research Article |
Corresponding author: Takahiro Taguchi ( mm7ttgctk@gmail.com ) Academic editor: Virmantas Stunžėnas
© 2022 Rei Kawakami, Takahiro Taguchi, Joshua Vacarizas, Masumi Ito, Takuma Mezaki, Akira Tominaga, Satoshi Kubota.
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:
Kawakami R, Taguchi T, Vacarizas J, Ito M, Mezaki T, Tominaga A, Kubota S (2022) Karyotypic analysis and isolation of four DNA markers of the scleractinian coral Favites pentagona (Esper, 1795) (Scleractinia, Anthozoa, Cnidaria). Comparative Cytogenetics 16(1): 77-92. https://doi.org/10.3897/compcytogen.v16.i1.79953
|
We performed conventional and molecular cytogenetic studies on the Favites pentagona Esper, 1795, a scleractinian coral mostly found along the west coast of Japan. Karyotype analysis of F. pentagona by G-banding revealed a karyogram containing a homogenously staining region (HSR) on chromosome 10 in more than 50% of the examined metaphase spreads. This HSR consisted of sequences from 18S ribosomal RNA (rRNA) genes, as demonstrated by fluorescence in situ hybridization (FISH) and DNA sequencing. We highlighted the development of four chromosomal FISH markers from repetitive genes such as U2 small nuclear RNA linked to 5S rRNA sequence (U2 snRNA-5S), 18S rRNA, histone H3, and uncharacterized gene FP-9X. The chromosomal locations of the U2 snRNA-5S and 18S RNA were on the terminal end of long arm of chromosomes 2 and 10, respectively, while the histone H3 and the uncharacterized gene were located near the centromeres of chromosomes 1 and 9, respectively. These FISH markers will improve the karyotyping of F. pentagona from mitotic preparations which helps in widening our understanding of coral genetic structure and chromosome organization. In addition, these improvements in karyotyping will provide the basis in constructing of chromosome-level genome assembly for F. pentagona.
chromosome, FISH, histone, HSR, karyotype, rRNA, scleractinian coral
Cytogenetic information from karyotypic analysis gives us a deeper understanding the way genetic material is packaged inside a nucleus of a cell and how certain genetic diseases are associated with chromosome defects and aberrations (
In this study, we reported the detailed molecular cytogenetic analysis of stony coral Favites pentagona Esper, 1758, from family Merulinidae. F. pentagona is commonly observed along the west coast of Japan (Veron, 2000). Colonies of F. pentagona range from massive, encrusting to columnar forms. The valleys with colonies are usually long and relatively straight at colony margins, becoming increasingly short, sinuous, and contorted towards the colony center; septa have thin walls and are highly irregular (Veron, 2000).
Cytogenetic analysis of F. pentagona was conducted using conventional and molecular cytogenetic techniques, such as fluorescence in situ hybridization (FISH). We identified a homogenously staining region (HSR) on F. pentagona chromosome 10 using G-banding and 4’,6-diamidino-2-phenylindole (DAPI) staining, followed by karyotyping. Furthermore, the chromosomal locations of four tandemly repetitive genes were identified for F. pentagona. The development of four FISH markers was described, and the FISH signals of each gene were characterized showing the effectivity of these markers to identify specific chromosomes from mitotic cells.
F. pentagona gametes were collected from spawning colonies at Nishidomari (32°46'N, 132°43'E), Kochi Prefecture, Japan (Fig.
Coral chromosome preparations were conducted according to the method described by
Genomic DNA was extracted from F. pentagona sperm (approximately 0.1 ml) using a Wizard Genomic DNA Purification Kit (Promega Corporation, Madison, WI, USA) according to the manufacturer’s instructions.
Target genes (18S rRNA, U2 snRNA-5S, histone H3, and uncharacterized gene FP-9X) were amplified by PCR using the Emerald PCR master mix (Takara, Japan). The primer sets used are shown in Table
Primer set | Genes | Sequence (5’-3’) | Reference | Species |
---|---|---|---|---|
1 | 18S rRNA | F-GGTTGATCCTGCCAGTAGTCATATGCTTG |
|
Zooxanthella |
R-GATCCTTCCGCAGGTTCACCTACGGAAACC | ||||
2 | histone H3 | F-ATGGCTCGTACCAAGCAGACVGC |
|
Stony coral |
R-ATATCCTTRGGCATRATRGTGAC | ||||
3 | U2 snRNA-5S | F-CTTCCGTGATCGGACGAGAA |
|
Hydra |
R-TATAATATTGGAACAGAATT | ||||
4 | Uncharacterized gene FP-9X | F-CTTCCGTGATCGGACGAGAA |
|
Hydra |
R-CCAATTTTGTAGACATCTTGAAG |
|
Hydra |
DNA inserts from plasmids were sequenced with the M13 forward and reverse primers using the BigDye Terminator v3.1 Cycle Sequencing Kit (GE Healthcare, Japan) and ABI PRISM 3130 Genetic Analyzer (Thermo Fisher Scientific, Tokyo, Japan). DNA sequences were aligned, and homology searches were performed using Gapped BLAST and PSI-BLAST: a new generation of protein database search programs to search the GenBank database (http://www.ddbj.nig.ac.jp).
FISH analysis was performed as previously reported (
FISH slides were examined under a fluorescence microscope (Olympus BX-50, Tokyo, Japan) equipped with a cooled charge-coupled device. Images of suitable metaphase spreads were acquired using an Olympus DP70 workstation and the FISH analysis software. The mirror units used for each fluorescence light (FITC, Cy-3, and DAPI) were U-NIBA, U-MWU, and U-MWIB (Olympus), respectively.
Chromosomes in metaphase cells were karyotyped by conventional trypsin G-banding, and an HSR in terminal end of one of the chromosomes was observed in approximately 50% of the observed metaphase spreads (Fig.
Relative lengths and centromere indices of the 14 chromosome pairs, shown as means and standard deviations obtained from the eight metaphase spreads.
Chromosome number | Short arm (μm) | Long arm (μm) | Total length (μm) | Arm ratio | Overall length ratio | Chromosome type* |
---|---|---|---|---|---|---|
1 | 2.21±0.75 | 3.94±0.95 | 6.15±1.5 | 1.88±0.57 | 0.94±0.08 | sm |
2 | 1.52±0.48 | 3.3±0.82 | 4.82±1.12 | 2.3±0.71 | 0.74±0.06 | sm |
3 | 1.55±0.52 | 2.91±0.83 | 4.46±1.08 | 1.99±0.62 | 0.68±0.04 | sm |
4 | 1.48±0.53 | 2.74±0.62 | 4.22±0.98 | 1.98±0.61 | 0.65±0.04 | sm |
5 | 1.41±0.35 | 2.63±0.74 | 4.04±0.95 | 1.92±0.48 | 0.62±0.03 | sm |
6 | 1.49±0.26 | 2.36±0.74 | 3.85±0.9 | 1.6±0.38 | 0.59±0.03 | m |
7 | 1.39±0.26 | 2.34±0.62 | 3.74±0.8 | 1.7±0.36 | 0.57±0.04 | sm |
8 | 1.47±0.38 | 2.15±0.43 | 3.62±0.79 | 1.49±0.17 | 0.56±0.03 | m |
9 | 1.32±0.28 | 2.14±0.51 | 3.46±0.73 | 1.64±0.32 | 0.53±0.04 | m |
10 | 1.26±0.23 | 2.05±0.49 | 3.31±0.67 | 1.63±0.26 | 0.51±0.04 | m |
11 | 1.31±0.3 | 1.9±0.41 | 3.21±0.63 | 1.49±0.33 | 0.5±0.04 | m |
12 | 1.2±0.34 | 1.85±0.4 | 3.05±0.66 | 1.6±0.33 | 0.47±0.04 | m |
13 | 1.12±0.23 | 1.53±0.35 | 2.65±0.49 | 1.41±0.38 | 0.41±0.04 | m |
14 | 0.94±0.23 | 1.25±0.27 | 2.2±0.45 | 1.37±0.31 | 0.34±0.05 | m |
FISH signals for the 18S rRNA gene locus were identified at the terminal ends of the long arm of chromosome 10 (Fig.
FISH image showing hybridization signals of uncharacterized gene FP-9X probe (red; arrowheads) and 18S rRNA gene probe (green; arrows) (a). Chromosomes were karyotyped according to size and centromere positions showing uncharacterized gene FP-X9 and 18S rRNA gene probe hybridization on chromosome 9 and chromosome 10, respectively (c, above alignment). DAPI-only channel revealing the HSR region pointed by the arrow (b) and its karyogram (c, below alignment). Scale bar: 2 μm.
Cloning and sequencing were performed for the amplicons from which FISH probes were prepared. Positive clones were designated as FP-18S for 18S rRNA gene, FP-H3 for histone H3 gene, FP-U2-5S for U2 snRNA-5S, and FP-X9 for uncharacterized gene FP-X9. Sequence analysis of FP-18S clone (1,732 bp) with the GenBank database revealed a difference of a single nucleotide from the partial sequence of F. pentagona 18S rRNA gene (Accession No. LC644154). The FP-H3 clone (329 bp) completely matched with the partial sequence of the F. pentagona histone H3 gene (Accession No. LC644156). The FP-U2-5S (824 bp) sequence contained U2 spliceosomal small nuclear RNA (snRNA) gene sequence and region of 5S rRNA gene (Accession No. LC644155) (Figs
FISH image showing hybridization signal of histone H3 gene probe (red; arrowheads) (a). Chromosomes were karyotyped according to size and centromere positions showing the hybridization signal on chromosome 1 (c, above alignment). DAPI-only channel revealing the HSR region pointed by the arrow (b) and its karyogram (c, below alignment). Scale bar: 2 μm.
To solve the difficulties in taxonomically classifying stony corals (
FISH image showing hybridization signal of U2 snRNA-5S gene probe (red; arrowheads) (a). Chromosomes were karyotyped according to size and centromere positions showing hybridization signal on chromosome 2 (c, above alignment). Few background signals were seen; one background signal was on long arm telomere of chromosome 1 (a and c). DAPI-only channel without HSR region (b) and its karyotype (c, below alignment). Scale bar: 2 μm.
We carried out conventional G-bandings to establish the karyotype of F. pentagona embryos. In general, obtaining high-quality G-banding in invertebrate chromosomes is difficult because of the relatively small chromosome size and the weak effect of trypsin on G-banding. Karyotyping of F. pentagona revealed the three chromosome groups that cannot be precisely identified because of their similar lengths. Furthermore, differences in chromosome condensation depending on the stage of the cell cycle at which cells were fixed sometimes made it difficult to measure the precise lengths of chromosomes. To develop a coral chromosome study, it is necessary to identify each chromosome precisely using a painting probe (
The FISH marker for histone H3 gene was observed at the centromeric region of chromosome 1. The core histone genes are highly conserved and repetitive, and their loci can thus be detected using FISH probes containing the sequence of a single array composed of tandem repeats (
Information on 5S rDNA gene among stony corals is very limited (
Schematic diagram of FISH probe sequences of FP-U2-5S which contains the U2 spliceosomal snRNA-like region and partial sequence of 5S rRNA gene sequence (a). FP-X9 is similar to the 5'-untranslated region of uncharacterized gene of a Merulinidae coral (Orbicella faveolata (Ellis et Solander, 1786)) (b). Rectangles in both ends of bars show the primer positions and relative lengths.
Each of the FISH markers derived from the four different amplicons (FP-18S, FP-H3, FP-U2-5S, and FP-X9) were observed at a single site (locus), even in uncontracted prometaphase spreads with elongated chromosomes. As the specificity of the markers is very high due to the highly repetitive and conserved nature of these genes, these markers will be useful for karyotyping and identifying specific chromosomes containing similarity of sequences within closely related species.
The series of cytogenetic studies on stony corals including the development of specific FISH markers may contribute to understand changes in chromosomal structures across taxa thereby gain insight into its evolutionary processes (
We highlighted the development of four chromosomal FISH markers for U2 snRNA-5S, 18S rRNA, histone H3, and uncharacterized FP-9X genes, which were found to be located on chromosomes 2, 10, 1, and 9, respectively. The loci of the gene histone H3 were mapped in the chromosomes of stony corals for the first time. The isolation of four FISH markers for F. pentagona will also promote gene mapping and understand genome structure and organization for this species. This cytogenetic information on stony coral along with morphological and molecular characteristics may contribute to understand its evolutionary processes and resolve taxonomic problems in stony coral taxonomy.
TT: designed and performed experiments, organized the figures, and drafted manuscript. RK, MI, and JV: performed experiments, organized the figures and the tables. TM: did sampling and identification of the specimens. RK and JV: corrected the manuscript. AT, SK, and TT: supervised the research and corrected the manuscript. All authors read, discussed, and approved the final version of the manuscript.
This work was supported by grants from the Japan Society for the Promotion of Science (15K14789, 17H03861, and 21K05734: all to T.T.).
Takahiro Taguchi https://orcid.org/0000-0002-9095-2456