Show simple item record

dc.contributor.authorLee, Yung-Ien
dc.contributor.authorYap, Jing Weien
dc.contributor.authorIzan, Shairulen
dc.contributor.authorLeitch, Ilia J.en
dc.contributor.authorFay, Michael F.en
dc.contributor.authorLee, Yi-Chingen
dc.contributor.authorHidalgo, Orianeen
dc.contributor.authorDodsworth, Stevenen
dc.contributor.authorSmulders, Marinus J.M.en
dc.contributor.authorGravendeel, Barbaraen
dc.contributor.authorLeitch, Andrew R.en
dc.date.accessioned2019-02-11T12:46:23Z
dc.date.available2019-02-11T12:46:23Z
dc.date.issued2017-11-24
dc.identifier.citationLee Y., Yap J., Izan S., Leitch I., Fay M., Lee Y., Hidalgo O., Dodsworth S., Smulders M., Gravendeel B., Leitch A. (2018) 'Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization', BMC Genomics, 19 (578), pp.-.en
dc.identifier.issn1471-2164
dc.identifier.pmid30068293
dc.identifier.doi10.1186/s12864-018-4956-7
dc.identifier.urihttp://hdl.handle.net/10547/623130
dc.description.abstractBackground: Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across the genus). A new satellite repeat in Paphiopedilum subgenus Parvisepalum, SatA, was identified and characterized using the RepeatExplorer pipeline in HiSeq Illumina reads from P. armeniacum (2n = 26). Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA. Results: SatA comprises c. 14.5% of the P. armeniacum genome and is specific to subgenus Parvisepalum. It is composed of four primary monomers that range from 230 to 359 bp and contains multiple inverted repeat regions with hairpin loop motifs. A new karyotype of P. vietnamense (2n = 28) is presented and shows that the chromosome number in subgenus Parvisepalum is not conserved at 2n = 26, as previously reported. The physical locations of SatA sequences were visualised on the chromosomes of all seven Paphiopedilum species of subgenus Parvisepalum (2n = 26–28), together with the 5S and 45S rDNA loci using FISH. The SatA repeats were predominantly localisedin the centromeric, peri-centromeric and sub-telocentric chromosome regions, but the exact distribution pattern was species-specific. Conclusions: We conclude that the newly discovered, highly abundant and rapidly evolving satellite sequence SatA is specific to Paphiopedilum subgenus Parvisepalum. SatA and rDNA chromosomal distributions are characteristic of species, and comparisons between species reveal that the distribution patterns generate a strong phylogenetic signal. We also conclude that the ancestral chromosome number of subgenus Parvisepalum and indeed of all Paphiopedilum could be either 2n = 26 or 28, if P. vietnamense is sister to all species in the subgenus as suggested by the ITS data.
dc.description.sponsorshipThis work was supported by the Ministry of Science and Technology, Taiwan, ROC [NSC 102–2313-B-178-001-MY3] and National Museum of Natural Science, Taiwan, ROC to YIL in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.en
dc.language.isoenen
dc.publisherBioMed Central Ltd.en
dc.relation.urlhttps://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4956-7en
dc.rightsGreen - can archive pre-print and post-print or publisher's version/PDF
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.subjectFISHen
dc.subjectsatellite DNAen
dc.subjectPaphiopedilumen
dc.subjectFluorescent in situ hybridizationen
dc.subjectKaryotypeen
dc.subjectC400 Geneticsen
dc.titleSatellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridizationen
dc.typeArticleen
dc.identifier.journalBMC Genomicsen
dc.identifier.pmcidPMC6090851
dc.date.updated2019-02-11T12:04:27Z
dc.description.noteOA article Creative Commons Attribution 4.0 International License
html.description.abstractBackground: Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across the genus). A new satellite repeat in Paphiopedilum subgenus Parvisepalum, SatA, was identified and characterized using the RepeatExplorer pipeline in HiSeq Illumina reads from P. armeniacum (2n = 26). Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA. Results: SatA comprises c. 14.5% of the P. armeniacum genome and is specific to subgenus Parvisepalum. It is composed of four primary monomers that range from 230 to 359 bp and contains multiple inverted repeat regions with hairpin loop motifs. A new karyotype of P. vietnamense (2n = 28) is presented and shows that the chromosome number in subgenus Parvisepalum is not conserved at 2n = 26, as previously reported. The physical locations of SatA sequences were visualised on the chromosomes of all seven Paphiopedilum species of subgenus Parvisepalum (2n = 26–28), together with the 5S and 45S rDNA loci using FISH. The SatA repeats were predominantly localisedin the centromeric, peri-centromeric and sub-telocentric chromosome regions, but the exact distribution pattern was species-specific. Conclusions: We conclude that the newly discovered, highly abundant and rapidly evolving satellite sequence SatA is specific to Paphiopedilum subgenus Parvisepalum. SatA and rDNA chromosomal distributions are characteristic of species, and comparisons between species reveal that the distribution patterns generate a strong phylogenetic signal. We also conclude that the ancestral chromosome number of subgenus Parvisepalum and indeed of all Paphiopedilum could be either 2n = 26 or 28, if P. vietnamense is sister to all species in the subgenus as suggested by the ITS data.


Files in this item

Thumbnail
Name:
Leeetal.2018Paphiopedilum.pdf
Size:
2.559Mb
Format:
PDF

This item appears in the following Collection(s)

Show simple item record

Green - can archive pre-print and post-print or publisher's version/PDF
Except where otherwise noted, this item's license is described as Green - can archive pre-print and post-print or publisher's version/PDF