Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization

Abstract Background 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 repr...

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Main Authors: Yung-I Lee, Jing Wei Yap, Shairul Izan, Ilia J. Leitch, Michael F. Fay, Yi-Ching Lee, Oriane Hidalgo, Steven Dodsworth, Marinus J. M. Smulders, Barbara Gravendeel, Andrew R. Leitch
Format: Article
Language:English
Published: BMC 2018-08-01
Series:BMC Genomics
Subjects:
Online Access:http://link.springer.com/article/10.1186/s12864-018-4956-7
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spelling doaj-ac5abfc7b21f475ea94de192c5ff8e642020-11-25T00:40:30ZengBMCBMC Genomics1471-21642018-08-0119111410.1186/s12864-018-4956-7Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridizationYung-I Lee0Jing Wei Yap1Shairul Izan2Ilia J. Leitch3Michael F. Fay4Yi-Ching Lee5Oriane Hidalgo6Steven Dodsworth7Marinus J. M. Smulders8Barbara Gravendeel9Andrew R. Leitch10Biology Department, National Museum of Natural ScienceSchool of Biological and Chemical Sciences, Queen Mary University of LondonPlant Breeding, Wageningen University & ResearchDepartment of Comparative Plant and Fungal Biology, Royal Botanic GardensJodrell Laboratory, Royal Botanic GardensBiology Department, National Museum of Natural ScienceJodrell Laboratory, Royal Botanic GardensJodrell Laboratory, Royal Botanic GardensPlant Breeding, Wageningen University & ResearchEndless Forms Group, Naturalis Biodiversity CenterSchool of Biological and Chemical Sciences, Queen Mary University of LondonAbstract Background 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.http://link.springer.com/article/10.1186/s12864-018-4956-7PaphiopedilumKaryotypeSatellite DNAFluorescent in situ hybridizationFISH
collection DOAJ
language English
format Article
sources DOAJ
author Yung-I Lee
Jing Wei Yap
Shairul Izan
Ilia J. Leitch
Michael F. Fay
Yi-Ching Lee
Oriane Hidalgo
Steven Dodsworth
Marinus J. M. Smulders
Barbara Gravendeel
Andrew R. Leitch
spellingShingle Yung-I Lee
Jing Wei Yap
Shairul Izan
Ilia J. Leitch
Michael F. Fay
Yi-Ching Lee
Oriane Hidalgo
Steven Dodsworth
Marinus J. M. Smulders
Barbara Gravendeel
Andrew R. Leitch
Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization
BMC Genomics
Paphiopedilum
Karyotype
Satellite DNA
Fluorescent in situ hybridization
FISH
author_facet Yung-I Lee
Jing Wei Yap
Shairul Izan
Ilia J. Leitch
Michael F. Fay
Yi-Ching Lee
Oriane Hidalgo
Steven Dodsworth
Marinus J. M. Smulders
Barbara Gravendeel
Andrew R. Leitch
author_sort Yung-I Lee
title Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization
title_short Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization
title_full Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization
title_fullStr Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization
title_full_unstemmed Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization
title_sort satellite dna in paphiopedilum subgenus parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization
publisher BMC
series BMC Genomics
issn 1471-2164
publishDate 2018-08-01
description Abstract Background 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.
topic Paphiopedilum
Karyotype
Satellite DNA
Fluorescent in situ hybridization
FISH
url http://link.springer.com/article/10.1186/s12864-018-4956-7
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