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He Z, Luo X, Lei Y, Zhang W. Five Species of Taxus Karyotype Based on Oligo-FISH for 5S rDNA and (AG 3T 3) 3. Genes (Basel) 2022; 13:genes13122209. [PMID: 36553477 PMCID: PMC9778077 DOI: 10.3390/genes13122209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/07/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
As a relict plant, Taxus is used in a variety of medicinal ingredients, for instance to treat a variety of cancers. Taxus plants are difficult to distinguish from one another due to their similar morphology; indeed, some species of Taxus cytogenetic data still are unclear. Oligo-FISH can rapidly and efficiently provide insight into the genetic composition and karyotype. This is important for understanding the organization and evolution of chromosomes in Taxus species. We analysed five Taxus species using two oligonucleotide probes. (AG3T3)3 signals were distributed at the chromosome ends and the centromere of five species of Taxus. The 5S rDNA signal was displayed on two chromosomes of five species of Taxus. In addition to Taxus wallichiana var. mairei, 5S rDNA signals were found proximal in the remaining four species, which signals a difference in its location. The karyotype formula of Taxus wallichiana was 2n = 2x = 24m, its karyotype asymmetry index was 55.56%, and its arm ratio was 3.0087. Taxus × media's karyotype formula was 2n = 2x = 24m, its karyotype asymmetry index was 55.09%, and its arm ratio was 3.4198. The karyotype formula of Taxus yunnanensis was 2n = 2x = 24m, its karyotype asymmetry index was 55.56%, and its arm ratio was 2.6402. The karyotype formula of Taxus cuspidate was 2n = 2x = 24m, its karyotype asymmetry index was 54.67%, its arm ratio was 3.0135, and two chromosomes exhibited the 5S rDNA signal. The karyotype formula of T. wallichiana var. mairei was 2n= 2x = 22m + 2sm, its karyotype asymmetry index was 54.33%, and its arm ratio was 2.8716. Our results provide the karyotype analysis and physical genetic map of five species of Taxus, which contributes to providing molecular cytogenetics data for Taxus.
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New chromosome number and cyto-molecular characterization of the African Baobab (Adansonia digitata L.) - "The Tree of Life". Sci Rep 2020; 10:13174. [PMID: 32764541 PMCID: PMC7413363 DOI: 10.1038/s41598-020-68697-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/22/2020] [Indexed: 11/08/2022] Open
Abstract
The African baobab (Adansonia digitata L.), also referred to as the "Tree of Life", is a majestic, long-lived and multipurpose tree of sub-Saharan Africa. Internationally, a growing demand for baobab products in the food, pharmaceutical and cosmetics industries has been observed. Considering this, there is a need for scientific information on the genetics and breeding of A. digitata, including cytogenetics, genetic diversity and reproductive biology. The objectives of our cytogenetic research were to determine the genome size, chromosome number, and organization of ribosomal DNA (45S and 5SrDNA) of A. digitata. Flow cytometry analysis revealed a 2C-DNA value of 3.8 ± 0.6 pg (1Cx monoploid genome size 919.1 ± 62.9 Mbp). Using our improved chromosome preparation technique, we were able to unequivocally count the chromosomes resulting in 2n = 4x = 168, a revised chromosome number for A. digitata. Fluorescent in situ hybridization (FISH) analysis revealed two massively large variants of 45S rDNA and their corresponding nucleolus organizer regions (NOR). The NOR variants were about two to four times larger than the main body of their respective chromosomes. To our knowledge, this is the first report of this phenomenon in a plant species. Furthermore, we found that FISH analysis using the Arabidopsis-type telomere repeat sequence probe clarified and confirmed the new chromosome number and characterized the 45S rDNA structural organization.
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Hizume M, Yamasaki Y, Kan M. Fluorescent Chromosome Banding Patterns in Six Species of Abies, Pinaceae. CYTOLOGIA 2016. [DOI: 10.1508/cytologia.81.61] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Hizume M, N. Ohtaka K, Takeda KM, Fujii S, Yamasaki Y, Kondo K. Chromosome banding in the genus Pinus IV. Fluorescent banding patterns of chromosomes in eight taxa of haploxylone pines. ACTA ACUST UNITED AC 2016. [DOI: 10.3199/iscb.11.61] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Masahiro Hizume
- Faculty of Education, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Kozue N. Ohtaka
- Faculty of Education, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Kaoru M. Takeda
- Faculty of Education, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Satomi Fujii
- Faculty of Education, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Yoko Yamasaki
- Faculty of Education, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Katsuhiko Kondo
- Institute of Evolutionary Biology, 2-4-28 Kamiyouga, Setagaya-Ku, Tokyo 158-0098, Japan
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Shibata F, Matsusaki Y, Hizume M. A Comparative Analysis of Multi-Probe Fluorescence In Situ Hybridisation (FISH) Karyotypes in 26 Pinus Species (Pinaceae). CYTOLOGIA 2016. [DOI: 10.1508/cytologia.81.409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Pavia I, Carvalho A, Rocha L, Gaspar MJ, Lima-Brito J. Physical location of SSR regions and cytogenetic instabilities in Pinus sylvestris chromosomes revealed by ND-FISH. J Genet 2015; 93:567-71. [PMID: 25189261 DOI: 10.1007/s12041-014-0412-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Ivo Pavia
- Institute for Biotechnology and Bioengineering (IBB), Centre of Genomics and Biotechnology (CGB), University of Tras-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
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Hizume M. Fluorescent banding pattern in chromosomes of Tsuga forrestii and T. sieboldii, Pinaceae. ACTA ACUST UNITED AC 2015. [DOI: 10.3199/iscb.10.95] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Masahiro Hizume
- Faculty of Education, Ehime University, Matsuyama 790-8577, Japan
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Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA gene (rDNA) organisation. Heredity (Edinb) 2013; 111:23-33. [PMID: 23512008 PMCID: PMC3692318 DOI: 10.1038/hdy.2013.11] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In higher eukaryotes, the 5S rRNA genes occur in tandem units and are arranged either
separately (S-type arrangement) or linked to other repeated genes, in most cases to rDNA
locus encoding 18S–5.8S–26S genes (L-type arrangement). Here we used Southern
blot hybridisation, PCR and sequencing approaches to analyse genomic organisation of rRNA
genes in all large gymnosperm groups, including Coniferales, Ginkgoales, Gnetales and
Cycadales. The data are provided for 27 species (21 genera). The 5S units linked to the
35S rDNA units occur in some but not all Gnetales, Coniferales and in Ginkgo
(∼30% of the species analysed), while the remaining exhibit separate
organisation. The linked 5S rRNA genes may occur as single-copy insertions or as short
tandems embedded in the 26S–18S rDNA intergenic spacer (IGS). The 5S transcript may
be encoded by the same (Ginkgo, Ephedra) or opposite
(Podocarpus) DNA strand as the 18S–5.8S–26S genes. In addition,
pseudogenised 5S copies were also found in some IGS types. Both L- and S-type units have
been largely homogenised across the genomes. Phylogenetic relationships based on the
comparison of 5S coding sequences suggest that the 5S genes independently inserted IGS at
least three times in the course of gymnosperm evolution. Frequent transpositions and
rearrangements of basic units indicate relatively relaxed selection pressures imposed on
genomic organisation of 5S genes in plants.
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Nkongolo K, Mehes-Smith M. Karyotype evolution in the Pinaceae: implication with molecular phylogeny. Genome 2012. [DOI: 10.1139/g2012-061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The family Pinaceae is made up mostly of diploid species (2n = 24). Systematization of karyotype analysis was developed to make comparison of intra- and interspecific karyotypes among the Pinaceae more accurate and reliable. Considering all parameters, the genera Pseudotsuga and Pseudolarix have the “most derived” (or advanced) and asymmetric karyotypes in the Pinaceae, followed by Larix, Picea, Abies, and Cedrus. The genus Pinus was the “least derived” (or ancestral) of all the genera of the Pinaceae analyzed. Differences in karyotype formulae and asymmetry indices were found among species within the same genera, suggesting that structural changes may have contributed to the diversification of the genus. This review is a detailed analysis of comparative karyotyping based on similar parameters, including numeric data and cytogenetic information. Telomeric sequence repeats and rDNA distribution in the Pinaceae were surveyed. The role of transposition in rDNA chromosome distribution is analyzed. Cytogenetic implications of hybridization between related species are reported. Likewise, the relationships between molecular phylogenetic and karyotype evolution is discussed in light of several reports. Within many genera, chromosomal organization was conserved despite independent molecular divergence and adaptation through the evolutionary history of the species of the Pinaceae.
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Affiliation(s)
- K.K. Nkongolo
- Department of Biology and Biomolecular Science Program, Laurentian University, Sudbury, ON P3E 2C6, Canada
| | - M. Mehes-Smith
- Department of Biology and Biomolecular Science Program, Laurentian University, Sudbury, ON P3E 2C6, Canada
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Bogunić F, Siljak-Yakovlev S, Muratović E, Ballian D. Different karyotype patterns among allopatric Pinus nigra (Pinaceae) populations revealed by molecular cytogenetics. PLANT BIOLOGY (STUTTGART, GERMANY) 2011; 13:194-200. [PMID: 21143741 DOI: 10.1111/j.1438-8677.2010.00326.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
To examine variation and taxonomic recognition of Pinus nigra (European black pine) at the intraspecific level, chromosomal distribution of 5S and 18S-5.8S-26S rDNA loci revealed by fluorescent in situ hybridisation (FISH) and fluorochrome banding with chromomycin A(3) and DAPI were analysed among allopatric populations belonging to different subspecies. Despite prevalent opinion on predominantly conserved and homogenous conifer karyotypes, several patterns were observed. Surprisingly, interstitial 18S rDNA loci and DAPI heterochromatin staining after FISH showed variations in distribution and localisation. Three subspecies shared a pattern with nine 18S rDNA loci (ssp. nigra, pallasiana and laricio) while ssp. dalmatica and salzmannii had eight rDNA loci. DAPI banding displayed two patterns, one with a high number of signals (ssp. nigra, pallasiana and dalmatica) and the other with a lower number of signals (ssp. salzmannii and laricio). We conclude that our results cannot provide proof for either classification scheme for the P. nigra complex, but rather demonstrate the variability of different heterochromatin fractions at the intraspecific level.
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Affiliation(s)
- F Bogunić
- Faculty of Forestry, University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
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Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 2010; 11:420. [PMID: 20609256 PMCID: PMC2996948 DOI: 10.1186/1471-2164-11-420] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 07/07/2010] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND In today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24). The size and complexity of these genomes have prompted much speculation as to the feasibility of completing a conifer genome sequence. Conifer genomes are reputed to be highly repetitive, but there is little information available on the nature and identity of repetitive units in gymnosperms. The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda. RESULTS We present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS) sequences representing 7.5% of the genome. Computational annotation of ten BACs predicts three putative protein-coding genes and at least fifteen likely pseudogenes in nearly one megabase of sequence. We found three conifer-specific LTR retroelements in the BACs, and tentatively identified at least 15 others based on evidence from the distantly related angiosperms. Alignment of WGS sequences to the BACs indicates that 80% of BAC sequences have similar copies (> or = 75% nucleotide identity) elsewhere in the genome, but only 23% have identical copies (99% identity). The three most common repetitive elements in the genome were identified and, when combined, represent less than 5% of the genome. CONCLUSIONS This study indicates that the majority of repeats in the P. taeda genome are 'novel' and will therefore require additional BAC or genomic sequencing for accurate characterization. The pine genome contains a very large number of diverged and probably defunct repetitive elements. This study also provides new evidence that sequencing a pine genome using a WGS approach is a feasible goal.
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Affiliation(s)
- Allen Kovach
- Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Jill L Wegrzyn
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Genis Parra
- Genome Center, Division of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Carson Holt
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - George E Bruening
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Carol A Loopstra
- Department of Ecological Science and Management, Texas A&M University, College Station, TX 77843, USA
| | - James Hartigan
- Beckman Coulter Genomics (formerly Agencourt Biosciences), Danvers, MA 01923, USA
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Charles H Langley
- Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ian Korf
- Genome Center, Division of Biological Sciences, University of California, Davis, CA 95616, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Institute of Forest Genetics, USDA Forest Service, Davis, CA, 95616, USA
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12
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Begum R, Alam SS, Menzel G, Schmidt T. Comparative molecular cytogenetics of major repetitive sequence families of three Dendrobium species (Orchidaceae) from Bangladesh. ANNALS OF BOTANY 2009; 104:863-72. [PMID: 19635741 PMCID: PMC2749531 DOI: 10.1093/aob/mcp178] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 05/05/2009] [Accepted: 06/12/2009] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Dendrobium species show tremendous morphological diversity and have broad geographical distribution. As repetitive sequence analysis is a useful tool to investigate the evolution of chromosomes and genomes, the aim of the present study was the characterization of repetitive sequences from Dendrobium moschatum for comparative molecular and cytogenetic studies in the related species Dendrobium aphyllum, Dendrobium aggregatum and representatives from other orchid genera. METHODS In order to isolate highly repetitive sequences, a c(0)t-1 DNA plasmid library was established. Repeats were sequenced and used as probes for Southern hybridization. Sequence divergence was analysed using bioinformatic tools. Repetitive sequences were localized along orchid chromosomes by fluorescence in situ hybridization (FISH). KEY RESULTS Characterization of the c(0)t-1 library resulted in the detection of repetitive sequences including the (GA)(n) dinucleotide DmoO11, numerous Arabidopsis-like telomeric repeats and the highly amplified dispersed repeat DmoF14. The DmoF14 repeat is conserved in six Dendrobium species but diversified in representative species of three other orchid genera. FISH analyses showed the genome-wide distribution of DmoF14 in D. moschatum, D. aphyllum and D. aggregatum. Hybridization with the telomeric repeats demonstrated Arabidopsis-like telomeres at the chromosome ends of Dendrobium species. However, FISH using the telomeric probe revealed two pairs of chromosomes with strong intercalary signals in D. aphyllum. FISH showed the terminal position of 5S and 18S-5.8S-25S rRNA genes and a characteristic number of rDNA sites in the three Dendrobium species. CONCLUSIONS The repeated sequences isolated from D. moschatum c(0)t-1 DNA constitute major DNA families of the D. moschatum, D. aphyllum and D. aggregatum genomes with DmoF14 representing an ancient component of orchid genomes. Large intercalary telomere-like arrays suggest chromosomal rearrangements in D. aphyllum while the number and localization of rRNA genes as well as the species-specific distribution pattern of an abundant microsatellite reflect the genomic diversity of the three Dendrobium species.
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Affiliation(s)
- Rabeya Begum
- Department of Botany, University of Dhaka, Dhaka 1000, Bangladesh
| | | | - Gerhard Menzel
- Institute of Botany, Dresden University of Technology, D-01062 Dresden, Germany
| | - Thomas Schmidt
- Institute of Botany, Dresden University of Technology, D-01062 Dresden, Germany
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She CW, Liu JY, Song YC. CPD staining: an effective technique for detection of NORs and other GC-rich chromosomal regions in plants. Biotech Histochem 2009; 81:13-21. [PMID: 16760123 DOI: 10.1080/10520290600661414] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Mitotic chromosome spreads of 16 plant species belonging to six families were analyzed using an improved combined PI and DAPI (CPD) staining procedure. Fluorescence in situ hybridization (FISH) with 45S rDNA probe was conducted sequentially on the same spreads to evaluate the efficiency and sensitivity of the technique. Fluorochrome staining with chromomycin A3 (CMA)-DAPI also was conducted to clarify the properties of the sequences involved in the CPD banded regions. Our results revealed that all of the NORs (rDNA sites) in the species tested were efficiently shown as red bands by CPD staining, and the number and position of the bands corresponded precisely to those of the 45S rDNA FISH signals, indicating that the detection sensitivity of CPD staining is similar to that of FISH. In 10 of the species tested including Aegilops squarrosa, Allium sativum, Oryza sativum ssp. indica, Oryza officinalis, Pisum sativum, Secale cereale, Setaria italica, Sorghum vulgare, Vicia faba and Zea mays, CPD bands were exhibited exclusively in their NORs, while in other six species including Hordeum vulgare, Allium cepa, Psophocarpus tetragonolobus, Arabidopsis thaliana, Brassica oleracea var. capitata and Lycopersicon esculentum, CPD bands appeared in chromosomal regions other than their NORs. The CPD bands were in accordance with the CMA bands in all species tested, indicating GC-rich sequences in the CPD bands and that the improved CPD staining procedure is specific for GC-rich regions in plant genomes. Our investigation not only elucidated the banding mechanisms of CPD, but also demonstrated that the CPD staining technique, which may be preferable to CMA staining, is an effective tool for detecting NORs and other GC-rich chromosomal regions in plants.
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Affiliation(s)
- C W She
- Key Laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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Puizina J, Sviben T, Krajacić-Sokol I, Zoldos-Pećnik V, Siljak-Yakovlev S, Papes D, Besendorfer V. Cytogenetic and molecular characterization of the Abies alba genome and its relationship with other members of the Pinaceae. PLANT BIOLOGY (STUTTGART, GERMANY) 2008; 10:256-67. [PMID: 18304200 DOI: 10.1111/j.1438-8677.2007.00018.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Genome size, karyotype structure, heterochromatin distribution, position and number of ribosomal genes, as well as the ITS2 sequence of the internal transcribed spacer (ITS) were analysed in silver fir (Abies alba Mill.). The analysis also included characterization of the Arabidopsis-type of telomeric repeats in silver fir and in related species. The results were compared with results from other species of the Pinaceae, to evaluate phylogeny and chromosomal and molecular evolution in the Pinaceae. Integrated chromosomal data provided insights into chromosome and karyotype evolution in the Pinaceae. The evolutionary trend for GC-rich heterochromatic blocks seems to involve loss of blocks that are not associated with rDNA. Similarly, numerous large blocks of interstitial plant telomeric repeats that are typical for all analysed species of the genus Pinus were not observed in the evolutionarily younger genera, such as Abies, Picea and Larix. On the contrary, the majority of telomeric sequences in these three genera appeared confined to the chromosome ends. We confirmed the current position of Abies and Tsuga in subfamily Abietoideae and the position of Pinus in the subfamily Pinoideae based on ITS2 sequences. Pseudotsuga is placed together with Larix into the subfamily Laricoideae. We conclude that the current position of the genus Picea in the subfamily Abietoideae should be reconsidered and, possibly, the genus Picea should be reclassified as a separate subfamily, Piceoideae, as recently proposed.
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Affiliation(s)
- J Puizina
- Department of Biology, Faculty of Natural Sciences, Mathematics and Education, University of Split, Split, Croatia
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Deng HS, Zhang DM, Fu CX, Hong DY. Behavior of meiotic chromosomes in Pinus wallichiana, P. strobus and their hybrid and nrDNA localization in pollen mother cells of the hybrid by using FISH. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2008; 50:360-367. [PMID: 18713369 DOI: 10.1111/j.1744-7909.2007.00475.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The complete process of meiosis was investigated in Pinus wallichiana, P. strobus and their artificial hybrid (F1) using microsporocytes. It is revealed that there were slightly lower chiasma frequency, lower ring bivalent frequency, lower meiotic index and distinctly higher frequency of aberrance (chromosomal bridges, fragments or micronuclei) in pollen mother cells (PMCs) of the hybrid (F1) than those of the parental species, which showed a certain degree of differentiation between homologous chromosomes of the two parents. However, relatively higher frequency of ring bivalents and higher meiotic index in all the three entities indicate the great stability of genomes of parental species, and the differentiation of genomes between the two parents must have been slight. Total nineteen signal loci of 18S rDNA were observed in nine bivalents of the hybrid (F1), among which one bivalent bears two loci, while the others have only one. It is suggested that distinct differentiation at genetic level existed in homologous chromosomes of the two parental species, whereas only slight differentiation at karyotypic and genomic levels take place between the parent species.
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Affiliation(s)
- Hui-Sheng Deng
- College of Life Science, Zhejiang University, Hangzhou 310029, China
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Ribeiro T, Barão A, Viegas W, Morais-Cecíli L. Molecular cytogenetics of forest trees. Cytogenet Genome Res 2008; 120:220-7. [DOI: 10.1159/000121070] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2007] [Indexed: 01/03/2023] Open
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Islam-Faridi MN, Nelson CD, Kubisiak TL. Reference karyotype and cytomolecular map for loblolly pine (Pinus taeda L.). Genome 2007; 50:241-51. [PMID: 17546089 DOI: 10.1139/g06-153] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A reference karyotype is presented for loblolly pine (Pinus taeda L., subgenus Pinus, section Pinus, subsection Australes), based on fluorescent in situ hybridization (FISH), using 18S-28S rDNA, 5S rDNA, and an Arabidopsis-type telomere repeat sequence (A-type TRS). Well separated somatic chromosomes were prepared from colchicine-treated root meristems, using an enzymatic digestion technique. Statistical analyses performed on chromosome-arm lengths, centromeric indices, and interstitial rDNA and telomeric positions were based on observations from 6 well-separated metaphase cells from each of 3 unrelated trees. Statistically, 7 of the 12 loblolly pine chromosomes could be distinguished by their relative lengths. Centromeric indices were unable to distinguish additional chromosomes. However, the position and relative strength of the rDNA and telomeric sites made it possible to uniquely identify all of the chromosomes, providing a reference karyotype for use in comparative genome analyses. A dichotomous key was developed to aid in the identification of loblolly pine chromosomes and their comparison to chromosomes of other Pinus spp. A cytomolecular map was developed using the interstitial 18S-28S rDNA and A-type TRS signals. A total of 54 bins were assigned, ranging from 3 to 5 bins per chromosome. This is the first report of a chromosome-anchored physical map for a conifer that includes a dichotomous key for accurate and consistent identification of the P. taeda chromosomes.
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Affiliation(s)
- M Nurul Islam-Faridi
- Forest Tree Molecular Cytogenetics Laboratory, Southern Institute of Forest Genetics, Southern Research Station, USDA Forest Service, Texas A&M University, 2585-TAMU, College Station, TX 77843-2585, USA.
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Mondin M, Santos-Serejo JA, Aguiar-Perecin ML. Karyotype characterization of Crotalaria juncea (L.) by chromosome banding and physical mapping of 18S-5.8S-26S and 5S rRNA gene sites. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000100013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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CAI QING, ZHANG DAMING, LIU ZHANLIN, WANG XIAORU. Chromosomal localization of 5S and 18S rDNA in five species of subgenus Strobus and their implications for genome evolution of Pinus. ANNALS OF BOTANY 2006; 97:715-22. [PMID: 16481361 PMCID: PMC2803414 DOI: 10.1093/aob/mcl030] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Studying the genome structure of pines has been hindered by their large genomes and uniform karyotypes. Consequently our understanding of the genome organization and evolutionary changes in different groups of pines is extremely limited. However, techniques are now available that can surmount these difficulties. The purpose of this study was to exploit some of these techniques to characterize the genome differentiation between the two subgenera of Pinus: Pinus and Strobus. METHODS Double-probe fluorescence in-situ hybridization (FISH) was used to localize the 5S and 18S rDNA loci on chromosomes of five species from the subgenus Strobus: P. bungeana, P. koraiensis, P. armandii, P. wallichiana and P. strobus. * KEY RESULTS The rDNA FISH pattern varied considerably among the five species, with P. bungeana being the most distinct. By comparing the results obtained with those of previous rDNA FISH studies of members of the subgenus Pinus, several general features of rDNA loci distribution in the genus Pinus can be discerned: (a) species of subgenus Strobus generally have more rDNA loci than species of subgenus Pinus, correlating with their larger genomes in the subgenus Strobus; (b) there is a clear differentiation in 5S and 18S rDNA loci linkage patterns between the two subgenera; (c) variations in the rDNA FISH pattern correlate with phylogenetic relationships among species within the subgenus; (d) P. bungeana has fewer 18S rDNA sites than other pines investigated to date, but they give intense signals, and may reflect the primary distribution of the 18S-25S rDNA loci in the genus. CONCLUSIONS The stable differentiation in rDNA FISH pattern between the subgenera suggests that chromosomal rearrangements played a role in the splitting of the two subgenera, and transpositional events rather than major structural changes are likely responsible for the variable rDNA distribution patterns among species of the same subgenus with conserved karyotypes.
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Affiliation(s)
- QING CAI
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China and Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education, 710069 Xi'an, China
| | - DAMING ZHANG
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China and Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education, 710069 Xi'an, China
| | - ZHAN-LIN LIU
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China and Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education, 710069 Xi'an, China
| | - XIAO-RU WANG
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China and Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University, Ministry of Education, 710069 Xi'an, China
- For correspondence. E-mail
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Besendorfer V, Krajacić-Sokol I, Jelenić S, Puizina J, Mlinarec J, Sviben T, Papes D. Two classes of 5S rDNA unit arrays of the silver fir, Abies alba Mill.: structure, localization and evolution. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 110:730-41. [PMID: 15657739 DOI: 10.1007/s00122-004-1899-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2004] [Accepted: 12/01/2004] [Indexed: 05/09/2023]
Abstract
The structure and organization of the 5S ribosomal DNA units of the silver fir, Abies alba Mill., as well as their position in the chromosome complement were investigated. PCR amplification of the gene and nontranscribed spacer region, sequence analysis and Southern hybridization, using a homologous probe, detected DNA sequences of approximately 550 bp and 700 bp. Sequence analysis of the spacers revealed that the difference in length between the sequences occurred in the middle spacer region as a result of the amplification of a 75-bp sequence of the short unit class, which is organized in four 54- to 68-bp tandem repeats in the long spacer unit. The 5S rDNA transcribed region is 120 bp long and shows high sequence similarity with other gymnosperm species. The comparative analysis of 5' and 3' flanking sequences of 5S rRNA genes of silver fir and other gymnosperms indicates that A. alba spacer units have the same rate of evolution and are more closely related to Larix and Pseudotsuga than to Pinus and Picea. Southern hybridization and fluorescence in situ hybridization of metaphase chromosomes of A. alba suggest that the short and long spacer units are organized as separate tandem arrays at two chromosomal loci on chromosomes V and XI.
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Affiliation(s)
- Visnja Besendorfer
- Department of Molecular Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
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21
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Campbell CS, Wright WA, Cox M, Vining TF, Major CS, Arsenault MP. Nuclear ribosomal DNA internal transcribed spacer 1 (ITS1) in Picea (Pinaceae): sequence divergence and structure. Mol Phylogenet Evol 2005; 35:165-85. [PMID: 15737589 DOI: 10.1016/j.ympev.2004.11.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2004] [Revised: 10/17/2004] [Accepted: 11/07/2004] [Indexed: 11/29/2022]
Abstract
The nrDNA ITS1 of Picea is 2747-3271 bp, the longest known of all plants. We obtained 24 cloned ITS1 sequences from six individuals of Picea glehnii, Picea mariana, Picea orientalis, and Picea rubens. Mean sequence divergence within these individuals (0.018+/-0.009) is more than half that between the species (0.031+/-0.011) and may be maintained against concerted evolution by separation of Picea 18S-26S rDNA repeats on multiple chromosomes. Picea ITS1 contains three subrepeats with a motif (5'-GGCCACCCTAGTC) that is conserved across Pinaceae. Two subrepeats are tandem, remote from the third, and more closely related and significantly more similar to one another than either is to the third subrepeat. This correlation between similarity and proximity may be the result of subrepeat duplication or concerted evolution within rDNA repeats. In inferred secondary structures, subrepeats generally form long hairpins, with a portion of the Pinaceae conserved motif in the terminal loop, and tandem subrepeats pair with one another over most of their length. Coalescence of ITS1 sequences occurs in P. orientalis but not in the other species.
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22
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Nkongolo KK, Kim NS, Michael P. Detection and physical mapping of the 18S-5.8S-26S rDNA and the pKFJ660 probe with microsatellite sequences derived from the rice blast fungus (Magnaporthe grisea) in conifer species. Hereditas 2004; 140:70-8. [PMID: 15032949 DOI: 10.1111/j.1601-5223.2004.01691.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Sequences homologous to the pKFJ660 probe, a fragment of DNA derived from the rice blast fungus (Magnaporthe grisea) carrying TC/AG repeat microsatellite sequences and 30 bp direct repeats were identified in the genome of Picea (spruce) and Pinus (pine) species by fluorescence in situ hybridization (FISH) and slot blot analyses. Slot blot analysis using the pKFJ660 probe revealed hybridization signals with genomic DNAs from various pine and spruce species. Further analyses indicated that the copy number of the (AG)30 motif was higher than 5 x 10(4) per plant genome for all plant samples tested, but the copy number of the sequences homologous to the whole pKFJ660 probe varies considerably among the 25 plant species tested. In situ hybridization of metaphase chromosomes from Pinus resinosa, P. banksiana and P. strobus showed the presence of sequences homologous to this probe on several chromosomes in a dispersed pattern. Major signals were observed on a few chromosomes indicating that some of these sequences are clustered in specific genomic locations. The locations of these repeats were compared to those of 18S-5.8S-26S rDNA in pine species. Chromosomal distribution of 18S-5.8S-26S rDNA varied among the three pine species (P. resinosa, P. banksiana and P. strobus) studied. Ribosomal DNA (rDNA) sites were identified on 14 to 20 chromosomes in these pine species.
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Affiliation(s)
- K K Nkongolo
- Department of Biological Sciences, Laurentian University, Sudbury, Ontario, Canada.
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23
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Hajdera I, Siwinska D, Hasterok R, Maluszynska J. Molecular cytogenetic analysis of genome structure in Lupinus angustifolius and Lupinus cosentinii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 107:988-96. [PMID: 14523528 DOI: 10.1007/s00122-003-1303-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2002] [Accepted: 01/20/2003] [Indexed: 05/10/2023]
Abstract
Molecular cytogenetic analysis of Lupinus angustifolius and Lupinus cosentinii was performed using flow cytometry, fluorescence in situ hybridisation (FISH) and differential chromosome staining. Genome size was determined as 2.07 pg for L. angustifolius and 1.54 pg for L. cosentinii. Analysis of nuclear DNA amount in cells during plant development has shown endopolyploidisation in different organs. The highest level of endopolyploidy was in cotyledons and reached 32C in L. angustifolius and 64C in L. cosentinii. Both of the investigated Lupinus species belong to the polysomatic type of plants. Double FISH with rDNA probes provided chromosomal landmarks for 10 out of 40 chromosomes for L. angustifolius and 8 out of 32 chromosomes for L. cosentinii. In L. angustifolius, the number and localisation of 25S rDNA hybridisation signals precisely corresponded to the chromomycin A3 (CMA(+)) bands, while in L. cosentinii both 25S and 5S rDNA loci overlapped with CMA(+) bands. Silver staining revealed that only 45S rRNA genes located in secondary constriction regions were transcriptionally active. FISH with Arabidopsis-type telomeric arrays revealed the presence of signals at termini of all chromosomes. Despite the application of different DNA probes for FISH and different chromosome staining, a relatively small proportion of chromosomes in the Lupinus karyotypes can be distinguished. Identification of all chromosomes requires the use of more chromosome-specific markers.
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Affiliation(s)
- Inga Hajdera
- Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
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24
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Vischi M, Jurman I, Bianchi G, Morgante M. Karyotype of Norway spruce by multicolor FISH. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 107:591-597. [PMID: 12827248 DOI: 10.1007/s00122-003-1306-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2002] [Accepted: 02/17/2003] [Indexed: 05/24/2023]
Abstract
The chromosomes (2n = 2 x = 24) of Norway spruce are very large since their size reflects the huge amount of genomic DNA (2C = 30 x 10(9) bp). However, the identification of homologous pairs is hampered by their high degree of similarity at the morphological level. Data so far presented in the literature were not sufficient to solve all the ambiguities in chromosome identification. Several genomic Norway spruce DNA clones containing highly repetitive sequences have been identified and characterised in our laboratory. Three of them were selected for fluorescent in situ hybridization (FISH) experiments because of their strong signals and suitability for chromosome identification: PATR140 hybridized at the centromeric site of three chromosome pairs; PAF1 hybridized in six subtelomeric and two centromeric sites; 1PABCD6 co-localized with the subtelomeric sites identified by PAF1. The statistical analysis of microscopic measurements of chromosomes in combination with the FISH signals of these probes allowed the unambiguous construction of Norway spruce karyotype. We also compared the karyotype of Norway spruce with that of other spruce species to infer the number and kind of rearrangements that have occurred during the evolution of these species.
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Affiliation(s)
- M Vischi
- Dipartimento di Produzione Vegetale e Tecnologie Agrarie, Via delle Scienze 208, 33100 Udine, Italy.
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Komulainen P, Brown GR, Mikkonen M, Karhu A, García-Gil MR, O'Malley D, Lee B, Neale DB, Savolainen O. Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 107:667-678. [PMID: 12827250 DOI: 10.1007/s00122-003-1312-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2002] [Accepted: 03/10/2003] [Indexed: 05/24/2023]
Abstract
A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F(1) progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.
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Affiliation(s)
- P Komulainen
- Department of Biology, University of Oulu, FIN-90014 University of Oulu, Finland
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26
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WILLIAMS CLAIREG, JOYNER KARENL, AUCKLAND LISAD, JOHNSTON SPENCER, PRICE HJAMES. Genomic consequences of interspecific Pinus spp. hybridization. Biol J Linn Soc Lond 2002. [DOI: 10.1046/j.1095-8312.2002.00038.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Gernandt DS, Liston A, Piñero D. Variation in the nrDNA ITS of Pinus subsection Cembroides: implications for molecular systematic studies of pine species complexes. Mol Phylogenet Evol 2001; 21:449-67. [PMID: 11741386 DOI: 10.1006/mpev.2001.1026] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The pinyon pines (Pinus subsection Cembroides), distributed in semiarid regions of the western United States and Mexico, include a mixture of relictual and more recently evolved taxa. To investigate relationships among the pinyons, we screened and partially sequenced 3000-bp clones of the nuclear ribosomal DNA internal transcribed spacer (ITS) region for 16 taxa from subsect. Cembroides and nine representatives from four other subsections of subgenus Strobus. Restriction digests of clones reveal within-individual heterogeneity, suggesting that concerted evolution is operating slowly on the ITS in pine species. Two ITS clones were identified as pseudogenes. Tandem subrepeats in the ITS1 form stem loops comparable to those in other genera of Pinaceae and may be promoting recombination between rDNA repeats, resulting in ITS1 chimeras. Within the pinyon clade, phylogenetic structure is present, but different clones from the same (or different) individuals of a species are polyphyletic, indicating that coalescence of ITS copies within individual genomes predates evolutionary divergence in the group. At the level of subsection and above, the ITS region corresponds well with morphological and cpDNA evidence. Except for P. nelsonii, the pinyons are monophyletic, with both subsect. Cembroides and P. nelsonii forming a clade with the foxtail and bristlecone pines (subsect. Balfourianae) of western North America.
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Affiliation(s)
- D S Gernandt
- Departamento de Ecología Evolutiva, Universidad Nacional Autónoma de Mexico, Ciudad Universitaria, Codigo Postal, 04510, México
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Friesen N, Brandes A, Heslop-Harrison JS. Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers. Mol Biol Evol 2001; 18:1176-88. [PMID: 11420359 DOI: 10.1093/oxfordjournals.molbev.a003905] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We examined the diversity, evolution, and genomic organization of retroelements in a wide range of gymnosperms. In total, 165 fragments of the reverse transcriptase (RT) gene domain were sequenced from PCR products using newly designed primers for gypsy-like retrotransposons and well-known primers for copia-like retrotransposons; representatives of long interspersed nuclear element (LINE) retroposons were also found. Gypsy and copia-like retroelements are a major component of the gymnosperm genome, and in situ hybridization showed that individual element families were widespread across the chromosomes, consistent with dispersion and amplification via an RNA intermediate. Most of the retroelement families were widely distributed among the gymnosperms, including species with wide taxonomic separation from the Northern and Southern Hemispheres. When the gymnosperm sequences were analyzed together with retroelements from other species, the monophyletic origin of plant copia, gypsy, and LINE groups was well supported, with an additional clade including badnaviral and other, probably virus-related, plant sequences as well as animal and fungal gypsy elements. Plant retroelements showed high diversity within the phylogenetic trees of both copia and gypsy RT domains, with, for example, retroelement sequences from Arabidopsis thaliana being present in many supported groupings. No primary branches divided major taxonomic clades such as angiosperms, monocotyledons, gymnosperms, or conifers or (based on smaller samples) ferns, Gnetales, or Sphenopsida (Equisetum), suggesting that much of the existing diversity was present early in plant evolution, or perhaps that horizontal transfer of sequences has occurred. Within the phylogenetic trees for both gypsy and copia, two clearly monophyletic gymnosperm/conifer clades were revealed, providing evidence against recent horizontal transfer. The results put the evolution of the large and relatively conserved genome structure of gymnosperms into the context of the diversity of other groups of plants.
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Affiliation(s)
- N Friesen
- Botanical Garden of the University of Osnabrück, Osnabrück, Germany
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29
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Fourré JL. Somaclonal Variation and Genetic Molecular Markers in Woody Plants. MOLECULAR BIOLOGY OF WOODY PLANTS 2000. [DOI: 10.1007/978-94-017-2311-4_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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McGrath JM, Hickok LG. Multiple ribosomal RNA gene loci in the genome of the homosporous fern Ceratopteris richardii. ACTA ACUST UNITED AC 1999. [DOI: 10.1139/b99-093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genomes of homosporous ferns are largely uncharacterized, but they appear to differ from gymnosperms and angiosperms in key aspects, such as high chromosome numbers at the diploid level, and thus provide a unique perspective on plant genome structure and evolution. Using the model homosporous fern Ceratopteris richardii, loci encoding ribosomal RNA sequences (rDNA genes) were detected using fluorescent in situ hybridization. At least two major rDNA loci were visible in all cases, and six or more weakly hybridizing signals were observed in most cytological preparations. These results are consistent with models of homosporous fern evolution via cycles of polyploidy followed by gene silencing. They are also consistent with other models of fern genome evolution. With the exception of the weakly hybridizing signals, these data are similar to analogous reports of one or two major rDNA loci in diploid angiosperms. These results suggest that the gross morphology of rDNA loci are similar between diploid homosporous ferns and angiosperms, but that important clues to rDNA gene and chromosome evolution in homosporous ferns may reside in the analysis of their minor rDNA sequences.Key words: rDNA, in situ hybridization, homosporous ferns, evolution, gene silencing, polyploidy.
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Trontin JF, Grandemange C, Favre JM. Two highly divergent 5S rDNA unit size classes occur in composite tandem array in European larch (Larix decidua Mill.) and Japanese larch (Larix kaempferi (Lamb.) Carr.). Genome 1999. [DOI: 10.1139/g99-015] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 5S ribosomal DNA unit structure and organization have been investigated in Larix decidua and Larix kaempferi using selective amplification of gene and spacer, sequence analysis and homologous probe hybridization. Two highly divergent unit size classes of approximately 650 and 870 bp were detected in both species. Sequence analysis in Larix decidua revealed that length variations occur in the middle spacer region and are the result of duplications (in the long spacers) and considerable sequence heterogeneity. Conversely, the transcribed region is of uniform length (120 bp), and the nucleotide sequence of one Larix decidua clone is similar to that reported for other gymnosperms. Sequence comparison of the larch spacers with two other Pinaceae species (Pinus radiata and Picea glauca) showed that the 5' and 3' regions flanking the gene (40 and 60 bp, respectively) are quite conserved, suggesting a regulatory role. Moreover, a small element of about 70 bp located in the middle spacer region was found to be common to the larch long units and the six Pinus radiata spacer clones previously sequenced (64% sequence identity). The short and long unit size classes are mainly organized in composite tandem array(s) with evidence of extensive zones of strict alternation in both species. Mechanisms underlying this unusual association of divergent units in larch 5S rDNA arrays are discussed.Key words: 5S rRNA genes, spacer variations, cluster organization, sequence comparison, Gymnosperms.
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32
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Murray BG, Davies BJ. An improved method for preparing the chromosomes of pines and other gymnosperms. Biotech Histochem 1996; 71:115-7. [PMID: 8724435 DOI: 10.3109/10520299609117146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A simple technic is described to produce well spread gymnosperm chromosomes. Root tip meristems are digested with a pectinase:cellulase mixture to produce a cell suspension which then is squashed to yield flat, well spread chromosome complements that can be stained or used for in situ hybridization.
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Affiliation(s)
- B G Murray
- School of Biological Sciences, University of Auckland, New Zealand
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Abstract
Comprehensive genetic maps are now available for all of the world's important crop species. Data show a remarkable conservation of order of markers over family-wide taxonomic groupings and illuminate species relationships and mechanisms of genome evolution. Comparison of genetic and physical maps has revealed differences in genetic distance throughout genomes with implications for genome organization, gene isolation and transformation.
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Affiliation(s)
- T Schwarzacher
- Department of Cereal Research, John Innes Centre, Coney, Norwich, UK
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