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Heitkam T, Schulte L, Weber B, Liedtke S, Breitenbach S, Kögler A, Morgenstern K, Brückner M, Tröber U, Wolf H, Krabel D, Schmidt T. Comparative Repeat Profiling of Two Closely Related Conifers ( Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs. Front Genet 2021; 12:683668. [PMID: 34322154 PMCID: PMC8312256 DOI: 10.3389/fgene.2021.683668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/25/2021] [Indexed: 12/26/2022] Open
Abstract
In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 giga base pairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers' accumulative genome evolution mode. For this, we applied low-coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs' organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.
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Affiliation(s)
- Tony Heitkam
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Luise Schulte
- Institute of Botany, Technische Universität Dresden, Dresden, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Beatrice Weber
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Susan Liedtke
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Sarah Breitenbach
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Anja Kögler
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Kristin Morgenstern
- Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, Tharandt, Germany
| | | | - Ute Tröber
- Staatsbetrieb Sachsenforst, Pirna, Germany
| | - Heino Wolf
- Staatsbetrieb Sachsenforst, Pirna, Germany
| | - Doris Krabel
- Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, Tharandt, Germany
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
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Yuyama PM, Pereira LFP, dos Santos TB, Sera T, Vilas-Boas LA, Lopes FR, Carareto CMA, Vanzela ALL. FISH using a gag-like fragment probe reveals a common Ty3-gypsy-like retrotransposon in genome of Coffea species. Genome 2012; 55:825-33. [PMID: 23231601 DOI: 10.1139/gen-2012-0081] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The genus Coffea possesses about 100 species, and the most economically important are Coffea canephora and Coffea arabica. The latter is predominantly self-compatible with 2n = 4x = 44, while the others of the genus are diploid with 2n = 2x = 22 and mostly self-incompatible. Studies using molecular markers have been useful to detect differences between genomes in Coffea; however, molecular and cytogenetic studies have produced only limited information on the karyotypes organization. We used DOP-PCR to isolate repetitive elements from genome of Coffea arabica var. typica. The pCa06 clone, containing a fragment of 775 bp length, was characterized by sequencing and used as a probe in chromosomes of C. arabica and six other species: C. canephora, Coffea eugenioides, Coffea kapakata, Coffea liberica var. dewevrei, Coffea racemosa, and Coffea stenophylla. This insert shows similarities with a gag protein of the Ty3-gypsy-like super-family. Dot blot and FISH analyses demonstrated that pCa06 is differentially accumulated between species and chromosomes. Signals appeared scattered and clustered on the chromosomes and were also associated with heterochromatic regions. While the literature shows that there is a high karyotype similarity between Coffea species, our results point out differences in the accumulation and dispersion of this Ty3-gypsy-like retrotransposon during karyotype differentiation of Coffea.
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Affiliation(s)
- Priscila Mary Yuyama
- Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Caixa Postal 6001, CEP 86051-990 Londrina, PR, Brazil
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