Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae)

Hamon, Perla; Duroy, Pierre‐Olivier; Tranchant‐Dubreuil, Christine; Costa, Paulo Mafra D’Almeida; Duret, Caroline; Razafinarivo, Norosoa J.; Couturon, Emmanuel; Hamon, Serge; Kochko, Alexandre de; Poncet, Valérie; Guyot, Romain

doi:10.1007/s00438-011-0617-0

Cited by 22 publications

(25 citation statements)

References 49 publications

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“…In addition, C. salvatrix and P. travancorensis beans share the same characteristic, they are practically caffeine-free (Campa et al, 2005;Santa Ram et al, 2005). Recently, two Ty1-copia-like retrotransposons (Nana and Divo) were isolated from some coffee species and from P. ebracteolatus by Hamon et al (2011), which strengthen the greater closeness of both genera.…”

Section: Discussionmentioning

confidence: 90%

A Karyological Study in Some Species of Coffea L. and in the Closest Relative Psilanthus travancorensis (Wight & Arn.) J.-F. Leroy

Pierozzi

Borghi

Silvarolla

2012

Not Bot Hort Agrobot Cluj

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Chromosome characterization were carried out in Coffea kapakata A. Chev (Bridson), C. racemosa Lour., C. salvatrix Swynn. & Philipson and in Psilanthus travancorensis (Wight & Arn.) J.-F. Leroy (2n=22) by employing the conventional acetic orcein technique as well as by C-and NOR-banding aiming further comparative studies. Although C. canephora and C. dewevrei have already been studied and depict a C-band karyotype, they have also been included for further comparisons, since NOR-banding and some other morphometric data have not been obtained yet. However, there were observed some differences among the species regarding chromosomal morphometry. The karyotype formula obtained was 3m+6sm+2sm s for C. salvatrix and P. travancorensis, 1M +2m + 6sm + 2sm s for C. kapakata and 2M +1m + 6sm + 2sm s for C. racemosa. All species displayed a moderate karyotype asymmetry and according to Stebbins system, C. canephora, C. dewevrei, C. kapakata and C. racemosa were classified as 3B while C. salvatrix and P. travancorensis were classified as 2A. Among the four indices used to assess karyotype asymmetry, Paszko AI index along with Stebbins were best suited to individualize the species. C-bands were preferentially situated at a pericentromeric/centromeric position. Two pairs of chromosomes, with secondary constriction and satellite segments, were observed in all the species following acetic orcein staining. C. racemosa and C. salvatrix showed NOR-band in both pairs, while only one chromosome pair carrying NOR-band was seen in C. canephora, C. dewevrei, C. kapakata and P. travancorensis. Data on chromosome morphometry, asymmetry indices and NOR-banding were suitable for the characterization of the species.

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Section: Discussionmentioning

confidence: 90%

A Karyological Study in Some Species of Coffea L. and in the Closest Relative Psilanthus travancorensis (Wight & Arn.) J.-F. Leroy

Pierozzi

Borghi

Silvarolla

2012

Not Bot Hort Agrobot Cluj

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“…For example, in vegetatively propagated grape clones, TE insertional polymorphisms constitute the largest class of mutations [10]. Genetic diversity associated with TE polymorphisms has been commonly explored in plant varieties and species such as pepper and tomato [2, 11], barley [12], strawberry [13], coffee [14], blue agave [15] and cashew [16]. …”

Section: Introductionmentioning

confidence: 99%

Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions

et al. 2016

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BackgroundInitial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity. Flax, where accessions are bred mainly for seed nutritional properties or for fibers, constitutes a good model for studying the relationship of transpositional activity with diversification and breeding. In this study, we estimated copy number and used a type of transposon display known as Sequence-Specific Amplification Polymorphisms (SSAPs), to characterize six families of Ty1-copia elements across 14 flax accessions. Polymorphic insertion sites were sequenced to find insertions that could potentially alter gene expression, and a preliminary test was performed with selected genes bearing transposable element (TE) insertions.ResultsQuantification of six families of Ty1-copia elements indicated different abundances among TE families and between flax accessions, which suggested diverse transpositional histories. SSAPs showed a high level of polymorphism in most of the evaluated retrotransposon families, with a trend towards higher levels of polymorphism in low-copy number families. Ty1-copia insertion polymorphisms among cultivars allowed a general distinction between oil and fiber types, and between spring and winter types, demonstrating their utility in diversity studies. Characterization of polymorphic insertions revealed an overwhelming association with genes, with insertions disrupting exons, introns or within 1 kb of coding regions. A preliminary test on the potential transcriptional disruption by TEs of four selected genes evaluated in three different tissues, showed one case of significant impact of the insertion on gene expression.ConclusionsWe demonstrated that specific Ty1-copia families have been active since breeding commenced in flax. The retrotransposon-derived polymorphism can be used to separate flax types, and the close association of many insertions with genes defines a good source of potential mutations that could be associated with phenotypic changes, resulting in diversification processes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3337-3) contains supplementary material, which is available to authorized users.

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“…Few of these genetic elements have been described in Coffea. Hamon et al (2011) isolated two Ty1-copialike retrotransposons (Nana and Divo) from BAC libraries of Coffea canephora. These two retrotransposons were found to be common in species of Coffea and in Psilanthus ebracteolatus Hiern but with different activity rates, which has permitted the differentiation of species and accessions as well.…”

Section: Introductionmentioning

confidence: 99%

FISH using a gag-like fragment probe reveals a common Ty3-gypsy-like retrotransposon in genome of Coffea species

Yuyama

Pereira

Santos

et al. 2012

Genome

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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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Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae)

Cited by 22 publications

References 49 publications

A Karyological Study in Some Species of Coffea L. and in the Closest Relative Psilanthus travancorensis (Wight & Arn.) J.-F. Leroy

A Karyological Study in Some Species of Coffea L. and in the Closest Relative Psilanthus travancorensis (Wight & Arn.) J.-F. Leroy

Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions

FISH using a gag-like fragment probe reveals a common Ty3-gypsy-like retrotransposon in genome of Coffea species

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