The Tvv1 retrotransposon family is conserved between plant genomes separated by over 100 million years

Cedric Moisy , Alan H. Schulman, Ruslan Kalendar, Jan P. Buchmann, Frédérique Pelsy

Research output: Contribution to journalArticleScientificpeer-review

Abstract

Retrotransposons are ubiquitous throughout the genomes of the vascular plants, but individual retrotransposon families tend to be confined to the level of plant genus or at most family. This restricts the general applicability of a family as molecular markers. Here, we characterize a new plant retrotransposon named Tvv1_Sdem, a member of the Copia superfamily of LTR retrotransposons, from the genome of the wild potato Solanum demissum. Comparative analyses based on structure and sequence showed a high level of similarity of Tvv1_Sdem with Tvv1-VB, a retrotransposon previously described in the grapevine genome Vitis vinifera. Extending the analysis to other species by in silico and in vitro approaches revealed the presence of Tvv1 family members in potato, tomato, and poplar genomes, and led to the identification of full-length copies of Tvv1 in these species. We were also able to identify polymorphism in UTL sequences between Tvv1_Sdem copies from wild and cultivated potatoes that are useful as molecular markers. Combining different approaches, our results suggest that the Tvv1 family of retrotransposons has a monophyletic origin and has been maintained in both the rosids and the asterids, the major clades of dicotyledonous plants, since their divergence about 100 MYA. To our knowledge, Tvv1 represents an unusual plant retrotransposon metapopulation comprising highly similar members disjointedly dispersed among very distant species. The twin features of Tvv1 presence in evolutionarily distant genomes and the diversity of its UTL region in each species make it useful as a source of robust molecular markers for diversity studies and breeding.

Original languageEnglish
JournalTheoretical and Applied Genetics
Volume127
Issue number5
Pages (from-to)1223-1235
Number of pages13
ISSN0040-5752
DOIs
Publication statusPublished - 1 May 2014
MoE publication typeA1 Journal article-refereed

Fields of Science

  • 1184 Genetics, developmental biology, physiology

Cite this

@article{8649b162112447f191f48a124eeea4b4,
title = "The Tvv1 retrotransposon family is conserved between plant genomes separated by over 100 million years",
abstract = "Retrotransposons are ubiquitous throughout the genomes of the vascular plants, but individual retrotransposon families tend to be confined to the level of plant genus or at most family. This restricts the general applicability of a family as molecular markers. Here, we characterize a new plant retrotransposon named Tvv1_Sdem, a member of the Copia superfamily of LTR retrotransposons, from the genome of the wild potato Solanum demissum. Comparative analyses based on structure and sequence showed a high level of similarity of Tvv1_Sdem with Tvv1-VB, a retrotransposon previously described in the grapevine genome Vitis vinifera. Extending the analysis to other species by in silico and in vitro approaches revealed the presence of Tvv1 family members in potato, tomato, and poplar genomes, and led to the identification of full-length copies of Tvv1 in these species. We were also able to identify polymorphism in UTL sequences between Tvv1_Sdem copies from wild and cultivated potatoes that are useful as molecular markers. Combining different approaches, our results suggest that the Tvv1 family of retrotransposons has a monophyletic origin and has been maintained in both the rosids and the asterids, the major clades of dicotyledonous plants, since their divergence about 100 MYA. To our knowledge, Tvv1 represents an unusual plant retrotransposon metapopulation comprising highly similar members disjointedly dispersed among very distant species. The twin features of Tvv1 presence in evolutionarily distant genomes and the diversity of its UTL region in each species make it useful as a source of robust molecular markers for diversity studies and breeding.",
keywords = "1184 Genetics, developmental biology, physiology",
author = "Cedric Moisy and Schulman, {Alan H.} and Ruslan Kalendar and Buchmann, {Jan P.} and Fr{\'e}d{\'e}rique Pelsy",
year = "2014",
month = "5",
day = "1",
doi = "10.1007/s00122-014-2293-z",
language = "English",
volume = "127",
pages = "1223--1235",
journal = "Theoretical and Applied Genetics",
issn = "0040-5752",
publisher = "Springer",
number = "5",

}

The Tvv1 retrotransposon family is conserved between plant genomes separated by over 100 million years. / Moisy , Cedric; Schulman, Alan H.; Kalendar, Ruslan; Buchmann, Jan P.; Pelsy, Frédérique .

In: Theoretical and Applied Genetics, Vol. 127, No. 5, 01.05.2014, p. 1223-1235.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - The Tvv1 retrotransposon family is conserved between plant genomes separated by over 100 million years

AU - Moisy , Cedric

AU - Schulman, Alan H.

AU - Kalendar, Ruslan

AU - Buchmann, Jan P.

AU - Pelsy, Frédérique

PY - 2014/5/1

Y1 - 2014/5/1

N2 - Retrotransposons are ubiquitous throughout the genomes of the vascular plants, but individual retrotransposon families tend to be confined to the level of plant genus or at most family. This restricts the general applicability of a family as molecular markers. Here, we characterize a new plant retrotransposon named Tvv1_Sdem, a member of the Copia superfamily of LTR retrotransposons, from the genome of the wild potato Solanum demissum. Comparative analyses based on structure and sequence showed a high level of similarity of Tvv1_Sdem with Tvv1-VB, a retrotransposon previously described in the grapevine genome Vitis vinifera. Extending the analysis to other species by in silico and in vitro approaches revealed the presence of Tvv1 family members in potato, tomato, and poplar genomes, and led to the identification of full-length copies of Tvv1 in these species. We were also able to identify polymorphism in UTL sequences between Tvv1_Sdem copies from wild and cultivated potatoes that are useful as molecular markers. Combining different approaches, our results suggest that the Tvv1 family of retrotransposons has a monophyletic origin and has been maintained in both the rosids and the asterids, the major clades of dicotyledonous plants, since their divergence about 100 MYA. To our knowledge, Tvv1 represents an unusual plant retrotransposon metapopulation comprising highly similar members disjointedly dispersed among very distant species. The twin features of Tvv1 presence in evolutionarily distant genomes and the diversity of its UTL region in each species make it useful as a source of robust molecular markers for diversity studies and breeding.

AB - Retrotransposons are ubiquitous throughout the genomes of the vascular plants, but individual retrotransposon families tend to be confined to the level of plant genus or at most family. This restricts the general applicability of a family as molecular markers. Here, we characterize a new plant retrotransposon named Tvv1_Sdem, a member of the Copia superfamily of LTR retrotransposons, from the genome of the wild potato Solanum demissum. Comparative analyses based on structure and sequence showed a high level of similarity of Tvv1_Sdem with Tvv1-VB, a retrotransposon previously described in the grapevine genome Vitis vinifera. Extending the analysis to other species by in silico and in vitro approaches revealed the presence of Tvv1 family members in potato, tomato, and poplar genomes, and led to the identification of full-length copies of Tvv1 in these species. We were also able to identify polymorphism in UTL sequences between Tvv1_Sdem copies from wild and cultivated potatoes that are useful as molecular markers. Combining different approaches, our results suggest that the Tvv1 family of retrotransposons has a monophyletic origin and has been maintained in both the rosids and the asterids, the major clades of dicotyledonous plants, since their divergence about 100 MYA. To our knowledge, Tvv1 represents an unusual plant retrotransposon metapopulation comprising highly similar members disjointedly dispersed among very distant species. The twin features of Tvv1 presence in evolutionarily distant genomes and the diversity of its UTL region in each species make it useful as a source of robust molecular markers for diversity studies and breeding.

KW - 1184 Genetics, developmental biology, physiology

U2 - 10.1007/s00122-014-2293-z

DO - 10.1007/s00122-014-2293-z

M3 - Article

VL - 127

SP - 1223

EP - 1235

JO - Theoretical and Applied Genetics

JF - Theoretical and Applied Genetics

SN - 0040-5752

IS - 5

ER -