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Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data.
G3 (Bethesda) 2016; 6(8):2299-308G

Abstract

The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny.

Authors+Show Affiliations

Division of Biology, Kansas State University, Manhattan, Kansas 66506 htetre@ksu.edu.Division of Biology, Kansas State University, Manhattan, Kansas 66506.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

27233667

Citation

Tetreault, Hannah M., and Mark C. Ungerer. "Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred From Next-Generation Sequence Data." G3 (Bethesda, Md.), vol. 6, no. 8, 2016, pp. 2299-308.
Tetreault HM, Ungerer MC. Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data. G3 (Bethesda). 2016;6(8):2299-308.
Tetreault, H. M., & Ungerer, M. C. (2016). Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data. G3 (Bethesda, Md.), 6(8), pp. 2299-308. doi:10.1534/g3.116.029082.
Tetreault HM, Ungerer MC. Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred From Next-Generation Sequence Data. G3 (Bethesda). 2016 08 9;6(8):2299-308. PubMed PMID: 27233667.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data. AU - Tetreault,Hannah M, AU - Ungerer,Mark C, Y1 - 2016/08/09/ PY - 2016/5/29/entrez PY - 2016/5/29/pubmed PY - 2017/11/29/medline KW - Helianthus KW - Helianthus agrestis KW - LTR retrotransposons KW - genome size evolution KW - transposable elements SP - 2299 EP - 308 JF - G3 (Bethesda, Md.) JO - G3 (Bethesda) VL - 6 IS - 8 N2 - The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny. SN - 2160-1836 UR - https://www.unboundmedicine.com/medline/citation/27233667/Long_Terminal_Repeat_Retrotransposon_Content_in_Eight_Diploid_Sunflower_Species_Inferred_from_Next_Generation_Sequence_Data_ L2 - http://www.g3journal.org/cgi/pmidlookup?view=long&pmid=27233667 DB - PRIME DP - Unbound Medicine ER -