biy-39-5-11-1501-77.pdf (4.15 MB)
Identification and evolutionary genomics of novel LTR retrotransposons in Brassica
journal contribution
posted on 2016-01-15, 16:40 authored by Faisal Nouroz, Shumaila Noreen, John Seymour Heslop-HarrisonRetrotransposons (REs) are the most abundant and diverse elements identified from eukaryotic genomes. Using computational
and molecular methods, 262 intact LTR retrotransposons were identified from Brassica genomes by dot plot analysis and data mining.
The Copia superfamily was dominant (206 elements) over Gypsy (56), with estimated intact copies of ~1596 Copia and 540 Gypsy
and ~7540 Copia and 780 Gypsy from Brassica rapa and Brassica oleracea whole genomes, respectively. Canonical Copia and Gypsy
gag-pol polyprotein organizations were observed in most elements with a few displaying 1–3 additional or internally deleted domains.
The PBS and PPT motifs were identified with tRNA complementary to tRNAMet or, rarely, other tRNA types. PCR amplification of
RT regions revealed their abundance and distribution among A-, B-, and C-genome Brassicas indicating a common ancestor. The
evolutionary relationship of Brassica REs resolved them into superfamily-specific (Copia/Gypsy) lineages. The phylogenetic analysis
of 130 Brassica Copia clustered them into 2 clades and 10 sub-clades of 18 families; Gypsy elements clustered into 2 clades. The results
enabled identification and understanding of the structure and nature of full-length REs and their derivatives in Brassica. The markers
derived here will be useful for examining chromosome and genome evolution in Brassica.
Funding
This work was supported by Hazara University Mansehra, Pakistan, and the Higher Education Commission of Pakistan. We are thankful to them for the funding and support of this work. We thank Dr Graham Teakle and Dr Guy Barker from Warwick University, UK, and Dr Xianhong Ge from University of Wuhan, China, for supplying seeds or DNA from the Brassica accessions.
History
Citation
Turkish Journal of Biology, 2015, 39 (5), pp. 740-+ (20)Author affiliation
/Organisation/COLLEGE OF MEDICINE, BIOLOGICAL SCIENCES AND PSYCHOLOGY/MBSP Non-Medical Departments/Department of GeneticsVersion
- VoR (Version of Record)
Published in
Turkish Journal of BiologyPublisher
TÜBİTAK Scientific and Technical Research Council of Turkeyissn
1300-0152eissn
1303-6092Acceptance date
2015-03-23Available date
2016-01-15Publisher DOI
Publisher version
http://journals.tubitak.gov.tr/biology/issues/biy-15-39-5/biy-39-5-11-1501-77.pdfLanguage
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Science & TechnologyLife Sciences & BiomedicineBiologyLife Sciences & Biomedicine - Other TopicsLTR retrotransposonsBrassicaCopiaGypsyevolutionary relationshipRTAP markersTY1-COPIA GROUP RETROTRANSPOSONSTERMINAL REPEAT RETROTRANSPOSONSWIDE COMPARATIVE-ANALYSISTRANSPOSABLE ELEMENTSGENETIC DIVERSITYPLANT RETROTRANSPOSONSARABIDOPSISSEQUENCESFAMILIESL.
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