التفاصيل البيبلوغرافية
| العنوان: |
Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L. |
| المؤلفون: |
Alipour, Atefeh, Tsuchimoto, Suguru, Sakai, Hiroe, Ohmido, Nobuko, Fukui, Kiichi |
| بيانات النشر: |
BioMed Central Ltd. |
| سنة النشر: |
2013 |
| المجموعة: |
BioMed Central |
| مصطلحات موضوعية: |
Jatropha curcas L, copia-type retrotransposon, Retrotransposon-based insertion polymorphism (RBIP), Fluorescence in situ hybridization (FISH) |
| الوصف: |
Background Recently, Jatropha curcas L. has attracted worldwide attention for its potential as a source of biodiesel. However, most DNA markers have demonstrated high levels of genetic similarity among and within jatropha populations around the globe. Despite promising features of copia -type retrotransposons as ideal genetic tools for gene tagging, mutagenesis, and marker-assisted selection, they have not been characterized in the jatropha genome yet. Here, we examined the diversity, evolution, and genome-wide organization of copia -type retrotransposons in the Asian, African, and Mesoamerican accessions of jatropha, then introduced a retrotransposon-based marker for this biofuel crop. Results In total, 157 PCR fragments that were amplified using the degenerate primers for the reverse transcriptase (RT) domain of copia -type retroelements were sequenced and aligned to construct the neighbor-joining tree. Phylogenetic analysis demonstrated that isolated copia RT sequences were classified into ten families, which were then grouped into three lineages. An in-depth study of the jatropha genome for the RT sequences of each family led to the characterization of full consensus sequences of the jatropha copia -type families. Estimated copy numbers of target sequences were largely different among families, as was presence of genes within 5 kb flanking regions for each family. Five copia -type families were as appealing candidates for the development of DNA marker systems. A candidate marker from family Jc7 was particularly capable of detecting genetic variation among different jatropha accessions. Fluorescence in situ hybridization (FISH) to metaphase chromosomes reveals that copia -type retrotransposons are scattered across chromosomes mainly located in the distal part regions. Conclusion This is the first report on genome-wide analysis and the cytogenetic mapping of copia -type retrotransposons of jatropha, leading to the discovery of families bearing high potential as DNA markers. Distinct dynamics of ... |
| نوع الوثيقة: |
report |
| اللغة: |
English |
| Relation: |
http://www.biotechnologyforbiofuels.com/content/6/1/129 |
| الاتاحة: |
http://www.biotechnologyforbiofuels.com/content/6/1/129 |
| Rights: |
Copyright 2013 Alipour et al.; licensee BioMed Central Ltd. |
| رقم الانضمام: |
edsbas.7E12434A |
| قاعدة البيانات: |
BASE |