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首页> 外文期刊>Journal of Nematology, with Annual of Applied Nematology >Secondary structure models of D2-D3 expansion segments of 28S rRNA for Hoplolaiminae species
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Secondary structure models of D2-D3 expansion segments of 28S rRNA for Hoplolaiminae species

机译：Hoplolaiminae物种的28S rRNA的D2-D3扩展片段的二级结构模型

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The D2-D3 expansion segments of the 28S ribosomal RNA (rRNA) were sequenced and compared to predict secondary structures for Hoplolaiminae species based on free energy minimization and comparative sequence analysis. The free energy based prediction method provides putative stem regions within primary structure and these base pairings in stems were confirmed manually by compensatory base changes among closely and distantly related species. Sequence differences ranged from identical between Hoplolaimuscolumbus and H. seinhorsti to 20.8% between Scutellonema brachyurum and H. concaudajuveneus. The comparative sequence analysis and energy minimization method yielded 9 stems in the D2 and 6 stems in the D3 which showed complete or partial compensatory base changes. At least 75% of nucleotides in the D2 and 68% of nucleotides in the D3 were related with formation of base pairings to maintain secondary structure. GC contents in stems ranged from 61 to 73% for the D2 and from 64 to 71% for the D3 region.These ranges are higher than G-C contents in loops which ranged from 37 to 48% in the D2 and 33-45% in the D3. In stems, G-C/C-G base pairings were the most common in the D2 and the D3 and also non-canonical base pairs including A centre dot A and U centre dot U, C centre dot U/U centre dot C, and G centre dot A/A centre dot G occurred in stems. The predicted secondary model and new sequence alignment based on predicted secondary structures for the D2 and D3 expansion segments provide useful informationto assign positional nucleotide homology and reconstruction of more reliable phylogenetic trees.
机译：对28S核糖体RNA（rRNA）的D2-D3扩增片段进行测序，并进行比较，以基于自由能最小化和比较序列分析预测Hoplolaiminae物种的二级结构。基于自由能的预测方法在一级结构中提供了假定的茎区域，并且茎中的这些碱基配对已通过近亲和远缘物种之间的补偿性碱基变化手动确认。序列差异范围从Hoplolaimuscolumbus和H. seinhorsti之间相同，到Scutellonema brachyurum和H. concaudajuveneus之间为20.8％。比较序列分析和能量最小化方法在D2中产生了9个茎，在D3中产生了6个茎，这些茎表现出完全或部分补偿性碱基变化。 D2中至少75％的核苷酸和D3中68％的核苷酸与碱基配对的形成有关，以维持二级结构。 D2茎的GC含量从61％到73％，D3区域的茎的GC含量从64％到71％不等，高于D2茎的GC含量从37％到48％，D2区域的33-45％不等。 D3。在茎中，GC / CG碱基对是D2和D3中最常见的，也是非规范碱基对，包括A中心点A和U中心点U，C中心点U / U中心点C和G中心点A / A中心点G出现在茎中。预测的二级模型和基于D2和D3扩展段的预测二级结构的新序列比对提供有用的信息，以分配位置核苷酸同源性和更可靠的系统树的重建。

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