Yin Hao, Wu Xiao, Shi Dongqing, Chen Yangyang, Qi Kaijie, Ma Zhengqiang, Zhang Shaoling
Center of Pear Engineering Technology Research, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
Mob DNA. 2017 Oct 27;8:14. doi: 10.1186/s13100-017-0098-8. eCollection 2017.
Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes. Common LTR-RTs contain the palindromic dinucleotide 5'-'TG'-'CA'-3' motif at the ends. Thus, further analyses of non-canonical LTR-RTs with non-palindromic motifs will enhance our understanding of their structures and evolutionary history.
Here, we report two new LTR-RT subfamilies ( and ) with atypical dinucleotide ends of 5'-'TG'-'TT'-3', and 5'-'AA'-'CA'-3' in pear, apple, peach and mei. In total, 91 intact LTR-RTs were identified and classified into four and four families. A structural annotation analysis showed that the four families, together with and , belong to the -like superfamily, whereas and appeared to be TRIM elements. The average amplification time frames for the eight families ranged from 0.05 to 2.32 million years. Phylogenetics coupled with sequence analyses revealed that the elements of peach were horizontally transferred from apple. In addition, 32 elements from two and three families had detectable transcriptional activation, and a qRT-PCR analysis indicated that their expression levels varied dramatically in different species, organs and stress treatments.
Two novel LTR-RT subfamilies that terminated with non-palindromic dinucleotides at the ends of their LTRs were identified in four Rosaceae species, and a deep analysis showed their recent activity, horizontal transfer and varied transcriptional levels in different species, organs and stress treatments. This work enhances our understanding of the structural variation and evolutionary history of LTR-RTs in plants and also provides a valuable resource for future investigations of LTR-RTs having specific structures in other species.
长末端重复逆转座子（LTR-RTs）是植物基因组的主要组成部分。常见的LTR-RTs在末端含有回文二核苷酸5'-'TG'-'CA'-3'基序。因此，对具有非回文基序的非经典LTR-RTs进行进一步分析将增进我们对其结构和进化历史的理解。
在此，我们报道了梨、苹果、桃和梅中两个新的LTR-RT亚家族（ 和 ），其LTR末端具有非典型二核苷酸末端5'-'TG'-'TT'-3'和5'-'AA'-'CA'-3'。总共鉴定出91个完整的LTR-RTs，并将其分为四个 和四个 家族。结构注释分析表明，四个 家族与 和 属于 -样超家族，而 和 似乎是TRIM元件。八个家族的平均扩增时间范围为0.05至232万年。系统发育分析结合序列分析表明，桃的 元件是从苹果水平转移而来的。此外，来自两个 和三个 家族的32个元件具有可检测的转录激活，qRT-PCR分析表明它们在不同物种、器官和胁迫处理中的表达水平差异很大。
在四个蔷薇科物种中鉴定出两个新的LTR-RT亚家族，其LTR末端以非回文二核苷酸终止，深入分析表明它们具有近期活性、水平转移以及在不同物种、器官和胁迫处理中不同的转录水平。这项工作增进了我们对植物中LTR-RTs结构变异和进化历史的理解，也为未来研究其他物种中具有特定结构的LTR-RTs提供了宝贵资源。
