PMID- 29046683 OWN - NLM STAT- PubMed-not-MEDLINE LR - 20201001 IS - 1664-462X (Print) IS - 1664-462X (Electronic) IS - 1664-462X (Linking) VI - 8 DP - 2017 TI - The Diversity of Sequence and Chromosomal Distribution of New Transposable Element-Related Segments in the Rye Genome Revealed by FISH and Lineage Annotation. PG - 1706 LID - 10.3389/fpls.2017.01706 [doi] LID - 1706 AB - Transposable elements (TEs) in plant genomes exhibit a great variety of structure, sequence content and copy number, making them important drivers for species diversity and genome evolution. Even though a genome-wide statistic summary of TEs in rye has been obtained using high-throughput DNA sequencing technology, the accurate diversity of TEs in rye, as well as their chromosomal distribution and evolution, remains elusive due to the repetitive sequence assembling problems and the high dynamic and nested nature of TEs. In this study, using genomic plasmid library construction combined with dot-blot hybridization and fluorescence in situ hybridization (FISH) analysis, we successfully isolated 70 unique FISH-positive TE-related sequences including 47 rye genome specific ones: 30 showed homology or partial homology with previously FISH characterized sequences and 40 have not been characterized. Among the 70 sequences, 48 sequences carried Ty3/gypsy-derived segments, 7 sequences carried Ty1/copia-derived segments and 15 sequences carried segments homologous with multiple TE families. 26 TE lineages were found in the 70 sequences, and among these lineages, Wilma was found in sequences dispersed in all chromosome regions except telomeric positions; Abiba was found in sequences predominantly located at pericentromeric and centromeric positions; Wis, Carmilla, and Inga were found in sequences displaying signals dispersed from distal regions toward pericentromeric positions; except DNA transposon lineages, all the other lineages were found in sequences displaying signals dispersed from proximal regions toward distal regions. A high percentage (21.4%) of chimeric sequences were identified in this study and their high abundance in rye genome suggested that new TEs might form through recombination and nested transposition. Our results also gave proofs that diverse TE lineages were arranged at centromeric and pericentromeric positions in rye, and lineages like Abiba might play a role in their structural organization and function. All these results might help in understanding the diversity and evolution of TEs in rye, as well as their driving forces in rye genome organization and evolution. FAU - Zhang, Yingxin AU - Zhang Y AD - Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. AD - Center for Life Science, University of Chinese Academy of Sciences, Beijing, China. FAU - Fan, Chengming AU - Fan C AD - Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. FAU - Li, Shuangshuang AU - Li S AD - Department of Life Science, Henan Normal University, Xinxiang, China. FAU - Chen, Yuhong AU - Chen Y AD - Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. FAU - Wang, Richard R-C AU - Wang RR AD - Forage and Range Research Laboratory, United States Department of Agriculture, Agricultural Research Service, Utah State University, Logan, UT, United States. FAU - Zhang, Xiangqi AU - Zhang X AD - Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. FAU - Han, Fangpu AU - Han F AD - Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. FAU - Hu, Zanmin AU - Hu Z AD - Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. AD - Center for Life Science, University of Chinese Academy of Sciences, Beijing, China. LA - eng PT - Journal Article DEP - 20171004 PL - Switzerland TA - Front Plant Sci JT - Frontiers in plant science JID - 101568200 EIN - Front Plant Sci. 2017 Nov 21;8:2020. PMID: 29206242 PMC - PMC5632726 OTO - NOTNLM OT - Secale cereale OT - TE lineages OT - fluoresence in situ hybridization OT - nested transposition OT - variation EDAT- 2017/10/20 06:00 MHDA- 2017/10/20 06:01 PMCR- 2017/01/01 CRDT- 2017/10/20 06:00 PHST- 2017/06/21 00:00 [received] PHST- 2017/09/19 00:00 [accepted] PHST- 2017/10/20 06:00 [entrez] PHST- 2017/10/20 06:00 [pubmed] PHST- 2017/10/20 06:01 [medline] PHST- 2017/01/01 00:00 [pmc-release] AID - 10.3389/fpls.2017.01706 [doi] PST - epublish SO - Front Plant Sci. 2017 Oct 4;8:1706. doi: 10.3389/fpls.2017.01706. eCollection 2017.