Zhang, C.; Wang, L.; Dou, L.; Yue, B.; Xing, J.; Li, J. Transposable Elements Shape the Genome Diversity and the Evolution of Noctuidae Species. Genes2023, 14, 1244.
Zhang, C.; Wang, L.; Dou, L.; Yue, B.; Xing, J.; Li, J. Transposable Elements Shape the Genome Diversity and the Evolution of Noctuidae Species. Genes 2023, 14, 1244.
Zhang, C.; Wang, L.; Dou, L.; Yue, B.; Xing, J.; Li, J. Transposable Elements Shape the Genome Diversity and the Evolution of Noctuidae Species. Genes2023, 14, 1244.
Zhang, C.; Wang, L.; Dou, L.; Yue, B.; Xing, J.; Li, J. Transposable Elements Shape the Genome Diversity and the Evolution of Noctuidae Species. Genes 2023, 14, 1244.
Abstract
Noctuidae is known to have high species diversity, although the genomic diversity of Noctuidae species have not been studied extensively. Investigation of transposable elements (TEs) in this family can improve our understanding on the genomic diversity of Noctuidae. In this study, we annotated and characterized genome-wide TEs in ten noctuid species belonging to seven genera. With multiple annotation pipelines, we constructed a consensus sequence library containing 1,038 –2,826 TE consensus. The genome content of TEs showed high variation in the ten Noctuidae genomes, ranging from 11.3% to 45.0%. The relatedness analysis indicated that the TE content, especially the content of LINEs and DNA transposons, are positively correlated with the genome size (r=0.86, p-value=0.001). We identified SINE/B2 as a lineage-specific subfamily in Trichoplusia ni, a species-specific expansion of LTR/Gypsy subfamily in Spodoptera exigua, and a recent expansion of SINE/5S subfamily in Busseola fusca. We further revealed that of the four TE classes, only LINEs showed phylogenetic signal with high confidence. We also examined how the expansion of TEs contributed to the evolution of noctuid genomes. Moreover, we identified a total of 56 horizontal transfer TE (HTT) events among the ten noctuid species and at least three HTT events between the nine Noctuidae species and 11 non-noctuid arthropods. One of HTT events caused by a Gypsy transposon might have caused the recent expansion of Gypsy subfamily in the S.exigua genome. By determining the TE content, dynamics, and HTT events in the Noctuidae genomes, our study emphasized that TE activities and HTT events had substantial impacts on the Noctuidae genome evolution.
Keywords
Noctuidae; transposable elements; genomic diversity; phylogeny; horizontal transfer TE (HTT) events
Subject
Biology and Life Sciences, Insect Science
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
