AUTHOR=Zhang Guo-Jun , Jia Ke-Li , Wang Jin , Gao Wu-Jun , Li Shu-Fen 

TITLE=Genome-wide analysis of transposable elements and satellite DNA in Humulus scandens, a dioecious plant with XX/XY1Y2 chromosomes

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1230250

DOI=10.3389/fpls.2023.1230250

ISSN=1664-462X

ABSTRACT=<p>Transposable elements (TEs) and satellite DNAs, two major categories of repetitive sequences, are expected to accumulate in non-recombining genome regions, including sex-linked regions, and contribute to sex chromosome evolution. The dioecious plant, <italic>Humulus scandens</italic>, can be used for studying the evolution of the XX/XY<sub>1</sub>Y<sub>2</sub> sex chromosomes. In this study, we thoroughly examined the repetitive components of male and female <italic>H. scandens</italic> using next-generation sequencing data followed by bioinformatics analysis and florescence <italic>in situ</italic> hybridization (FISH). The <italic>H. scandens</italic> genome has a high overall repetitive sequence composition, 68.30% in the female and 66.78% in the male genome, with abundant long terminal repeat (LTR) retrotransposons (RTs), including more Ty3/<italic>Gypsy</italic> than Ty1/<italic>Copia</italic> elements, particularly two Ty3/<italic>Gypsy</italic> lineages, Tekay and Retand. Most LTR-RT lineages were found dispersed across the chromosomes, though CRM and Athila elements were predominately found within the centromeres and the pericentromeric regions. The Athila elements also showed clearly higher FISH signal intensities in the Y<sub>1</sub> and Y<sub>2</sub> chromosomes than in the X or autosomes. Three novel satellite DNAs were specifically distributed in the centromeric and/or telomeric regions, with markedly different distributions on the X, Y<sub>1</sub>, and Y<sub>2</sub> chromosomes. Combined with FISH using satellite DNAs to stain chromosomes during meiotic diakinesis, we determined the synapsis pattern and distinguish pseudoautosomal regions (PARs). The results indicate that the XY<sub>1</sub>Y<sub>2</sub> sex chromosomes of <italic>H. scandens</italic> might have originated from a centric fission event. This study improves our understanding of the repetitive sequence organization of <italic>H. scandens</italic> genome and provides a basis for further analysis of their chromosome evolution process.</p>