Genome-Wide Analysis of Transposable Elements and Satellite DNAs in Spinacia Species to Shed Light on Their Roles in Sex Chromosome Evolution

Abstract

Sex chromosome evolution has mostly been studied in species with heteromorphic sex chromosomes. The Spinacia genus serves as an ideal model for investigating evolutionary mechanisms underlying the transition from homomorphic to heteromorphic sex chromosomes. Among evolutionary factors, repetitive sequences play multiple roles in sex chromosome evolution while their forces have not been fully explored in Spinacia species. Here, we identified major repetitive sequence classes in male and female genomes of Spinacia species and their ancestral relative sugar beet to elucidate the evolutionary processes of sex chromosome evolution using next-generation sequencing (NGS) data. Comparative analysis revealed that the repeat elements of Spinacia species are considerably higher than of sugar beet, especially the Ty3/Gypsy and Ty1/Copia retrotransposons. The long terminal repeat retroelements (LTR) Angela, Athila, and Ogre may be accounted for the higher proportion of repeats in the spinach genome. Comparison of the repeats proportion between female and male genomes of three Spinacia species indicated the different representation in Spinacia tetrandra samples but not in the S. oleracea or S. turkestanica samples. From these results, we speculated that emergence of repetitive DNA sequences may correlate the formation of sex chromosome and the transition from homomorphic sex chromosomes to heteromorphic sex chromosomes as heteromorphic sex chromosomes exclusively existed in Spinacia tetrandra. Three novel sugar beet-specific satellites were identified and confirmed by fluorescence in situ hybridization (FISH); six out of eight new spinach-specific satellites were mapped to the short arm of sex chromosomes. A total of 141 copies of SolSat01-171-s were found in the sex determination region (SDR). Thus, the accumulation of satellite DNA on the short arm of chromosome 1 may be involved in the sex chromosome evolution in Spinacia species. Our study provides a fundamental resource for understanding repeat sequences in Spinacia species and their roles in sex chromosome evolution.

Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets

“…Further previously described ‘satDNAs’ and minisatellites (i.e. Dione/ Fok I-satellite and Niobe/ Alu I-satellite: Zakrzewski et al 2010, 2014; BvMSats: Zakrzewski et al 2010; BvuSats: Li et al 2021) were not included as we found that these repeats are not arranged in long arrays and therefore we consider them tandem repeats rather than satDNA. The monomer sequences of newly identified satDNAs can be found in Additional file 1: Data S1.…”

“…76% in quinoa: Heitkam et al ., 2020; approx. 51% in spinach: Li et al ., 2021). Discrepancies in repeat abundances to a previous RepeatExplorer2 analysis in B. vulgaris (Kowar et al ., 2016) are moderate and result from the exclusion of organellar DNA from our read set as well as the improvement of the repeat annotation by including a more comprehensive, custom repeat database.…”

The Comparative Analysis of the DNA Repeat Composition among <em>Cannabis Sativa</em> L., <em>Humulus Lupulus</em> L. And <em>Humulus Japonicus</em> Siebold & Zucc. With Heteromorphic Sex Chromosomes

“…The similar results were presented in Spinacia oleracea L. (with homomorphic sex chromosomes) and S. tetrandra Stev. (with heteromorphic sex chromosomes) [56]. Li et al (2021) showed that the proportion of Ale and Retand was higher in the female genome than in the male genome, while the proportion of Angela, Bianca, CRM, Tekay, LINE, EnSpm_CACTA, and rDNA was higher in male genome than in the female genome of S. oleracea.…”

A rapid method for assembly of single chromosome and identification of sex determination region based on single‐chromosome sequencing

“…Then, FISH was performed as described previously by Li et al . (2021). The slides were observed and photographed under Olympus BX63 fluorescence microscope and then processed with P hotoshop v.7.0.…”

“…The PCR reaction procedure is as follows: denaturation at 95°C for 3 min; denaturation at 94°C for 25 s, annealing at 55°C for 30 s, and extension at 72°C for 40 s, 35 cycles; finally, extension at 72°C for 10 min. The mixed probe (STUYsdr‐1 and STUYsdr‐2) was labeled with Texas Red‐5‐dCTP, and 45S rDNA was labeled with Chroma Tide Alexa Fluor 488‐5‐dUTP using nick translation method (Li et al ., 2021) and stored at −20°C. The chromosome slides at metaphase, meiotic pachytene, diakinesis, metaphase I, and other stages were prepared.…”