Analysis of transposable elements and organellar DNA in male and female genomes of a species with a huge Y chromosome reveals distinct Y centromeres

Abstract

Few angiosperms have distinct Y chromosomes. Among those that do are Silene latifolia (Caryophyllaceae), Rumex acetosa (Polygonaceae) and Coccinia grandis (Cucurbitaceae), the latter having a male/female difference of 10% of the total genome (female individuals have a 0.85 pg genome, male individuals 0.94 pg), due to a Y chromosome that arose about 3 million years ago. We compared the sequence composition of male and female C. grandis plants and determined the chromosomal distribution of repetitive and organellar DNA with probes developed from 21 types of repetitive DNA, including 16 mobile elements. The size of the Y chromosome is largely due to the accumulation of certain repeats, such as members of the Ty1/copia and Ty3/gypsy superfamilies, an unclassified element and a satellite, but also plastome- and chondriome-derived sequences. An abundant tandem repeat with a unit size of 144 bp stains the centromeres of the X chromosome and the autosomes, but is absent from the Y centromere. Immunostaining with pericentromere-specific markers for anti-histone H3Ser10ph and H2AThr120ph revealed a Y-specific extension of these histone marks. That the Y centromere has a different make-up from all the remaining centromeres raises questions about its spindle attachment, and suggests that centromeric or pericentromeric chromatin might be involved in the suppression of recombination.

Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants

“…In another dioecious plant, Carica papaya, NUPTs are localized within the male-specific region of the Y chromosome (MSY) and HSY approximately 12 times the rate in the X chromosome counterpart and four times that of the genome wide average [74]. NUPTs/NUMTs accumulate in the sex chromosomes of other dioecious plants, such as Rumex acetosa [84] and Coccinia grandis [85]. In A. officinalis, the number and total length of NUPTs in Y chromosome were larger than those in other chromosomes.…”

“…It is believed that the sex chromosomes originate from autosomes, and the evolutionary process involves some essential events, such as sex-determining gene emergence, recombination restriction, and Y chromosome degeneration [86]. In addition, sex chromosomes can recruit abundant TEs and organellar DNAs [74,85], and these novel sequences may benefit the structural differentiation and recombination restriction of sex chromosomes and contribute to Y chromosome degeneration [49]. The gathering of such novel sequences in sex chromosomes can promote recombination suppression of the sex chromosomes; when recombination is suppressed, such sequences can accumulate rapidly in the recombination-free region.…”

A high-throughput segregation analysis identifies the sex chromosomes ofCannabis sativa

“…Old animal sex chromosomes systems are usually heteromorphic with the Y being smaller than the X (Charlesworth et al 2005;Bachtrog 2013). Heteromorphic systems in plants are much more recent and in the case of Silene latifolia and Coccinia grandis, the Y is larger than the X (Matsunaga et al 1994;Sousa et al 2013), probably due to accumulation of DNA repeats on the Y (Sousa et al 2016;Hobza et al 2017). The Cannabaceae and related families (Urticaceae, Moraceae) family is expected to derive from a dioecious common ancestor (Zhang et al 2019).…”

Analysis of the small chromosomalPrionium serratum(Cyperid) demonstrates the importance of a reliable method to differentiate between mono- and holocentricity

“…The application of these antibodies in a wide range of species is possible due to the evolutionarily conserved amino acid sequence of histone H3. However, in some monocentric species, the application of anti-H2AT120ph resulted in additional non-pericentromeric signals (Baez et al, 2019;Sousa et al, 2016).…”