Evolution of the sex-determining region inGinkgo biloba

Abstract

Sex chromosomes or sex-determining regions (SDR) have been discovered in many dioecious plant species, including the iconic ‘living fossil' Ginkgo biloba , though the location and size of the SDR in G. biloba remain contradictory. Here we resolve these controversies and analyse the evolution of the SDR in this species. Based on transcriptome sequencing data from four genetic crosses we reconstruct male- and female-specific genetic maps and locate the SDR to the middle of chromosome 2. Integration of the genetic maps with the genome sequence reveals that recombination in and around the SDR is suppressed in a region of about 50 Mb in both males and females. However, occasional recombination does occur except a small, less than 5 Mb long region that does not recombine in males. Based on synonymous divergence between homologous X- and Y-linked genes in this region, we infer that the Ginkgo SDR is fairly old—at least of Cretaceous origin. The analysis of substitution rates and gene expression reveals only slight Y-degeneration. These results are consistent with findings in other dioecious plants with homomorphic sex chromosomes, where the SDR is typically small and evolves in a region with pre-existing reduced recombination, surrounded by long actively recombining pseudoautosomal regions. This article is part of the theme issue ‘Sex determination and sex chromosome evolution in land plants’.

Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes

“…Whether the PPR within A. palmeri MSY carries any restoration activity, i.e., has a post-transcriptional action on mitochondrial gene expression, is not known. Recently, a PPR was reported as one of the SDR genes in the gymnosperm plant, Gingko biloba [ 90 ]. Sex-linked genes in other dioecious plant species have been shown to exhibit male-specific coverages within the sex-determining regions, e.g., the sex-determinant factors, SOFF in garden asparagus ( Asparagus officinalis L.) [ 91 ], SyGI and FrBy in kiwifruit ( Actinidia sp) [ 40 ] and NRT1/PTR6.4 in spinach ( Spinacea oleracea L.) [ 45 ].…”

Heterochiasmy and Sex Chromosome Evolution in Silene

“…Not dissimilar to mammals and birds, sex chromosomes in S. latifolia are highly heteromorphic, though, unlike mammals and birds (where Y or W are typically small), the Y-chromosome in S. latifolia is the largest and the X is the second largest in the genome (e.g., [ 49 ]). The presence of highly distinct heteromorphic sex chromosomes in S. latifolia contrasts with many other dioecious plant species studied so far, such as papaya [ 50 ], persimmon [ 51 ], kiwifruit [ 52 ], asparagus [ 53 ], ginkgo [ 54 ] and Mercurialis [ 55 ], where sex chromosomes are cytologically indistinguishable (homomorphic) and have only small NRY that is flanked by long pseudoautosomal regions (PARs).…”

Genome-wide identification and expression analysis of MADS-box transcription factors reveal their involvement in sex determination of hardy rubber tree (Eucommia ulmoides oliv.)

“…In fig ( Ficus hispida L.), a MADS-box gene FhAG2 was found locating at the sex determination region of Y chromosome as potential male activator ( Zhang et al, 2020 ). Likewise, studies on cycad ( Cycas panzhihuaensis L. Zhou and S. Y. Yang) ( Liu et al, 2022 ), papaya ( Carica papaya L.) ( Yu et al, 2007 ), ginkgo ( Ginkgo biloba L.) ( Liao et al, 2020 ; Gong and Filatov, 2022 ), Nepenthes pitcher species ( Scharmann et al, 2019 ), and Silene latifolia Poir. ( Matsunaga et al, 2003 ).…”