“…Co-location of multiple markers indicates that recombination is suppressed or reduced in the region around the sex locus in both male and female maps. Recombination suppression in the region around the sex locus was confirmed once the genetic maps were integrated with the genome sequence [15]. Figure 1Male and female genetic maps for chromosome 2.…”
Section: Resultsmentioning
confidence: 98%
“…The combined analysis of the genetic map and the female reference genome [15] revealed that the order of genes is mostly colinear for all chromosomes, except chromosomes 1 and 4 (electronic supplementary material, figure S3). According to the genetic map, the first approximately 400 Mb of the scaffold for chromosome 1 is misplaced in the genome assembly—this region should either be on the other side of chromosome 1 or it may belong to a different chromosome, as recombination distance between markers in this region and the rest of the chromosome 1 is over 90 cM (electronic supplementary material, figure S3).…”
Section: Resultsmentioning
confidence: 99%
“…Focusing on chromosome 2 and the SDR, the integrated map and female genome sequence [15] revealed that the region with reduced recombination surrounding the sex locus is approximately 50 Mb long (figure 2). It is flanked by genes evm.chr2.722 and evm.chr2.564 (electronic supplementary material, table S3) located at 251.7 and 200.8 Mb on chromosome 2 in the female G. biloba genome reference assembly [15].…”
Section: Resultsmentioning
confidence: 99%
“…Focusing on chromosome 2 and the SDR, the integrated map and female genome sequence [15] revealed that the region with reduced recombination surrounding the sex locus is approximately 50 Mb long (figure 2). It is flanked by genes evm.chr2.722 and evm.chr2.564 (electronic supplementary material, table S3) located at 251.7 and 200.8 Mb on chromosome 2 in the female G. biloba genome reference assembly [15]. According to the annotation of the reference sequence, this region contains 159 protein-coding genes, however, we were able to genetically map only 34 of these genes in the genetic map, with other genes probably missing informative markers owing to lack of polymorphic sites and/or low expression in our transcriptome sequence-based genotyping analysis.…”
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’.
“…Co-location of multiple markers indicates that recombination is suppressed or reduced in the region around the sex locus in both male and female maps. Recombination suppression in the region around the sex locus was confirmed once the genetic maps were integrated with the genome sequence [15]. Figure 1Male and female genetic maps for chromosome 2.…”
Section: Resultsmentioning
confidence: 98%
“…The combined analysis of the genetic map and the female reference genome [15] revealed that the order of genes is mostly colinear for all chromosomes, except chromosomes 1 and 4 (electronic supplementary material, figure S3). According to the genetic map, the first approximately 400 Mb of the scaffold for chromosome 1 is misplaced in the genome assembly—this region should either be on the other side of chromosome 1 or it may belong to a different chromosome, as recombination distance between markers in this region and the rest of the chromosome 1 is over 90 cM (electronic supplementary material, figure S3).…”
Section: Resultsmentioning
confidence: 99%
“…Focusing on chromosome 2 and the SDR, the integrated map and female genome sequence [15] revealed that the region with reduced recombination surrounding the sex locus is approximately 50 Mb long (figure 2). It is flanked by genes evm.chr2.722 and evm.chr2.564 (electronic supplementary material, table S3) located at 251.7 and 200.8 Mb on chromosome 2 in the female G. biloba genome reference assembly [15].…”
Section: Resultsmentioning
confidence: 99%
“…Focusing on chromosome 2 and the SDR, the integrated map and female genome sequence [15] revealed that the region with reduced recombination surrounding the sex locus is approximately 50 Mb long (figure 2). It is flanked by genes evm.chr2.722 and evm.chr2.564 (electronic supplementary material, table S3) located at 251.7 and 200.8 Mb on chromosome 2 in the female G. biloba genome reference assembly [15]. According to the annotation of the reference sequence, this region contains 159 protein-coding genes, however, we were able to genetically map only 34 of these genes in the genetic map, with other genes probably missing informative markers owing to lack of polymorphic sites and/or low expression in our transcriptome sequence-based genotyping analysis.…”
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’.
“…Ginkgo biloba L., a fascinating and economically important gymnosperm, is the only living representative of the order Ginkgoales, which probably originated circa 280 million years ago [12]. It exhibits some unique features related to its sexual reproduction process, phylogenetic position, and evolutionary history [13][14][15]. At present, G. biloba has a wide Forests 2021, 12, 1255 2 of 16 distribution across different elevations and latitudes and generally has a long lifespan.…”
Ginkgo biloba is a well-known long-lived tree with important economical, ornamental and research value. New stems often resprout naturally from the trunk or roots of old trees to realize rejuvenation. However, the physiological and molecular mechanisms that underlie the resprouting from old trees are still unknown. In this study, we investigated a 544-year-old female ginkgo tree with vigorous resprouters along the trunk base in Yangzhou, China. We compared the morphological and physiological traits of leaves between resprouters (SL) and old branches (OL) and found a significantly higher thickness, fresh weight, and water content in SL. In particular, the depth and number of leaf lobes were dramatically increased in SL, suggesting the juvenile characteristics of sprouters in old ginkgo trees. Transcriptome data showed that the expression of genes related to photosynthetic capacity, the auxin signaling pathway, and stress-associated hormones was upregulated in SL. Importantly, levels of the most important secondary metabolites, including kaempferol, isorhamnetin, ginkgolide A, ginkgolide B, and ginkgolide C, were significantly higher in SL. We also identified high expression of key genes in SL, such as PAL and FLS, which are involved in flavonoid synthesis, and GGPS, which is involved in the synthesis of terpene lactones. These findings reveal the distinct physiological and molecular characteristics as well as secondary metabolite synthesis in leaves of resprouting stems in old ginkgo trees, providing new insight into rejuvenation physiology in old tree aging.
Conserving genetic diversity has been increasingly recognized as a keystone towards the protection of biodiversity and natural resources for future generations of humankind. In turn, the ongoing genomic revolution provides us with the technical innovations and expanded knowledge required to establish programs to integrate genomic approaches into programs to protect plant diversity and its genetic diversity. Although obtaining whole genomes of all organisms is still a far‐fetched dream, rapid progress in assembling whole genomes across the plant tree‐of‐life has provided access to reference genomes for many plants but, unfortunately, not all lineages of the plant tree‐of‐life. Addressing the existing taxon gaps is arguably best achieved by focusing on the genomes of plant species that experience high extinction threats or play a crucial role in ecosystem restoration. This review summarizes not only the recent progress in plant genomics with an emphasis on their importance to the conservation of plant diversity but also outlines steps to integrate genomics into plant conservation. Given the complexity of threats driving plant extinction, such as reduced genetic diversity, enhanced genome erosion, and loss of species integrity by hybridization, the integration of genomic research into our conservation efforts is crucial to understand extinction processes and, most importantly, to support the targets set to achieve “Harmony with Nature.”
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
