Polyploid Gene Expression and Regulation in Polysomic Polyploids

Polyploidization is one of the most crucial pathways in introducing speciation and broadening biodiversity, especially in the Plant Kingdom. Although the majority of studies have focused only on allopolyploid or disomic polyploids, polysomic polyploid species have occurred frequently in higher plants. Due to the occurrence of the capabilities of more copies of alleles in a locus which can have additive dosage effects and/or allelic interactions, polysomic polyploids can lead to unique gene regulations to silence or adjust the expression level to create variations in organ size, metabolic products, and abiotic stress tolerance and biotic stress resistance, etc. This review aims to comprehensively summarize the contemporary understanding and findings concerning the molecular mechanisms of gene expression as well as gene regulation in natural typed and resynthesized polysomic polyploid plants. The review investigates the molecular level of phenomena in polysomic polyploid plants such as 1) typically enlarging organ size and stabilizing meiosis, 2) increasing phytochemical content and metabolic products, 3) enhancing the ability to adapt with biotic and abiotic stress, and 4) changing in gene regulation to silence or adjust the expression levels involve in sequence elimination, methylation, gene suppression, subfunctionalization, neo-functionalization, and transposon activation.

Induction and characterization of polyploids from seeds of Rhododendron fortunei Lindl.

Most Rhododendron species are ornamental flowering species widely distributed in Asia,North America,and West Europe.Rhododendron fortunei,one of the endemic Rhododendron species in China,has beautiful flowers with bright colors and is being exploited to meet the needs of the flower market.Polyploid plants usually show superiority in growth,disease resistance,and adaption over their diploid relatives.Here,we report the first case of polyploid induction in R.fortunei.In order to induce polyploidy in R.fortunei,germinating seeds were treated with different concentrations of oryzalin for 16 h.By evaluating ploidy level with flow cytometry,a total of 34 polyploid R.fortunei lines,including 27 tetraploid lines and seven octoploid lines,were obtained.A comparison of treatments indicated that 7.5 mg L^-1 oryzalin was the optimal concentration for polyploid induction in seeds of R.fortunei.Compared with diploid plants,tetraploid and octoploid plants exhibited slower growth rates and had thicker and rounder curled leaves with more leaf epidermal hairs.Moreover,larger stomata at lower density were also observed in the leaves of polyploid plants.Chlorophyll contents were also significantly increased in polyploid plants,which leads to a darker green leaf color.Both small and large individuals exhibiting the same characteristics were observed among the obtained tetraploid plants.Overall,our study establishes a feasible method for polyploid induction in R.fortunei,thus providing a basis for breeding new R.fortunei varieties.

The occurrence,inheritance,and segregation of complex genomic structural variation in synthetic Brassica napus

"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.

Allotetraploidization event of Coptis chinensis shared by all Ranunculales

Coptis chinensis Franch.,also named Chinese goldthread is a member of Ranunculaceae in the order Ranunculales and represents an important lineage of early eudicots with traditional medicinal value.In our study,by using syntenic analysis combined with phylogenomic analysis of C.chinensis and four other representative genomes from basal and core eudicots,we confirmed that the WGD event in C.chinensis was shared by Aquilegia coerulea and Papaver somniferum L.and quickly occurred after Ranunculales diverged from other eudicots,likely a Ranunculales common tetraploidization(RCT).The synonymous nucleotide substitutions at synonymous sites distribution of syntenic blocks across these genomes showed that the evolutionary rate of the P.somniferum genome is faster than that of the C.chinensis genome by approximately 13.7%,possibly due to Papaveraceaes having an additional special tetraploidization event(PST).After Ks correction,the RCT dated to 115—130 million years ago(MYA),which was close to the divergence of Ranunculaceaes and Papaveraceaes approximately115.45—130.51 MYA.Moreover,we identified homologous genes related to polyploidization and speciation and constructed multiple sequence alignments with different reference genomes.Notably,the event-related subgenomes in the basal genomes all showed genomic fractionation bias,suggesting a likely allopolyploid nature of the RCT,PST and T-Alpha and T-Beta events in Tetracentron sinense.In addition,we detected that the sixteen P450 subfamilies were markedly expanded in the genomes of Ranunculales,and most of them were related to the RCT and PST events.We constructed a new platform for Early Eudicot Comparative Genomic Research(http://www.cgrpoee.top/index.html)to store more information.In summary,our findings support the WGD of C.chinensis shared by Ranunculales,which is likely an allotetraploidization event.This present effort offered new insights into the evolution of key polyploidization events and the genes related to secondary metabolites during the diversification of early eudicots.

A likely paleo-autotetraploidization event shaped the high conservation of Nyssaceae genome

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.

Natural and artificial polyploids in aquaculture

Genome polyploidy has been revealed to result in evolutionary advantages and novelties,and therefore,polyploid aquatic animals may possess excellent traits of economic interest including rapid growth,extensive adaptability and disease resistance.For this reason,numerous species of natural polyploid fishes,such as common carp,gibel carp,crucian carp,salmon,and sturgeon,were chosen as important target species for aquaculture.Many artificial polyploids have been commercially utilized for aquaculture and most of them were created from natural polyploid fishes of the Cyprinidae and Salmonidae.Thanks to the easy mass production and better economic traits in growth and flesh quality,the synthetized autopolyploids or allopolyploids from natural polyploid species in cyprinid fishes have been extensively applied to aquaculture throughout China.This review outlines polyploidy advantages and innovative opportunities,lists natural polyploid species used in aquaculture,and summarizes artificial polyploids that have been induced or synthetized,and used in aquaculture.Moreover,some main research trends on polyploid utilization and ploidy manipulation of aquaculture animals are also introduced and discussed in the review.

Evolutionary genetics of wheat mitochondrial genomes

The Triticum-Aegilops complex provides ideal models for the study of polyploidization,and mitochondrial genomes(mtDNA)can be used to trace cytoplasmic inheritance and energy production following polyploidization.In this study,gapless mitochondrial genomes for 19 accessions of five Triticum or Aegilops species were assembled.Comparative genomics confirmed that the BB-genome progenitor donated mtDNA to tetraploid T.turgidum(genome formula AABB),and that this mtDNA was then passed on to the hexaploid T.aestivum(AABBDD).T urartu(AA)was the paternal parent of T.timopheevii(AAGG),and an earlier Ae.tauschii(DD)was the maternal parent of Ae.cylindrica(CCDD).Genic sequences were highly conserved within species,but frequent rearrangements and nuclear or chloroplast DNA insertions occurred during speciation.Four highly variable mitochondrial genes(atp6,cob,nad6,and nad9)were established as marker genes for Triticum and Aegilops species identification.The BB/GG-specific atp6 and cob genes,which were imported from the nuclear genome,could facilitate identification of their diploid progenitors.Genic haplotypes and repeat-sequence patterns indicated that BB was much closer to GG than to Ae.speltoides(SS).These findings provide novel insights into the polyploid evolution of the Triticum/Aegilops complex from the perspective of mtDNA,advancing understanding of energy supply and adaptation in wheat species。

The lectin gene TRpL1 of tetraploid Robinia pseudoacacia L.response to salt stress

Lectins are natural proteins in animals,plants,and microorganisms and can be divided into 12 families.These lectins play important roles in various environmental stresses.Some polyploid plants show tolerance to environmental stresses and to insect pests.However,the mechanism of stress tolerance is unclear.Tetraploid Robinia pseudoacacia(4×)under salt stress showed higher tolerance than diploid R.pseudoacacia(2×).As lectin can improve stress tolerance,it was questioned whether the stress resistance of polyploid plants was related to the lectin protein.In this study,salt resistance of lectin gene TRpL1 was verified by its over-expression in plants.In addition,salt resistance of lectin protein by E.coli strains was detected.The data revealed that the over-expression transgenic plants of TRpL1 showed better salt tolerance than control plants under salt stress,and the TRpL1-expressing strain also grew better in the medium with added NaCl.Therefore,tetraploid plants can resist salt stress through TRpL1 protein regulation.

Megamitochondria Initiate Differentiation of Monolayer Cells into Detached Dome Cells That Proliferate by a Schizogony-Like Amitotic Process

Mitonucleon-initiated dome formation involves structural changes occurring over a 20 to 24 hour period in monolayer cells induced by a serum factor. The earliest observable change is the fusion of monolayer cells into a syncytium in which nuclei aggregate and become surrounded by a membrane that stains for endogenous biotin. Each of these structures is further surrounded by a fraction of the mitochondria that arise in the syncytium following initiation of dome formation. The mitochondria fuse around the chromatin aggregate in a structure we have called a mitonucleon. Within mitonucleons, a gaseous vacuole is generated that can be seen in protrusions of the apical membrane pressuring chromatin into a pyknotic state. Eventually that pressure, together with whatever enzymatic changes have occurred in the bolus of chromatin, results in DNA fragmentation. The fragments drawn out through the syncytium by a unipolar spindle are arrayed in a configuration that appears open both to epigenetic changes and to DNA repair and replication by polyteny. The fragmented DNA stretched across the syncytial space, hardly detectable by light microscopy, becomes visible approximately half way through the differentiation as the filaments thicken in what looks like replication by polyteny. This “recycling” of attached monolayer cells into detached dome cells must include DNA replication since the number of cells in the resulting domes is greater than the number of monolayer cells by 30% or more. The resulting DNA associates into a mass of chromatin which will “segment” into polyploid structures and then into what appear to be diploid nuclei over a period of 2 to 4 hours. When the layer of nuclei has filled the syncytium, the nuclei are cellularized, forming dome cells rising up from the monolayer and arching over a fluid cavity. Dome cells can extend into gland-like structures by the same mitonucleon dependent amitotic process observed in dome formation. Some of the characteristics of this process resemble the amitotic process of schizogony among single-celled eukaryotic parasites of the apicomplexan phylum. Mitonucleon initiated amitotic proliferation results in synthesis of dozens of dome cell nuclei in a period of 20 to 24 hours, so it is much more efficient than mitosis. Cells generated by this process and their progeny would also not be sensitive to agents that inhibit mitosis suggesting that the process, as an alternative to mitosis, might be activated in cancers that become resistant to some cytotoxic drugs.

Genome editing opens a new era of genetic improvement in polyploid crops

Sequence-specific nucleases(SSN) that generate double-stranded DNA breaks(DSBs) in genes of interest are the key to site-specific genome editing in plants. Genome editing has developed into one method of reducing undesirable traits in crops by the induction of knockout mutations. Different SSN-mediated genome-editing systems, including LAGLIDADG homing endonucleases or meganucleases, zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats, are emerging as robust tools for introducing functional mutations in polyploid crops including citrus, wheat, cotton, soybean, rapeseed, potato, grapes, Camelina sativa,dandelion, and tobacco. The approach utilizes knowledge of biological mechanisms for targeted induction of DSBs and their error-prone repair, allowing highly specific changes at designated genome loci. In this review, we briefly describe genome-editing technologies and their application to genetic improvement of polyploid crops.

Analysis of cytosine methylation in early generations of resynthesized Brassica napus

DNA methylation, an important epigenetic modification, serves as a key function in the polyploidization of numerous crops. In this study, early generations of resynthesized Brassica napus （F1,S1-S3）, ancestral parents B. rapa and B. oleracea were analyzed to characterize their DNA methylation status during polyploidization, applying DNA methylation-sensitive amplifica- tion polymorphism （MSAP） and high-performance liquid chromatography methods. In F, 53.4% fragments were inherited from both A- and C-genomes. Besides, 5.04 and 8.87% fragments in F were inherited from A- and C- genome, respectively. 5.85 and 0.8% fragments were newly appeared and disappeared in resynthesized B. napus, respectively. 13.1% of these gene sites were identified with methylation changes in F, namely, hypermethylation （7.86%） and hypomethylation （5.24%）. The lowest methylation status was detected in F （38.7%） compared with in S1-S3. In S3, 40.32% genes were methylated according to MSAP analysis. Sequencing of methylated fragments indicated that genes involved in multiple biological processes were modified, including transcription factors, protein modification, and transporters. Expression ananlysis of DNA methyltransferase I and DNA methyltransferase chromomethylase 3 in different materials was consistent to the DNA methylation status. These results can generally facilitate dissection of how DNA methylation contributes to genetic stability and improvement of B. napus during polypLoidization.

Karyotype and cytogeography of the genus Heracleum (Apiaceae) in the Hengduan Mountains

In the present study, the karyotypes of 34 populations belonging to 11 species and one variety of Heracleum from the Hengduan Mountains in China were examined. Chromosome numbers and the karyotypes of three species （H. souliei, H. la＇ngdoni, and H. wenchuanense） are reported for the first time, as are the karyotypes of H. moellendorffii and H. henryi （tetraploid）. Populations of H. candicans, H. franchetii, and H. kingdoni in the Hengduan Mountains were found to consist of a mixture of diploid and tetraploid plants. Except for four species of Heracleum, namely H. candicans, H. franchetii, H. henryi, and H.kingdoni, which have both diploid and tetraploid karyotypes, all other species of Heracleum are were found to be diploid. All karyotypes were found to belong to the 2A type of Stebbins, with the exception ofH. candicans var. obtusifolium, which belongs to 2B, and H. hemsleyanum and H. franchetii （Mt. Dujuan, Daocheng, Sichuan, China）, which belong to 1A. There was only a slight difference in the karyotype asymmetry index, which suggests a close kinship for species of Heracleum and that the entire phylogenetic development of Heracleum is relatively primitive. Species that exhibited advanced morphological features were also more advanced in karyotype structure, with the order ofkaryotype evolution being 1A→2A→2B. This phenomenon indicates that the species distributed in the Hengduan Mountains have not diverged completely and that the Hengduan Mountains are a relatively young and active area for the evolution of Heracleum. Polyploidization in Heracleum may be an important evolutionary mechanisms for some species, generating diversity. The biological attributes, distribution range, and the geological history of the genus have all played a part in accelerating the evolution through polyploidization or aneuploidization. It is known that as the distribution latitude of Heracleum decreases from north to south, the chromosome number, ploidy level, and asymmetry structure appear to increase. In the Hengduan Mountains, these tendencies are also evident. Finally, based on all the available cytogeographic data, we speculate that the more advanced tetraplont or aneuploid species of Heracleum in India may be derived from early diplont species that were distributed in the Caucasus region and Hengduan Mountains. The dispersal of Heracleum was from Eurasia to India, because this correlates with the emergence of the Himalayan Mountains through tectonic movement. Thus, the Hengduan Mountains are not only a center of diversity for Heracleurn, but also a center of active speciation in modern times.

Genomic footprints of wheat evolution in China reflected by a Wheat660K SNP array

Common wheat(Triticum aestiuum L.)is one of the most important crops because it provides about 20%of the total calories for humans.T.aestiuum is an excellent modern species for studying concerted evolution of sub-genomes in polyploid species,because of its large chromosome size and three well-known genome donors.Establishment of common wheat genome reference sequence and development of high-density SNP chips provide an excellent foundation to answer questions of wheat evolution and breeding at the genomic level.By genotyping more than 600 accessions of common wheat and their diploid and tetraploid ancestors using a Wheat660 K SNP array,we found dramatic genome changes due to tetraploidization and hexaploidization,in contrast to weaker influences of domestication and breeding on them.Further,since common wheat was introduced in China in 1500 BCE,Chinese landraces formed two subgroups(T.aestiuum-L1 and T.aestiuum-L2)with considerably diverse geographic distributions and agronomic traits.T.aestiuum-L2,mainly distributed in central and east China is found to have more but smaller oval grains with early maturity characteristics.We found that variation and selection in intergenic regions of the A and B sub-genomes dominated this differentiation,in which chromosomes 7 A and 3 B took the leading roles due to the existence of putative genes related to defense responses and environmental adaption in the highly differentiated regions.Large haplotype blocks were detected on 3 B(232.6-398.3 Mb)and 7 A(211.7-272.9 Mb)in the landraces,forming two distinct haplotypes,respectively.We discovered that artificial crosses in breeding promoted recombination in the whole genome,however,this recombination and differentiation was highly asymmetric among the three sub-genomes in homoeologous regions.In addition,we found that the wide use of European and northern American cultivars in breeding at early era,led dramatic changes in Chinese wheat genome,whereas,the recent breeding functioned to optimize it.This study will provide the insight for reconsideration of wheat evolution and breeding,and a new strategy for parent selection in breeding.

Cross Breeding of Populus and Its Hybrids for Cold Resistance

Populus tomentosa was crossed with P.tremuloidis, P.grandidentata, P.alba×P.grandidentata and P.alba×Ulmuspumila in order to maintain its rapid growth and high wood quality and improve its resistance to cold. Two methods were used to increase the germination rate from 1.5% to 41.1% and the remaining rate from 1.7% to 44.2%. Forty crossing combinations were conducted and 2744 hybrid seedlings were obtained. MX4×P.grandidentata （G-1-58）, MX3×P.tremuloidis （T-44-60）, MX2×P.tremuloidis （1-13-87-37） and MX2×（P.alba×P.grandidentata） were regarded as superior combinations after analysis and selection. Thirty seedlings of these combinations and 11 triploid seedlings identified by counting their chromosomes were selected as super plants.

Mechanisms involved in selecting and maintaining neuroblastoma cancer stem cell populations, and perspectives for therapeutic targeting

Pediatric neuroblastomas(NBs)are heterogeneous,aggressive,therapy-resistant embryonal tumours that originate from cells of neural crest(NC)origin and in particular neuroblasts committed to the sympathoadrenal progenitor cell lineage.Therapeutic resistance,post-therapeutic relapse and subsequent metastatic NB progression are driven primarily by cancer stem cell(CSC)-like subpopulations,which through their self-renewing capacity,intermittent and slow cell cycles,drug-resistant and reversibly adaptive plastic phenotypes,represent the most important obstacle to improving therapeutic outcomes in unfavourable NBs.In this review,dedicated to NB CSCs and the prospects for their therapeutic eradication,we initiate with brief descriptions of the unique transient vertebrate embryonic NC structure and salient molecular protagonists involved NC induction,specification,epithelial to mesenchymal transition and migratory behaviour,in order to familiarise the reader with the embryonic cellular and molecular origins and background to NB.We follow this by introducing NB and the potential NC-derived stem/progenitor cell origins of NBs,before providing a comprehensive review of the salient molecules,signalling pathways,mechanisms,tumour microenvironmental and therapeutic conditions involved in promoting,selecting and maintaining NB CSC subpopulations,and that underpin their therapy-resistant,self-renewing metastatic behaviour.Finally,we review potential therapeutic strategies and future prospects for targeting and eradication of these bastions of NB therapeutic resistance,post-therapeutic relapse and metastatic progression.

Roles of cell fusion, hybridization and polyploid cell formation in cancer metastasis

Cell-cell fusion is a normal biological process playing essential roles in organ formation and tissue differentiation,repair and regeneration.Through cell fusion somatic cells undergo rapid nuclear reprogramming and epigenetic modifications to form hybrid cells with new genetic and phenotypic properties at a rate exceeding that achievable by random mutations.Factors that stimulate cell fusion are inflammation and hypoxia.Fusion of cancer cells with non-neoplastic cells facilitates several malignancy-related cell phenotypes,e.g.,reprogramming of somatic cell into induced pluripotent stem cells and epithelial to mesenchymal transition.There is now considerable in vitro,in vivo and clinical evidence that fusion of cancer cells with motile leucocytes such as macrophages plays a major role in cancer metastasis.Of the many changes in cancer cells after hybridizing with leucocytes,it is notable that hybrids acquire resistance to chemo-and radiation therapy.One phenomenon that has been largely overlooked yet plays a role in these processes is polyploidization.Regardless of the mechanism of polyploid cell formation,it happens in response to genotoxic stresses and enhances a cancer cell’s ability to survive.Here we summarize the recent progress in research of cell fusion and with a focus on an important role for polyploid cells in cancer metastasis.In addition,we discuss the clinical evidence and the importance of cell fusion and polyploidization in solid tumors.

Effect of X-rays on Expression of Caspase-3 and p53 in EL-4 Cells and Its Biological Implications

Objective To investigate the effect of X-rays on expression of caspase-3 and p53 protein in EL-4 cells and its implications in induction of apoptosis and polyploid cells. Methods Mouse lymphoma cell line （EL-4 cells） was used. Fluorescent staining and flow cytometry analysis were employed for measurement of protein expression, apoptosis, cell cycle, and polyploid cells. Results The expression of caspase-3 protein increased significantly at 8 h and 12 h, compared with that of sham-irradiated control （P〈0.05, respectively） and the expression of p53 protein increased significantly at 2, 4, 8, 12, and 24 h, compared with that of sham-irradiated control （P〈0.05-P〈0.01） in EL-4 cells after 4.0 Gy X-irradiation. Apoptosis of EL-4 cells was increased significantly at 2, 4, 8, 12, 24, 48, and 72 h after 4.0Gy exposure, compared with that of sham-irradiated control （P〈0.05-P〈0.001）. G2 phase cells were increased significantly at 4, 8, 12, 24, 48, and 72 h （P〈0,05-P〈0.001）. However, no marked change in the number of 8 C polyploid cells was found from 2 to 48 h after 4.0 Gy exposure. Conclusion The expressions of caspase-3 and p53 protein in EL-4 cells are induced by X-rays, which might play an important role in the induction of apoptosis, and the molecular pathway for polyploid formation might be p53-independent.

Lycophyte transcriptomes reveal two whole-genome duplications in Lycopodiaceae:Insights into the polyploidization of Phlegmariurus

Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds.They are an excellent study system for examining whole-genome duplications(WGDs),or polyploidization,in spore-dispersed vascular plants.However,a lack of genome sequence data limits the reliable detection of very ancient WGDs,small-scale duplications(SSDs),and recent WGDs.Here,we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites(Ks)of the transcriptomes of 13 species of lycophytes to identify,locate,and date multiple WGDs in the lycophyte family Lycopodiaceae.Additionally,we examined the genus Phlegmariurus for signs of genetic discordance,which can provide valuable insight into the underlying causes of such conflict(e.g.,hybridization,incomplete lineage sorting,or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae,with one occurring in the common ancestor of extant Phlegmariurus(Lycopodiaceae)approximately 22-23 million years ago(Mya)and the other occurring in the common ancestor of Lycopodiaceae around 206-214 Mya.Interestingly,we found significant genetic discordance in the genus Phlegmariurus,indicating that the genus has a complex evolutionary history.This study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.

Study on Floral and Pollen Characters of Tetraploid Rice

Polyploidization is the evolution trend of many crops, and the yield increased obviously after polyploidization. The polyploidization of rice often brings ＂gigas＂ of both vegetative organs and seeds. Howevere, in rice breeding, it is required for restoring lines to have not only big anthers but also abundant pollens. People often doubt that the enlargement of the floral organ may just be enlargement of cell size in polyploid rice. So, it is of significance to study characteristics of floral organs and pollens of several tetraploid rice varieties or lines. Floral organ and pollen characteristics of Sg99012 and HN2026 were studied comparatively by stages and different ploidy levels, with the materials 9311, HD9802S, and PA64S as the control. The results showed that chromosome doubling had much more influence on floral characteristics of every lines than seeding by stages, and the tetraploids of every lines displayed ＂gigas＂. In correlation analysis, spikelet length, spikelet width, and anther length had significant correlation; spikelet width and anther width had significant correlation, too. Both seeding by stages and chromosome doubling made the correlations of characters between every floral organ changed to some extent. Seeding by stages had little effect on pollen diameter and fertility of HN2026-4X and Sg99012-4X. But chromosome doubling increased pollen size of every lines remarkably, and also increased the pollen quantity of PMeS （polyploid meiosis stability） restoring line HN2026-4X and gene map restoring line 9311-4X remarkably, whereas only had little effect on that of sterile lines. Moreover, chromosome doubling changed pollen fertility and made the number of fertility pollen of 9311 reduced significantly, but the pollen fertility of HN2026 （PMeS restoring line） and PA64S （sterile line） almost had no change after chromosome doubling. The results showed that tetraploid restoring lines had advantage of abundant and big size pollens, and tetraploid sterile lines had the characters of big size pollens, few change of pollen quantity and stable sterile character. These results provided evidence in reproductive biology for utilizing heterosis of polyploid rice by two-line method.

Comparative genomic analyses reveal cis-regulatory divergence after polyploidization in cotton

Polyploidization has long been recognized as a driver for the evolutionary formation of superior plant traits coupled with gene expression novelty.However,knowledge of the effect of regulatory variation on expression changes following polyploidization remains limited.In this study,we characterized transcriptional regulatory divergence by comparing tetraploid cotton with its putative diploid ancestors.We identified 144,827,99,609,and 219,379 Tn5 transposase-hypersensitive sites(THSs)in Gossypium arboreum,G.raimondii,and G.hirsutum,respectively,and found that the conservation of promoter THSs was associated with coordination of orthologous genes expression.This observation was consistent with analysis of transcription-factor binding sites(TFBS)for 262 known motifs:genes with higher TFBS conservation scores(CS)showed less change than those genes with lower TFBS CS in expression levels.TFBS influenced by genomic variation were involved in the novel regulation networks between transcriptional factors and target genes in tetraploid cotton.We describe an example showing that the turnover of TFBS was linked to expression pattern divergence of genes involved in fiber development(fiber-related genes).Our findings reveal the regulatory divergence of the transcriptional network in cotton after polyploidization and characterizes the regulatory relationships of genes contributing to desirable traits.