[目的]赖草属植物是麦类作物遗传改良和育种的重要基因资源,但作为异源多倍体植物,其基因组来源仍存在较大争议.通过比较赖草、大赖草及新麦草基因组中重复序列分布,探索赖草属物种基因组来源以及种间基因组多样性的形成特性.[方法]通过构建赖草属物种赖草的Cot-1 DNA文库获得大量重复序列,利用荧光原位杂交技术和重复序列对赖草以及近缘物种大赖草和祖先供体物种新麦草进行染色体荧光原位杂交涂染.[结果](1)根据序列及基因组分布特性,赖草Cot-1 DNA可归为串联重复序列、散布重复序列、散布加串联混合重复序列以及未能鉴定类型,4种类型占比分别为32.4％、45.7％、12.4％和9.5％.(2)串联重复序列TaiI-family、Lt1-6、pTa-535和pSc250在不同物种及同一物种不同材料间信号数量存在较大变异,分别为7～20,1～14,17～26,0～24个.(3)10个反转座子序列在所有物种染色体的分布呈现3种方式:在所有染色体上杂交信号集中分布在着丝粒、近着丝粒及间质区;在所有染色体的所有区域都有分布;在大部分染色体上的分布方式与第1种相同,但是部分染色体端部也有分布.2个LTR/Copia序列仅在赖草染色体上有分布,其他序列在不同物种以及不同材料间均有分布,但在信号强度以及部分染色体上的分布方式存在多态性.[结论]赖草属物种中的一些重复序列具有快速进化的特性,支持赖草属物种多倍化过程,并存在散在重复序列向整个核基因组的快速同质化扩散.

Polyploidy is a major factor in the evolution of plants,yet we know little about the origin and evolution of polyploidy in intertidal species.This study aimed to identify the evolutionary transitions in three true-mangrove species of the genus Acanthus distributed in the Indo-West Pacific region.For this purpose,we took an integrative approach that combined data on morphology,cytology,climatic niche,phylogeny,and biogeography of 493 samples from 42 geographic sites.Our results show that the Acanthus ilicifolius lineage distributed east of the Thai-Malay Peninsula possesses a tetraploid karyotype,which is morphologically distinct from that of the lineage on the west side.The haplotype networks and phylogenetic trees for the chloroplast genome and eight nuclear genes reveal that the tetraploid species has two sub-genomes,one each from A.ilicifolius and A.ebracteatus,the paternal and maternal parents,respectively.Population structure analysis also supports the hybrid speciation history of the new tetraploid species.The two sub-genomes of the tetraploid species diverged from their diploid progenitors during the Pleistocene.Environmental niche models revealed that the tetraploid species not only occupied the near-entire niche space of the diploids,but also expanded into novel environments.Our findings suggest that A.ilicifolius species distributed on the east side of the Thai-Malay Peninsula should be regarded as a new species,A.tetraploideus,which originated from hybridization between A.ilicifolius and A.ebracteatus,followed by chromosome doubling.This is the first report of a true-mangrove allo-polyploid species that can reproduce sexually and clonally reproduction,which explains the long-term adaptive potential of the species.

Structural variations(SVs)have long been described as being involved in the origin,adaption,and domes-tication of species.However,the underlying genetic and genomic mechanisms are poorly understood.Here,we report a high-quality genome assembly of Gossypium barbadense acc.Tanguis,a landrace that is closely related to formation of extra-long-staple(ELS)cultivated cotton.An SV-based pan-genome(Pan-SV)was then constructed using a total of 182 593 non-redundant SVs,including 2236 inversions,97 398 insertions,and 82 959 deletions from 11 assembled genomes of allopolyploid cotton.The utility of this Pan-SV was then demonstrated through population structure analysis and genome-wide association studies(GWASs).Using segregation mapping populations produced through crossing ELS cotton and the landrace along with an SV-based GWAS,certain SVs responsible for speciation,domestication,and improvement in tetrapioid cottons were identified.Importantly,some of the SVs presently identified as associated with the yield and fiber quality improvement had not been identified in previous SNP-based GWAS.In particular,a 9-bp insertion or deletion was found to associate with elimination of the interspecific reproductive isolation between Gossypium hirsutum and G.barbadense.Collectively,this study provides new insights into genome-wide,gene-scale SVs linked to important agronomic traits in a major crop spe-cies and highlights the importance of SVs during the speciation,domestication,and improvement of culti-vated crop species.

Reconstructing a robust species phylogeny and disentangling the evolutionary and biogeographic history of the gymnosperm genus Ephedra,which has a large genome and rich polyploids,re-main a big challenge.Here we reconstructed a transcriptome-based phylogeny of 19 diploid Ephedra species,and explored evolutionary retic-ulations in this genus represented by 50 diploid and polyploid species,using four low-copy nuclear and nine plastid genes.The diploid species phylogeny indicates that the Mediterranean species diverged first,and the remaining species split into three clades,including the American species(Clade A),E.rhytidosperma,and all other Asian species(Clade B).The single-gene trees placed E.rhytido-sperma sister to Clade A,Clade B,or Clades A+B in similar proportions,suggesting that radiation and gene flow likely occurred in the early evolution of Ephedra.In addition,reticulate evolution occurred not only among the deep nodes,but also in the recently evolved South American species,which further caused difficulty in phylogenetic re-construction.Moreover,we found that allopolyploid speciation was pervasive in Ephedra.Our study also suggests that Ephedra very likely originated in the Tethys coast during the late Cretaceous,and the South American Ephedra species have a single origin by dispersal from Mexico or North America.

Dear Editor,Allopolyploid mustard (Brassica juncea L.)is an important part of the U's triangle model of Brassica comprising vegetable,oilseed,and condiment crops.Vegetable B.juncea varieties are widely distributed in China and have been cultivated for a long period of 6000-7000 years (Yang et al.,2016).Tremendous phenotypic variation can be observed in the vegetable varieties of B.juncea,which include leaf-type,stem-type,root-type,and stalk-type varieties according to their edible organs (Qi et al.,2007).Oilseed B.juncea,as one of three major sources of edible oil in Brassica,is mainly distributed in the Indian subcontinent and Northwest China (Chen et al.,2013;Yang et al.,2016).It is also used for canola crops in Canada and Australia (Woods et al.,1991;Burton et al.,2004),and condiment crops in Europe,China,and other regions (Vaughan and Hemingway,1959).

Gene loss following whole genome duplication (WGD) is often biased,with one subgenome retaining more ancestral genes and the other sustaining more gene deletions.While bias toward the greater expression of gene copies on one subgenome can explain bias in gene loss,this raises the question to what drives differences in gene expression levels between subgenomes.Differences in chromatin modifications and epigenetic markers between subgenomes in several model species are now being identified,providing an explanation for bias in gene expression between subgenomes.WGDs can be classified into duplications with higher,biased gene loss and bias in gene expression between subgenomes versus those with lower,unbiased rates of gene loss and an absence of detectable bias between subgenomes;however,the originally proposed link between these two classes and whether WGD results from an allo-or autopolyploid event is inconsistent with recent data from the allopolyploid Capsella bursa-pastoris.The gene balance hypothesis can explain bias in the functional categories of genes retained following WGD,the difference in gene loss rates between unbiased and biased WGDs,and how plant genomes have avoided being overrun with genes encoding dose-sensitive subunits of multiprotein complexes.Comparisons of gene expression patterns between retained transcription factor pairs in maize suggest the high degree of retention for WGD-derived pairs of transcription factors may instead be explained by the older duplication-degeneration-complementation model.

Previous research suggests that Gossypium has undergone a 5- to 6-fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspe-cific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole ge-nome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae-Bombacoideae and Sterculioideae-Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analy-sis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetra-ploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae-Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.

Polyploidy refers to two or more complete sets of chromosomes that are combined within a nucleus, and includes both autopolyploidy and allopolyploidy (Otto 2007). Polyploidy is a recurring theme in the evolution-ary history of plants and it has been considered an important mechanism for speciation and also for adaptability to changing environments (Shimizu-Inatsugi et al. 2017). In nature, about one-third of flowering plants are polyploids, and a great majority of them are allopolyploids. There are many cultivated allopolyploid species, such as cotton, Brassica and potato, the possible evolutionary history of which can be inferred with high certainty.

In this issue,Wu et al.(2019) describe the largest whole-genome resequencing dataset published to date for rapeseed (Brassica napus),an allopolyploid crop species that originated just a few thousand years ago under anthropogenic influence and rapidly evolved into one of the world's most important oilseed crops.In almost 1000 accessions spanning species-wide germplasm for oilseed rape,a comprehensive analysis of sequence diversity related to flowering-related traits uncovered selective sweeps associated with eco-geographic adaptation and human selection,attributable particularly to divergence among homoeologs of key flowering-time regulation and ethylene synthesis/ signaling genes.The authors further extend their analysis to retrospective,genome-based documentation of diversity footprints that trace the global expansion of the species across a century of breeding.The study contributes not only a rich catalog of genome-wide diversity for genetic analysis and future breeding of important agro-econornic traits but also a unique conceptional framework for ongoing selective adaptation of oilseed rape crops to emerging challenges presented by chang ing climatic conditions in key production areas.Selective sweeps were found to contain genes involved in stress adaptation and development,especially flowering time,indicating that climatic adaptation both in terms of local stress factors and of life-cycle adaptation was the major factor underlying agronomic selection for improved seed yield.

Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized.Bamboos comprise one diploid herbaceous and three polyploid woody lineages,and are members of the only major subfamily in grasses that diversified in forests,with the woody members having a tree-like lignified culm.In this study,we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels (diploid,tetraploid,and hexaploid).We also constructed a high-density genetic linkage map for a hexaploid species of bamboo,and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids.Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage,and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors.A shared but distinct subgenome was identified in all polyploid forms,and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos.Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found.Taken together,our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species,and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.