流式细胞术测定银叶真藓(Bryum argenteum Hedw.)基因组大小

银叶真藓(Bryum argenteum Hedw.)是藓类植物真藓科真藓属的模式种。世界广布种。该研究以银叶真藓为试材,采用流式细胞术,首先选用同属于藓类植物而且已公布基因组大小的小立碗藓(Physcomitrella patens)作为内参,估算得到银叶真藓基因组大小为568~589 Mb。鉴于参照的小立碗藓基因组大小为487 Mb是测序结果,可能在实际反映其基因组大小上有偏差,所以作者又选取了既有测序结果(125 Mb)又有流式细胞术估算基因组大小数据(157 Mb)的拟南芥(Arabidopsis thaliana)作为内参,对银叶真藓基因组大小进行了再次估算。结果表明,银叶真藓的基因组大小为728.09±77.84 Mb,1CDNA含量约为0.75 pg。该研究所得数据有助于银叶真藓基因组测序的研究。     

流式细胞术测定川贝母四种基源植物基因组大小

为揭示川贝母各基源植物间基因组大小与形态的内在差异和联系,本研究以已知基因组大小的银杏(8.92 Gb)作为内标,卷叶贝母、暗紫贝母、甘肃贝母、太白贝母的幼嫩叶片为材料,采用流式细胞术测定贝母属4种基源植物的基因组大小。结果表明,4种基源植物的基因组大小相近,其中,以卷叶贝母最小,为(29.73±0.34) Gb;甘肃贝母最大,为(31.80±0.06) Gb;暗紫贝母基因组大小为(31.46±0.36) Gb,太白贝母基因组大小为(31.68±0.17) Gb。本试验将为贝母属几种基源植物的基因组学研究、分子细胞遗传学、生物活性合成代谢通路的揭示以及种群进化研究提供基础数据参考。     

马齿苋的基因组大小估算及基因组调查测序

马齿苋作为蔬菜、传统中药和动物饲料具有悠久的应用历史。然而,马齿苋的分子生物学研究一直比较滞后,缺乏组学数据是一个重要的障碍。本研究以栽培品种‘北农1号’(BN1)为实验材料,采用流式细胞术和基因组调查测序等技术对马齿苋基因组特征进行了初步研究。细胞遗传学染色体计数表明马齿苋BN1的体细胞有52条染色体(2n=52)。流式细胞术分析估算BN1的基因组大小在1 089～1 445 Mb之间。运用第二代DNA测序技术和K-mer分析,估算马齿苋BN1的基因组大小约为1 295 Mb,基因组杂合率为0.103%,重复序列含量为59.27%。本研究进一步利用获得的DNA序列数据,从头组装了一个大小为963.2 Mb的马齿苋基因组,重叠群N50长度为20.1 kb。BUSCO分析表明基因组完整度为90.4%。本研究为马齿苋的基因组测序和分子育种研究提供了有价值的数据。     

基于流式细胞术的澳洲坚果基因组C值测定

为建立澳洲坚果基因组C值的流式细胞术测定方法,采用改良的OTTO细胞核提取液配方和PI荧光染料,以‘O.C’嫩叶为材料,以基因组DNA含量已知的Pisum sativum L. Ctirad和Zea mays L. CE-777为对照,运用流式细胞术对澳洲坚果基因组C值进行了测定。结果表明,澳洲坚果‘O.C’二倍体基因组DNA总量为1.91488599 pg,其C值为0.957443 pg;按1 pg DNA=0.978×109 bp来计算,‘O.C’基因组大小为1.872758×109 bp;采用2种不同对照材料作为内标测定的结果无显著差异。本研究发现,运用流式细胞术进行澳洲坚果基因组C值测定准确可靠,可为其他物种基因组C值测定提供参考。     

基于流式细胞术和K-mer分析测定两种车前属植物基因组的大小

车前属(Plantago)植物车前(Plantago asiatica)和大车前(Plantago major)是中国传统药用植物。本研究采用流式细胞术与K-mer分析方法对车前和大车前的基因组大小进行测定,为后续全基因组测序提供参考。实验过程采用木本植物缓冲液(woody plant buffer, WPB)解离并制备车前和大车前嫩叶材料的细胞核悬浮液,以玉米基因组DNA为对照,通过流式细胞仪测定经碘化丙啶(propidium iodide, PI)染色的车前属植物细胞核样品的荧光强度,计算基因组大小。此外,本研究采用高通量测序技术对车前和大车前进行双末端测序,同时利用K-mer法估计基因组大小,并分析杂合率、重复序列和GC含量等信息。结果显示,利用流式细胞术测得车前基因组大小约为2 386.01 Mb;大车前基因组大小约为743.14 Mb。而通过基因组测序,分别获得了78 Gb的车前和58 Gb的大车前基因组数据。K-mer分析的结果表明,车前基因组大小约为2 161.54 Mb,测序深度为36 X;大车前基因组大小约为701.17 Gb,测序深度为80 X,K-mer分布曲线图显示车前和大车前都是低杂合基因组,车前基因组含有较高比例的重复序列(51.72%)。研究结果为揭示车前属植物基因组大小的进化提供了重要证据,也为后续三代全基因高通量测序和组装提供了必要的数据参考。     

基于流式细胞术和基因组Survey测定药食同源植物赤苍藤的基因组大小

为了解药食同源植物赤苍藤的基因组大小、基本结构特征及确定适合该物种的基因组测序方案,本研究采用流式细胞术,结合基于K-mer分析的全基因组调查和生物信息学,测定和分析赤苍藤基因组。结果表明,流式细胞术估算赤苍藤的基因组大小为2.0～2.2 Gb;Survey分析获得赤苍藤有效数据152 Gb,估计基因组大小约为2 103.11 Mb,杂合率为0.90%,重复序列比例为75.20%,基因组GC含量约为38.50%,推测赤苍藤基因组大小约为2.1 Gb,并初步判断其具有较高的重复序列和杂合率。本研究结果确定了赤苍藤基因组为复杂基因组,可为后续开展全基因测序时的策略选择提供重要参考,为下一步开展全基因组图谱绘制、挖掘重要功能基因提供了有效数据。     

流式细胞术测定苎麻基因组大小

苎麻属于荨麻科苎麻属,是目前非常重要的纺织原料,有着广泛的开发前景。为了更好地研究苎麻基因组信息,拟通过流式细胞术测定苎麻基因组大小。本研究以水稻(Oryza sativa)日本晴为内标,湘苎3号为待测样品,分别分离水稻和苎麻叶片细胞的细胞核,PI染色,用流式细胞仪对水稻和苎麻样品的PI发射荧光强度进行测定。通过比较水稻和苎麻样品的荧光强度的倍数关系,计算得到苎麻基因组大小,并采用外标法和内标法同时进行测定和计算。以水稻日本晴为外标,苎麻3号为待测样品,测得苎麻基因组大小为332.5 Mb,而用内标法得到的苎麻基因组大小为300.5 Mb,相比之下内标法测定的变异系数更低,更为准确。苎麻基因组大小的测定为苎麻基因组文库的建立及其基因组相关研究提供了理论指导。     

山胡椒基因组大小的估测及其重要自然群体的倍性鉴定

山胡椒是一种果实富含油脂、根茎叶具较高药用价值的经济树种。现阶段山胡椒基本处于野生状态,分析山胡椒的基因组大小特征及自然群落个体倍性,对促进该物种种质挖掘利用具有重要意义。本研究通过流式细胞术和K-mer频数分析两种方法对山胡椒基因组大小进行预测,并利用前者分析三个山胡椒自然群体(河南鸡公山,贵州梵净山和台湾大肚山)的个体倍性。流式细胞术以山苍子(2n=2x=24)作为内标。K-mer频数分析通过对其基因组DNA进行Illumina测序,得到过滤数据218.64 Gb。流式细胞实验结果显示,山胡椒基因组大小约为2.32 Gb,而K-mer频数分析显示其基因组大小约为2.22 Gb,杂合率为1.42%,重复率为76.75%。本研究共检测了123份个体,获得结果 118份,结果显示全为二倍体。综合两种分析方法,本研究认为山胡椒是高杂合、高重复物种,基因组大小为2.22～2.32 Gb。个体倍性鉴定结果表明,不论是有性生殖还是孤雌生殖,中国境内的山胡椒野生型个体基本为二倍体,自然种群倍性处于稳定状态。研究结果可为后续山胡椒的基因组学、生殖学研究与利用等相关工作提供参考。     

基于流式细胞仪对杏属植物基因组大小的测定

基因组大小是植物最基本也是最重要的生物多样性特征参数,测定杏基因组大小,比较不同种、变种及品种之间基因组大小的差异,可为相关杏属植物的物种进化和分类研究以及基因组研究提供基础数据。采用流式细胞仪技术,对分属于普通杏、辽杏、西伯利亚杏、紫杏和仁用杏5个种或类型的13个杏品种资源的基因组大小进行了测定。结果显示,在所对比的3种内标植物中,金丝小枣最适于做杏基因组大小测定的内标。以金丝小枣为内标,通过比较待测样品和内标G0/G1期荧光峰,计算得出13份杏属植物材料中,普通杏及其变种基因组大小为(253.17±0.963)Mb(大优佳)～(300.60±1.181)Mb(陕梅),紫杏基因组最小,大小为(245.07±0.842)Mb,辽杏、属于西伯利亚杏的绿萼山杏和仁用杏品种龙王帽的基因组大小分别为(280.37±4.858),(273.66±4.334),(263.42±1.306)Mb,5个种或类型间差异均达显著水平。首次揭示了杏属植物不同种和品种间基因组大小的差异。研究结果可为杏基因组大小与其表型性状、种间分化以及植物学分类间关系的解释提供基础证据。     

浙江楠全基因组调查

浙江楠是重要的材用和园林绿化树种,但对其分子生物学的研究有限,全基因组测序成为深入研究浙江楠分子生物学的关键。本研究利用高通量测序技术(Illumina Hiseq 2500)开展了浙江楠基因组大小测定,并利用生物信息学方法对其基因组大小、杂合率及重复序列比例等一些基本信息进行统计。结果表明：浙江楠基因组大小为1 060.06 Mb,杂合率为2.18%,重复序列比例为58.81%,GC含量为40.81%。基因组各指标的统计结果表明,浙江楠基因组较大,且具有较高的杂合率,测序难度较大。后续浙江楠全基因组测序需要利用二代(Illumina)与三代(PacBio)测序技术相结合的方式进行,将有利于高质量全基因组的获得。     

Approaches and Prospects of Developing Tourism Value of Natural Bryophyte Resources in West Sichuan

Abundant bryophytes with high ecological and ornamental value are distributed in natural forests in west Sichuan. Through exploring the practices and forecasting the application of bryophytes from 2 aspects(using bryophytes in the natural world and building artificial moss garden), this paper proposed that the large-scale application of bryophytes could be realized via the development of bryophyte tourism products and commodities on the basis of ecological restoration and artificial cultivation experiment.     

Retrotransposons - a major driving force in plant genome evolution and a useful tool for genome analysis

As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to unforeseen transposition activities. Regulation of transposition is relatively complex and three factors such as maintaining structure for none- or cis- or trans-acting transposition, being controlled by the host genome and induction by biotic and abiotic stress may contribute altering its transposition activity. The important roles of retrotransposons to modify genome size, remodel genome structure, and displace gene functions in the plant genome have been proven by a growing number of research studies till date, which indicates that retrotransposons are important driving force in genome evolution. For this review, we summarized the latest theoretic and practical research progresses on plant retrotransposons for their distribution, regulation of activity, the impact on the architecture of plant genomes, and put forward the future prospects.     

Lysophosphatidylethanolamine effects on horticultural commodities: A review

Lysophosphatidylethanolamine (LPE) is a naturally occurring lipid with regulatory effects in senescence and ripening. When applied exogenously to horticultural crops, LPE affects growth, development, and postharvest longevity. The effects of exogenously applied LPE have been studied in a range of plant organs in more than a dozen horticultural species. The claimed horticultural benefits include delayed leaf senescence, stimulation of ripening in table grape, acceleration of color development and extension of shelf-life in cranberry and tomato, and increased vase life of cut flowers. Responses to LPE application are found to vary dramatically within horticultural commodity, developmental stage, and organ type. Effects on ethylene responses are contradictory. LPE inhibits phospholipase D and is reported to affect the activity of enzymes relevant for produce quality, such as phenylalanine ammonia lyase and acid invertase. The biochemical mode of action of LPE is poorly understood. In particular, a mechanism by which a plant growth regulator might delay senescence of plant organs and accelerate ripening-related changes is not obvious. The horticultural, physiological and biochemical effects of LPE are reviewed in an attempt to highlight the knowledge gaps regarding the putative regulatory role of exogenously applied LPE.     

Genome size variation among sex types in dioecious and trioecious Caricaceae species

Caricaceae is a small family consisting of 35 species of varying sexual systems and includes economically important fruit crop, Carica papaya, and other species of “highland papayas”. Flow cytometry was used to obtain genome sizes for 11 species in three genera of Caricaceae to determine if genome size differences can be detected between sexes. Genome sizes ranged from 442.5 to 625.9 megabases (Mb) likely due to variation in the accumulation of retrotransposons in the genomes. The C. papaya genome size was estimated to be 442.5 Mb, larger than previously reported. Significant differences were detected between male and female samples in Jacaratia spinosa, Vasconcellea horovitziana, and V. stipulata, and between male and hermaphrodite samples of V. cundinamarcensis, suggesting the presence of sex chromosomes for these species. The small size differences between genomes of the papaya sexes were not detected using flow cytometry. Vasconcellea horovitziana was discovered to have a larger female genome size than male, suggesting the possibility of a ZW sex chromosome system in the family. The estimated genome sizes of these 11 species will be used in sequencing their genomes and in sex chromosome research for this family.     

Genome size variation in three Saccharum species

Saccharum species are autopolyploids with ploidy level ranging from 5× to 16x, and are considered the most complex genomes among crop plants. In present study, the genome sizes of 28 Saccharum spontaneum accessions, 15 Saccharum officinarum accessions, 28 Saccharum robustum accessions, and 12 Saccharum hybrids spp. were analyzed using flow cytometry. The estimated genome sizes of S. officinarum accessions ranged from 7.50 to 8.55?Gb with an average size of 7.88?Gb. In S. robustum, the estimated genome sizes ranged from 7.65 to 11.78, reflecting the variation of ploidy level. In S. spontaneum, the estimated genome sizes varied widely, with a range from 3.36 to 12.64?Gb, also due to variation of ploidy level. The average monoploid genome size of S. officinarum was 985?Mb, and that of S. spontaneum was 843?Mb. The results also showed that genome sizes were correlated with chromosome numbers, and based which, that the unknown chromosome numbers of some accessions could be predicted. The estimated genome sizes of Saccharum germplasm also helped identify some mislabeled accessions and yielded information critical for sugarcane breeding and genome sequencing programs.     

Commercialization decisions and the economics of introduction

Summary A commercial horticultural industry that establishes plant-breeding nurseries for an exotic species throughout a regional economy will expand until the marginal profit of the last nursery established is zero. However, a regional government concerned with social welfare will take into account not only the profits of the horticultural industry but also any expected costs of an accidental invasion. The latter costs will consist of the discounted expected social damages due to an increase in the rate of invasion over time and the increase in expected damage cost per hectare caused by an additional nursery. A government can employ an “introducers' pay” tax equal to the latter social costs to ensure that the plant breeding industry establishes the optimal number of nurseries. We illustrate this outcome with the example of purple loosestrife (Lythrum salicaria) in North America. In the absence of any tax, the horticultural industry will establish n = 3528 nursery operations, and the expected damages from invasion are US$ 28.2 million per year. With the tax, only n = 300 nurseries are established but the expected damages from invasion are reduced to US$ 1.3 million per year. Although profits for the horticultural industry are lower from the tax, the net gains in overall social welfare more than offset the losses. Although these results are illustrative only, they show that the problem of plant invasives initiated by commercial operations is amenable to standard economic analysis and solutions, such as implementation of an “introducers' pay tax”.     

Chromosome-level de novo genome assemblies of over 100 plant species

Genome sequence analysis in higher plants began with the whole-genome sequencing of Arabidopsis thaliana. Owing to the great advances in sequencing technologies, also known as next-generation sequencing (NGS) technologies, genomes of more than 400 plant species have been sequenced to date. Long-read sequencing technologies, together with sequence scaffolding methods, have enabled the synthesis of chromosome-level de novo genome sequence assemblies, which has further allowed comparative analysis of the structural features of multiple plant genomes, thus elucidating the evolutionary history of plants. However, the quality of the assembled chromosome-level sequences varies among plant species. In this review, we summarize the status of chromosome-level assemblies of 114 plant species, with genome sizes ranging from 125 Mb to 16.9 Gb. While the average genome coverage of the assembled sequences reached up to 89.1%, the average coverage of chromosome-level pseudomolecules was 73.3%. Thus, further improvements in sequencing technologies and scaffolding, and data analysis methods, are required to establish gap-free telomere-to-telomere genome sequence assemblies. With the forthcoming new technologies, we are going to enter into a new genomics era where pan-genomics and the >1,000 or >1 million genomes’ project will be routine in higher plants.     

Comparative genomics of Brassicaceae crops

The family Brassicaceae is one of the major groups of the plant kingdom and comprises diverse species of great economic, agronomic and scientific importance, including the model plant Arabidopsis. The sequencing of the Arabidopsis genome has revolutionized our knowledge in the field of plant biology and provides a foundation in genomics and comparative biology. Genomic resources have been utilized in Brassica for diversity analyses, construction of genetic maps and identification of agronomic traits. In Brassicaceae, comparative sequence analysis across the species has been utilized to understand genome structure, evolution and the detection of conserved genomic segments. In this review, we focus on the progress made in genetic resource development, genome sequencing and comparative mapping in Brassica and related species. The utilization of genomic resources and next-generation sequencing approaches in improvement of Brassica crops is also discussed.     

FISHy Analysis of Tetrapioid Cotton Species

Fluorescent in situ hybridization (FISH) is an important technique in plant genome research,because it provides integrated information about DNA,chromosomes and genomes.Genomic in situ hybridization (GISH) is a modification of FISH that can be used to rapidly compare genorne content,relatedness,organization and/or behavior.GISH results often provide insight into genome evolution and species relationships.     

Transferability of rice SSR markers to bamboo

Simple sequence repeat (SSR) markers are widely applied in studies of plant molecular genetics due to their abundance in the genome, codominant nature, high repeatability, and transferability in cross-species applications. To investigate the possibility of applying rice SSR markers in bamboo, we selected 120 rice SSR markers that are evenly distributed on rice chromosomes and assessed these for their transferability to 21 different bamboo species. A total of 4847 bands of 2196 alleles were obtained from 82 SSR markers that were able to amplify products in the bamboo genome; the transferability was 68.3%. Seven markers specifically amplified individual bamboo species and are consequently valuable markers for species identification. SSR markers located on rice chromosome 7 and 1 showed the highest and lowest transferability, respectively to the bamboo genome. SSR markers located on some regions of the rice chromosomes could not be amplified in bamboo, suggesting that regional divergence occurred between rice and bamboo during evolution. A dendrogram was constructed. The dendrogram classified bamboo species into two major groups which coincided with rhizome type, runner, and clumper. The results of this study demonstrate that rice SSR markers can be a valuable source of markers for those genomes lacking useful marker systems.