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。     

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。     

我国完成短花药野生稻基因组测序及分析

在I-OMAP计划的框架下,中国科学院遗传与发育生物学研究所陈明生课题组通过与深圳华大基因、亚利桑那大学等合作,利用第二代测序技术完成了261Mb高质量的短花药野生稻(O.rachyantha)全基因组序列,并开展了稻属比较基因组学和基因组进化的研究。研究揭示了稻属基因组在基因组大小、基因移动和异染色质进化等方面新的分子机制。     

基于rps4基因探讨中国丛藓科苔藓植物系统学研究

本研究采用PCR直接测序法,对中国丛藓科苔藓植物42个不同样品的rps4序列进行系统学研究。结果表明,rps4总长度为562 bp,其中包含201个变异位点,132个信息位点,碱基之间的转换与颠换比为1.77,平均G+C含量为27.5%,遗传距离值最小为0,最大的是小墙藓属与扭口藓属为0.3。基于贝叶斯法构建系统发育树,结果显示,贝叶斯树分为3个大支,分别为毛口藓亚科、扭口藓亚科及丛藓亚科,同时支持毛口藓亚科为一并系群,扭口藓亚科为一单系群,表明rps4基因比较适合于研究中国丛藓科植物的分子系统学。     

7种苔藓植物水提液对玉米种子萌发及幼苗生长的影响

研究了7种苔藓植物配子体水提液对玉米种子萌发和幼苗生长及生理特性的影响。结果显示:垂枝藓(Rhytidium rugosum)、粗枝拟垂枝藓(Rhytidiadelphus squarrosus)、牛舌藓扁枝亚种(Anomodon minor subsp)、东亚砂藓(Racomitrium japonicum)和蛇苔(Conocephalum conicum)明显促进了玉米主胚根和胚芽的生长。7种苔藓植物配子体水提液均表现出抑制玉米侧根数增加。幼苗生长过程中的脯氨酸含量,早期均明显低于对照,胚根POD活性高于对照,说明本试验中部分苔藓植物水提取液能够促进幼苗生长,有利于玉米幼苗培育和壮苗。     

长雄野生稻(Oryza longistaminata)全基因组Fosmid文库构建

长雄野生稻(O.longistaminata)起源于非洲,具有和亚洲栽培稻相同的AA基因组,是栽培稻改良的重要遗传资源。本研究构建了长雄野生稻全基因组fosmid文库,共获得33.6万克隆,文库的平均插入片段大小约为40kb,其中94.7%的克隆插入片段大小在30~50kb之间。挑取其中约11万克隆并保存,可覆盖10倍栽培稻基因组,对任意基因或序列的筛选概率达到了99.99%。将剩余的22万个克隆进行了末端配对测序,显示其有助于长雄野生稻全基因组测序的拼接。所构建的fosmid文库为筛选和克隆长雄野生稻的有利基因提供了研究材料。     

鹅掌楸全基因组调查

鹅掌楸属树种是珍稀的第三纪孑遗树种,也是优良用材兼园林绿化树种。但其分子生物学研究进展缓慢,全基因组的破译成为鹅掌楸属树种分子生物学研究深入开展的关键。本研究基于Illumina测序平台首次对鹅掌楸基因组的大小进行测定,通过生物信息学方法对其重复序列情况和杂合率等基本信息进行了预估,并进行了初步组装。主要结果如下:(1)鹅掌楸全基因组大小预估为1.57 Gb;(2)鹅掌楸基因组的杂合率和重复序列比例分别为0.93%和58.58%;(3)鹅掌楸属于高重复高杂合基因组,建议后续可以采用二代+三代(Illumina+Pac Bio)测序技术相结合的策略,辅以Hi-C技术以及相应的拼接软件,有利于鹅掌楸高质量全基因组图谱的获得。     

南瓜与葡萄和冬瓜的比较基因组学分析

南瓜含有丰富的维生素,营养价值极高。两个栽培种中国南瓜(Cucurbita moschata Duch.)和印度南瓜(Cucurbita maxima Duch.)基因组测序完成,为南瓜的比较基因组学分析提供了基础材料。本研究以葫芦科中较保守的冬瓜,以及双子叶葡萄作为参考基因组,对南瓜基因组结构进行了深入分析,证实了南瓜与其他葫芦科共有一次祖先四倍体事件(CCT),并且南瓜属共有一次特异性四倍体事件(CST)。通过细致的基因组结构和共线性分析,发现南瓜基因组中约11%的重复基因由CCT产生;与CST关联的重复基因约占全基因组的40%。以葡萄和冬瓜基因组为参考,构建了南瓜为核心的多基因组与古老多倍化事件和物种分化关联的同源基因比对图谱。另外,多倍化对重要基因家族形成具有重要贡献,以南瓜乙烯合成酶为例,分析了不同多倍化事件在其拷贝数变化上起到了不同程度的作用。该项研究为理解南瓜多倍化过程提供了清晰的基因组同源结构分析证据,对于南瓜基因组形成和基因进化研究提供了重要的比较基因组学基础。     

7种灰藓目植物醇提液的体外抑菌作用

为研究7种灰藓目植物醇提取液对11种细菌生长的抑制作用,探讨灰藓目植物的药用价值。本研究采用贴滤纸片法对7种灰藓目植物的抑菌性进行研究。结果表明,与对照组相比,柔叶青藓、多蒴灰藓和宝岛绢藓具有广泛抗菌作用。此外,钙生灰藓对铜绿假单孢菌、乙型副伤寒沙门氏菌抑菌作用与对照组相比有极显著差异。本研究对药用苔藓植物的筛选和资源保护有一定帮助。     

毛竹全长LTR逆转座子的鉴定和进化分析

转座子和逆转座子的大量插入,是高等植物基因组进化的重要动力。作为植物基因组研究热点的禾本科植物之一,毛竹基因组大小约为2 Gb,60%为重复序列,长末端重复序列型逆转座子(LTR逆转座子)则占全部重复序列的一半以上,然而目前对毛竹基因组中LTR逆转座子及进化情况知之甚少。本研究利用已发表的毛竹基因组序列,首次通过大数据筛查预测获得9436个平均长度10.3 kb的全长LTR逆转座子。通过分析,我们估算出毛竹LTR逆转座子插入基因组的时间主要分布于200~500万年前,晚于毛竹基因组四倍化的时间。研究还发现了29个位于全长LTR逆转座子内部、有转录组序列支持的蛋白编码基因,这些毛竹基因均不符合所在基因组区段的毛竹-水稻基因共线性关系,且位于LTR逆转座子内部的基因与存在于染色体其他位置的同源基因在表达模式上有着较大差异。本研究首次尝试从LTR逆转座子的角度探索毛竹基因的进化历程,也为今后的植物基因组研究提供了重要的基础数据。     

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 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.     

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.     

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.     

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”.     

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.     

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.     

Plant genetic resources of Nepal: A guide for plant breeders of agricultural, horticultural and forestry crops

Summary Nepal is rich in indigenous wild and landrace plant genetic resources for agronomic, horticultural, forestry, or medicinal uses, but much of this germplasm remains uncollected and awaits economic development. We list 485 entries (species, or genera for ornamental plants) in 14 categories, and compare these to existing germplasm collections in Nepal and the United States to highlight collection and conservation needs. To help plant plant collecting, we outline the key botanical and logistical data and legal framework for planning field work in Nepal.