钩梢强度对麻竹生物量分配和生理特性的影响

以不钩梢为对照,对笋期内麻竹进行轻度、中度、重度钩梢处理,研究各钩梢处理立竹构件生物量分配、当年生枝条和商品叶生长,以及净光合速率(P_n)、蒸腾速率(T_r)、水分利用效率(WUE)和叶片水势(LWP)等的变化,分析麻竹对营林措施中钩梢强度的适应机制和生存策略.结果表明: 与对照相比,钩梢处理对麻竹生物量及分配影响显著,3个处理麻竹立竹的叶/枝、叶/秆、枝/秆生物量比均显著高于对照.轻度钩梢和中度钩梢处理当年生枝条数量、基径、长度均显著大于对照,其中,中度钩梢处理当年生枝条基径、数量、长度和商品叶数量分别比对照增加43.0%、53.3%、29.8%和39.5%.各钩梢处理麻竹P_n、T_r、WUE、LWP在笋期内大小为出笋盛期>末期>初期;钩梢后麻竹的P_n、T_r和WUE显著提高,其中,各处理出笋盛期和末期的P_n大小为中度钩梢>轻度钩梢>重度钩梢>对照,且出笋盛期和末期的P_n分别是对照的1.4和1.3倍.各处理出笋初期、盛期和末期的T_r均为重度钩梢>中度钩梢>轻度钩梢>对照.中度钩梢处理对麻竹立竹的生物量分配、商品叶产量和生理特性均有明显优势,并能有效提高麻竹立竹的水分可获得性.     

Reducing assembly complexity of microbial genomes with single-molecule sequencing

Background

The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem.

Results

To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads.

Conclusions

Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.     

转录组测序揭示翼盖蕨(Didymochlaena trancatula)的全基因组复制历史

全基因组复制在动植物中普遍存在, 被认为是促进物种进化的重要动力之一。作为蕨类植物的单种科物种, 翼盖蕨(Didymochlaena trancatula)是真水龙骨类I的基部类群, 在蕨类中具有独特的演化地位。本研究基于高通量测序, 通过同义替换率(Ks)分析、相对定年分析揭示翼盖蕨的全基因组复制发生情况。Ks分析表明, 翼盖蕨至少经历了两次全基因组复制事件, 其中一次发生于59-62 million years ago (Mya), 另一次发生于90-94 Mya, 这两次全基因组复制事件分别和白垩纪第三纪的Cretaceous-Tertiary (C-T)大灭绝事件以及翼盖蕨的物种分化时间相吻合。进一步对两次全基因组复制保留的基因进行功能注释和富集分析, 结果显示与转录及代谢调控相关的基因优势被保留。翼盖蕨的全基因组复制事件可能促进了该物种的分化及其对极端环境的适应性。     

Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar ‘Fielder’

We have established a high-quality, chromosome-level genome assembly for the hexaploid common wheat cultivar ‘Fielder’, an American, soft, white, pastry-type wheat released in 1974 and known for its amenability to Agrobacterium tumefaciens-mediated transformation and genome editing. Accurate, long-read sequences were obtained using PacBio circular consensus sequencing with the HiFi approach. Sequence reads from 16 SMRT cells assembled using the hifiasm assembler produced assemblies with N50 greater than 20 Mb. We used the Omni-C chromosome conformation capture technique to order contigs into chromosome-level assemblies, resulting in 21 pseudomolecules with a cumulative size of 14.7 and 0.3 Gb of unanchored contigs. Mapping of published short reads from a transgenic wheat plant with an edited seed-dormancy gene, TaQsd1, identified four positions of transgene insertion into wheat chromosomes. Detection of guide RNA sequences in pseudomolecules provided candidates for off-target mutation induction. These results demonstrate the efficiency of chromosome-scale assembly using PacBio HiFi reads and their application in wheat genome-editing studies.     

六妹羊肚菌PacBio基因组测序和DNA 6mA甲基化分析

羊肚菌属于子囊门真菌,是世界范围内最受欢迎的食用菌之一。本研究通过PacBio单分子实时测序技术对我国四川省成功栽培的六妹羊肚菌Morchella sextelata SCLS菌株进行全基因组测序,获得其高质量核基因组组装,大小为53.57Mb,重复序列含量为17.03%,包含42条重叠群（contigs）,重叠群N50高达1.82Mb,其中13条重叠群两端均含有端粒重复序列,为完整的染色体。通过链特异性RNA-seq测序和转录本拼接,并结合多种基因预测策略,预测到13 182个蛋白编码基因,包括267个碳水化合物活性酶,11个次生代谢产物合成基因簇。通过与内蒙古地区栽培的六妹羊肚菌菌株NZTD180501373基因组比较发现,六妹羊肚菌进化过程中可能发生过染色体重组事件,二者具有33 055个SNP和48 726个InDel位点差异,并且各自拥有超过6Mb的特有序列。此外,相比于梯棱羊肚菌M. importuna,六妹羊肚菌SCLS菌株中与逆转录转座酶有关的orthogroup发生了扩张,并且拥有5个成员数超过100的特有逆转录转座酶基因家族。对SCLS菌株中的DNA N⁶腺嘌呤甲基化（6mA）修饰进行了鉴定,发现SCLS菌株基因组中0.42%的腺嘌呤被6mA甲基化,其含量显著高于已报道的6种双核亚界（Dikarya）真菌。6mA甲基化位点在逆转录转座子上显著富集,表明六妹羊肚菌中6mA甲基化可能调控逆转录转座子的活性,这也是首次在真菌中报道6mA甲基化与转座子相关。     

Secondary Metabolite Analysis of Phomopsis sp. LGT-5 Based on the Dual Guidance of Whole-Genome Sequencing and HPLC-Q-ToF-MS/MS

Microorganisms produce a wealth of structurally diverse specialized metabolites with a remarkable range of biological activities. The Phomopsis sp. LGT-5 was obtained through tissue block and repeatedly crossed methods from Tripterygium wilfordii Hook. F. The antibacterial experiments of LGT-5 showed that it has high inhibitory activity against Staphylococcus aureus and Pseudomonas aeruginosa, and moderate inhibitory activity against Candida albicans. To research the generation of the antibacterial phenomenon of LGT-5 and provide support for further research and application, the whole genome sequencing (WGS) of LGT-5 was obtained by single-molecule real-time DNA sequencing platform Pacific Biosciences (PacBio) sequencing and Illumina paired-end sequencing. The final assembled LGT-5 genome is 54.79 Mb with a contig N50 of 290.07 kb; in addition, its secondary metabolites were detected through HPLC-Q-ToF-MS/MS. By comparing its MS/MS data, the secondary metabolites were analyzed based on visual network maps obtained on the Global Natural Products Social Molecular Networking (GNPS). The analysis results showed that the secondary metabolites of LGT-5 were triterpenes and various cyclic dipeptides.     

The Larix kaempferi genome reveals new insights into wood properties

Here, through single-molecule real-time sequencing,we present a high-quality genome sequence of the Japanese larch(Larix kaempferi), a conifer species with great value for wood production and ecological afforestation. The assembled genome is 10.97 Gb in size, harboring 45,828 protein-coding genes. Of the genome, 66.8% consists of repeat sequences, of which long terminal repeat retrotransposons are dominant and make up 69.86%. We find that tandem duplications have been responsible for the expansi...     

苦马豆叶绿体基因组结构及其特征分析

利用Illumina高通量测序平台对苦马豆（Sphaerophysa salsula）进行测序和组装,获得完整的苦马豆叶绿体基因组序列。组装结果表明,苦马豆叶绿体基因组全长123 327 bp,存在IR区丢失,不具有四分体结构;注释结果显示,苦马豆叶绿体基因组共编码108个基因,其中包含74个蛋白编码基因、4个rRNA基因和30个tRNA基因;叶绿体基因组序列上共检测到99个SSR位点,包含75个单核苷酸、17个二核苷酸和7个三核苷酸重复单元;系统发育分析显示,苦马豆和骆驼刺为姊妹群,亲缘关系最近。这为今后苦马豆遗传多样性、群体遗传结构和物种形成机制研究奠定了基础。     

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II’s sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.     

喜马红景天叶绿体基因组特征及其系统发育分析

以青藏高原特有药用植物——喜马红景天（Rhodiola himalensis）为试验材料,利用高通量测序技术对喜马红景天进行叶绿体基因组测序、组装和注释,获得完整的叶绿体基因组。结果显示：喜马红景天叶绿体基因组全长为151 074 bp,GC含量为37.8%,具有1个长单拷贝区、1个短单拷贝区和1对反向重复区的典型四分体结构,其序列长度分别为82 309、17 017、25 874 bp;叶绿体基因组共编码130个基因,其中编码蛋白的基因86个、编码tRNA的基因37个、编码rRNA的基因7个;叶绿体基因组共检测出25 513个密码子,其中编码亮氨酸（Leu）的密码子占比最大;喜马红景天IRa和IRb区的rps19和ycf1基因缺失,长单拷贝区的trnH基因收缩;喜马红景天与圣地红景天（R. sacra）亲缘关系最近;短单拷贝区域的单核苷酸多态性（SNP）变异频率最高。本研究报道了喜马红景天的叶绿体基因组,并对其进行了组装、注释和序列分析,为今后开展喜马红景天的遗传多样性研究和合理开发利用提供理论依据。     

Comparative analysis of complete plastid genome reveals powerful barcode regions for identifying wood of Dalbergia odorifera and D. tonkinensis (Leguminosae)

Dalbergia odorifera T. C. Chen (Leguminosae), a rare and endangered tree species endemic to Hainan Island of China, produces the most expensive and rarest wood in China. The wood characteristics of D. odorifera are remarkably similar to those of D. tonkinensis (a much less sought-after species from Vietnam), and the DNA from wood is often highly degraded, making it very difficult to identify the two species using anatomical features or DNA barcoding based on regular DNA markers. To solve the confusion of identifying wood reliably from the two species, we built and analyzed the plastome library of 26 samples from 18 Dalbergia species, of which 12 samples from eight closely related species of D. odorifera are newly sequenced in this study. Phylogenomic analysis suggested that the relationships among the 26 samples are mostly well resolved, and conspecific individuals from different populations of D. odorifera and D. tonkinensis clustered together. Between the plastid genomes of the two species, we identified 129 indels and 114 single nucleotide polymorphisms. By assessing a subset of 20 nucleotide polymorphisms and 10 indels using 37 population-level samples (20 samples of D. odorifera and 17 samples of D. tonkinensis), we recovered eight species-specific barcode regions that could be suitable for identifying the wood D. odorifera and D. tonkinensis. To examine their utility in wood identification, we amplified the eight DNA barcodes using six wood samples and recovered an amplification success rate of 83.3%, demonstrating a reliable method for precise wood identification of the two species.     

铁棍山药微型块茎遗传转化体系的建立

怀山药(Dioscorea opposita)遗传转化是对其进行基因功能分析和遗传改良的基础, 但目前国内外尚未见相关报道。以怀山药优良品种铁棍山药(D. opposita cv. ‘Tiegun’)的微型块茎为受体材料, 对影响遗传转化的因素进行优化, 建立了由根癌农杆菌介导的山药遗传转化体系。过表达质粒载体pCAMBIA1301-DoSERK2含GUS标记基因和潮霉素(Hyg)抗性筛选基因, 沉默质粒载体pART27-DoSERK2含卡那霉素(Kan)抗性筛选基因。根癌农杆菌抑制剂特美汀(Tim)的最佳浓度为500 mg·L ^-1; 再生芽和生根时, Hyg的最佳浓度分别为15和20 mg·L ^-1, Kan的最佳浓度分别为120和160 mg·L ^-1。对转化植株进行PCR和GUS组织化学检测, 结果显示外源基因已整合到铁棍山药转基因株系的基因组中并在细胞中表达。该研究建立了一套取材便利的铁棍山药遗传转化方法, 对其它品种山药的转化也具有参考价值。     

金钟藤入侵群落的种间联结及生态位特征

金钟藤(Decalobanthus boisianus)是林业有害植物, 其暴发生长和扩散对森林生态系统造成了严重破坏。本文以海南岛48个金钟藤典型分布群落为研究对象, 用方差比率法和贡献定律法探究群落的稳定性; 用χ ²统计量、联结系数(AC)、共同出现百分率(PC)、Ochiai指数和Dice指数分析金钟藤与伴生物种的种间联结关系; 用生态位宽度、生态位相似性系数和生态位重叠指数研究群落中各物种的生态位特征, 以期为金钟藤生物防治的植物物种筛选提供借鉴。结果表明: (1)金钟藤所在48个群落共有156种伴生植物, 其中大戟科、茜草科、桑科、无患子科和樟科植物占优势; (2)群落中优势物种呈正联结关系, 植物种类累积倒数百分比与累积相对频度交点坐标为(44.53, 55.47), 远离稳定交点坐标(20, 80), 说明群落处于不稳定状态; (3)金钟藤与芳槁润楠(Machilus suaveolens)、黄椿木姜子(Litsea variabilis)、岭南山竹子(Garcinia oblongifolia)、显脉杜英(Elaeocarpus dubius)、鸭脚木(Schefflera octophylla)和银柴(Aporusa dioica)都紧密关联, 说明金钟藤与这些物种的资源利用方式较相似; (4)金钟藤的生态位宽度最大, 与伴生物种间的生态位重叠度较高, 但伴生物种间的生态位重叠度较低。金钟藤的入侵导致群落处于不稳定状态, 并与伴生物种间存在激烈的竞争关系。因此, 建议在金钟藤已入侵的群落中大量栽种芳槁润楠、黄椿木姜子、显脉杜英、鸭脚木和银柴, 以遏制其蔓延; 大量栽种翻白叶树(Pterospermum heterophyllum)、海南菜豆树(Radermachera hainanensis)、九节(Psychotria rubra)和肉实树(Sarcosperma laurinum)用于金钟藤入侵群落的植被恢复。     

A de novo chromosome‐level genome assembly of Coregonus sp. “Balchen”: One representative of the Swiss Alpine whitefish radiation

Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life‐history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution. Although well‐curated genome assemblies exist for many species within Salmonidae, genomic resources for the subfamily Coregoninae are lacking. To assemble a whitefish reference genome, we carried out PacBio sequencing from one wild‐caught Coregonus sp. “Balchen” from Lake Thun to ~90× coverage. PacBio reads were assembled independently using three different assemblers, falcon , canu and wtdbg2 and subsequently scaffolded with additional Hi‐C data. All three assemblies were highly contiguous, had strong synteny to a previously published Coregonus linkage map, and when mapping additional short‐read data to each of the assemblies, coverage was fairly even across most chromosome‐scale scaffolds. Here, we present the first de novo genome assembly for the Salmonid subfamily Coregoninae. The final 2.2‐Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb and was 93.3% complete for BUSCOs. The assembly consisted of ~52% transposable elements and contained 44,525 genes.