Article Online

Articles Online (Volume 18, Issue 3)

review

The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms

Jiantao Guan, Diego F. Garcia, Yun Zhou, Rudi Appels, Aili Li, Long Mao

In the year 2018, the world witnessed the finale of the race to sequence the genome of the world’s most widely grown crop, the common wheat. Wheat has been known to bear a notoriously large and complicated genome of a polyploidy nature. A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries, taking a conventional strategy similar to that for sequencing Arabidopsis and rice, became ferocious over time as both sequencing technologies and genome assembling methodologies advanced. At different stages, multiple versions of genome sequences of the same variety (e.g., Chinese Spring) were produced by several groups with their special strategies. Finally, 16 years after the rice genome was finished and 9 years after that of maize, the wheat research community now possesses its own reference genome. Armed with these genomics tools, wheat will reestablish itself as a model for polyploid plants in studying the mechanisms of polyploidy evolution, domestication, genetic and epigenetic regulation of homoeolog expression, as well as defining its genetic diversity and breeding on the genome level. The enhanced resolution of the wheat genome should also help accelerate development of wheat cultivars that are more tolerant to biotic and/or abiotic stresses with better quality and higher yield.
基因组序列是研究一个物种的进化、基因功能和基因调控的重要信息和工具。六倍体小麦基因组是水稻基因组的40倍是玉米基因组的5倍。庞大且复杂的小麦基因组决定其测序过程将如三国演义，魏蜀吴争长相雄。该综述把小麦基因组测序过程分成黑暗、黎明、高潮和春天四个阶段，系统梳理了小麦及其供体种基因组测序的历史，介绍了不同基因组版本采取的测序技术和组装策略以及达到的组装水平，总结了近年来小麦功能基因组研究的部分主要进展。 故事从2005年成立由多个国家组成的国际小麦测序组织（IWGSC）讲起。早期，IWGSC尝试采取与拟南芥和水稻测序类似的常规策略来测定和组装小麦基因组，即通过构建细菌染色体(BAC)文库-物理图谱-最小物理通路BAC测序的方法。按照这个策略，光是构建物理图谱一项就需要花费几百万美元，而且由于基因组过于庞大，没有实验室能够单独完成这个工作。于是，IWGSC先用流式细胞仪器将一个个染色体甚至是染色体臂分离出来，分别建库，然后再运送到几十个国家的研究小组，分别构建物理图谱。在将近10年的时间里，由于经费、人员、技术、文库质量等诸多原因，小麦基因组测序踽踽前行，不知始终。而同一时期，另外两个禾本科作物-高粱和玉米的基因组分别于2009年和2010年得以完成。2012年小麦的兄弟种大麦的基因组也得到了破译。于是，就有科学家建议先行测定小麦的二倍体供体种基因组，以加快六倍体小麦的测序速度和功能基因组研究。 2013年，两个二倍体供体种基因组乌拉尔图小麦（AA）和山羊草（DD）的基因组草图由中国科学家在Nature发表。而作为IWGSC成员的英国诺丁汉大学的科学家也匆匆忙忙于2014年在Science发表了由混合BAC文库鸟枪法454测序序列组装的中国春草图（CSS）。同年，利用传统方法测定的3B染色体序列也由法国科学家发表。2017年英国约翰英尼斯研究所通过提高测序深度和改进组装算法获得了中国春基因组的改进版TGACv1，但只有78%的基因组序列被锚碇到染色体上。2017年一个新成立的以色列生物信息公司NRGene的出现，使得解决像小麦这样的复杂基因组的组装难题有了新的转机。这期间发表的野生二粒小麦（四倍体）、乌拉尔图小麦和山羊草的改进版本（2017）以及2019年发表的栽培二粒小麦（四倍体）多多少少都受惠于NRGene的DeNovoMAGIC2软件的使用。2017年由IWGSC主导，加州大学戴维斯分校领衔的高质量山羊草基因组在Science发表。2018年，通过13年的努力，一个基本达到参考基因组质量水平的中国春序列（Refseqv1.0）终于完成，并在Science上发表。 回顾小麦基因组测序的历程，我们发现几乎每个小麦基因组及其不同版本都发表在国际顶尖杂志上：乌拉尔图基因组产生了两个版本，均发表在Nature；山羊草基因组则有三个版本分别发表在Nature，Nature Plants和Science；而中国春的三个版本中有两个发表在Science，3B染色体也在Science发表。经过这些年三国演义式的左冲右突，在水稻基因组完成16年和玉米基因组完成9年之后，普通小麦的基因组测序终于尘埃落定，尽管其质量还有很大提升的空间。小麦基因组序列的获得开启了小麦重新作为多倍体植物的模型，用于研究年轻多倍体进化，驯化，部分同源基因表达调控的遗传和表观遗传机制的新纪元，大大推进了小麦产量抗病相关基因挖掘，加速了高产高抗优良品种的创制。 该综述于近期发表于Genomic Proteomics & Bioinformatics杂志，中国农业科学院作物科学研究所毛龙研究员为责任作者，实验室官健涛博士为第一作者。作者感谢国家自然基金和中国农科院创新工程大力支持。

Page 221-229

Original Research

Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis

Zhichao Xu, Ranran Gao, Xiangdong Pu, Rong Xu, Jiyong Wang, Sihao Zheng, Yan Zeng, Jun Chen, Chunnian He, Jingyuan Song

Scutellaria baicalensis (S. baicalensis) and Scutellaria barbata (S. barbata) are common medicinal plants of the Lamiaceae family. Both produce specific flavonoid compounds, including baicalein, scutellarein, norwogonin, and wogonin, as well as their glycosides, which exhibit antioxidant and antitumor activities. Here, we report chromosome-level genome assemblies of S. baicalensis and S. barbata with quantitative chromosomal variation (2n = 18 and 2n = 26, respectively). The divergence of S. baicalensis and S. barbata occurred far earlier than previously reported, and a whole-genome duplication (WGD) event was identified. The insertion of long terminal repeat elements after speciation might be responsible for the observed chromosomal expansion and rearrangement. Comparative genome analysis of the congeneric species revealed the species-specific evolution of chrysin and apigenin biosynthetic genes, such as the S. baicalensis-specific tandem duplication of genes encoding phenylalanine ammonia lyase and chalcone synthase, and the S. barbata-specific duplication of genes encoding 4-CoA ligase. In addition, the paralogous duplication, colinearity, and expression diversity of CYP82D subfamily members revealed the functional divergence of genes encoding flavone hydroxylase between S. baicalensis and S. barbata. Analyzing these Scutellaria genomes reveals the common and species-specific evolution of flavone biosynthetic genes. Thus, these findings would facilitate the development of molecular breeding and studies of biosynthesis and regulation of bioactive compounds.
新型冠状病毒肺炎（COVID-19）肆虐全球，中医药在新冠诊治方面发挥积极作用。中药黄芩和半枝莲具有清热解毒功效，其基原植物为唇形科黄芩属植物黄芩（Scutellaria baicalensis）和半枝莲（Scutellaria barbata），主要活性成分为黄酮类化合物，如黄芩素、汉黄芩素、野黄芩素及其糖苷类化合物。黄芩活性成分的生物合成途径及体外合成生物学研究受国际关注。本研究报道了黄芩和半枝莲的染色体水平基因组序列。通过单拷贝基因构建系统发育树揭示黄芩和半枝莲的分化时间（13.28MYA）远早于之前的报道（3.35MYA），基于同源基因的同义替换速率研究发现唇形科与胡麻科共享的全基因组复制（WGD）事件。半枝莲基因组中长末端重复序列的近期插入可能与其染色体的重排和扩张相关。比较基因组研究显示芹菜素和白杨素合成途径相关基因在黄芩和半枝莲中特异性的扩张，如黄芩特异的苯丙氨酸解氨酶（phenylalanine ammonia-lyase，PAL）和查尔酮合成酶（chalcone synthase，CHS）编码基因的串联复制，以及半枝莲特异的4-香豆酰辅酶A连接酶（4-coumarate CoA ligase, 4CL）的扩张。此外，基于基因组共线性及不同组织部位基因表达研究发现黄芩和半枝莲中黄酮羟化酶编码基因（CYP82Ds）的复制及功能差异。本研究将有助于理解黄芩和半枝莲黄酮类化合物的合成及进化机制，为中药黄芩和半枝莲的高品质分子辅助育种等研究奠定基础。

Page 230-240

Original Research

MicroRNAs Are Involved in Maize Immunity Against Fusarium verticillioides Ear Rot

Zijian Zhou, Yan Cao, Tao Li, Xinghao Wang, Jiafa Chen, Hang He, Wen Yao, Jianyu Wu, Huiyong Zhang

Fusarium ear rot (FER) caused by Fusarium verticillioides is one of the most common diseases affecting maize production worldwide. FER results in severe yield losses and grain contamination with health-threatening mycotoxins. Although most studies to date have focused on comprehensive analysis of gene regulation in maize during defense responses against F. verticillioides infection, less is known about the role of microRNAs (miRNAs) in this process. We used deep sequencing to compare small RNA libraries from the maize kernels of susceptible (N6) or resistant (BT-1) inbred lines from uninfected plants and upon F. verticillioides infection. We found that pathogen exposure was accompanied by dynamic alterations in expression levels of multiple miRNAs, including new members of previously annotated miRNA families. A combination of transcriptomic, degradomic, and bioinformatics analyses revealed that F. verticillioides-responsive miRNAs and their potential target genes displayed opposite expression patterns in the susceptible and resistant genotypes. Functional category analysis uncovered preferential enrichment of the pathogen-responsive miRNAs and their targets in the phenylpropanoid metabolic processes, plant–pathogen interactions, and plant phytohormone signal transduction pathways. Furthermore, transgenic maize plants overexpressing miR408b exhibited reduced resistance to F. verticillioides infection in a susceptible maize line. These findings provide new insights into the regulatory roles of miRNAs in maize immunity against FER and new resources for breeding disease resistance into maize.
拟轮枝镰孢菌引起的玉米穗粒腐病是一种世界性的真菌病害，它不仅造成玉米严重减产，而且病原菌产生的毒素严重威胁人畜健康安全。诸多研究表明玉米穗粒腐病抗性是复杂的数量性状，其中涉及到众多的基因调控网络，利用图位克隆方法鉴定了许多与玉米穗粒腐病抗性相关的QTL及候选抗病基因。但是，关于microRNA是否在转录后水平参与调控玉米穗粒腐病还不清楚。该研究利用穗粒腐病高抗自交系（BT-1）和感病自交系（N6）为材料，通过高通量测序比较分析两种材料籽粒在拟轮枝镰孢菌侵染前后microRNA的特异性表达，鉴定出一系列可能与穗粒腐病抗性相关的microRNA，它们显著富集在已知抗病QTL位点，并且调控植物抗病免疫通路中一些关键的因子。利用降解组和转录组分析其调控的下游靶基因，发现这些差异表达的靶基因主要与苯丙素代谢通路、植物激素信号传导等通路密切相关。最后，选择一个在抗感玉米自交系之间差异表达，并在植物中高度保守的miR408b进行转基因功能分析，发现miR408b的过量积累显著升高对拟轮枝镰孢菌的敏感性，说明其可能是穗粒腐病抗性的一个负调控因子。这些结果有助于从基因转录后调控水平阐明玉米穗粒腐病抗病遗传机制，为抗病玉米选育提供更丰富的育种元件及潜在的分子标记。

Page 241-255

Original Research

Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis

Jihong Hu, Tao Zeng, Qiongmei Xia, Liyu Huang, Yesheng Zhang, Chuanchao Zhang, Yan Zeng, Hui Liu, Shilai Zhang, Guangfu Huang, Wenting Wan, Yi Ding, Fengyi Hu, Congdang Yang, Luonan Chen, Wen Wang

Significantly increasing crop yield is a major and worldwide challenge for food supply and security. It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the highest yield worldwide. Yet, the gene regulatory mechanism underpinning this ultrahigh yield has been a mystery. Here, we systematically collected the transcriptome data for seven key tissues at different developmental stages using rice cultivated both at Taoyuan as the case group and at another regular rice planting place Jinghong as the control group. We identified the top 24 candidate high-yield genes with their network modules from these well-designed datasets by developing a novel computational systems biology method, i.e., dynamic cross-tissue (DCT) network analysis. We used one of the candidate genes, OsSPL4, whose function was previously unknown, for gene editing experimental validation of the high yield, and confirmed that OsSPL4 significantly affects panicle branching and increases the rice yield. This study, which included extensive field phenotyping, cross-tissue systems biology analyses, and functional validation, uncovered the key genes and gene regulatory networks underpinning the ultrahigh yield of rice. The DCT method could be applied to other plant or animal systems if different phenotypes under various environments with the common genome sequences of the examined sample. DCT can be downloaded from https://github.com/ztpub/DCT.
农作物产量的显著提升是关系到全世界食物供给和粮食安全的重大问题。在中国云南涛源地区，发现在自然条件下的水稻种植能获得超高的产量，然而，这种超高产水稻的调控机理一直是个尚未可知。为揭示这个谜团，本研究在持续4年大大田实验基础上，同时收集涛源和景洪（对照）地区影响水稻产量和生长发育的7个关键组织，进行转录组测序。利用自主开发的计算系统生物学算法，动态跨组织隐变量网络整合分析(dynamic cross-tissue，DCT) 对转录组数据进行系统的生物信息学分析，鉴定到了24个候选高产基因以及相关网络模块。与此同时，我们对其中一个未知功能的候选基因 OsSPL4，进行了基因编辑（CRISPR/Cas9）转基因实验，验证其确实能够显著增加幼穗分枝，进而提高水稻产量。本研究通过大量的田间实验，跨组织的系统生物学分析，功能验证，综合揭示了涛源水稻超高产的关键基因和关键调控网络。我们开发的DCT模型与算法将能广泛应用于其他动植物在相同基因组情况下，由于环境条件不同而引起表型显著差异的分子机理研究。DCT的程序包可以在https://github.com/ztpub/DCT获得。

Page 256-270

Original Research

Na2CO3-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics

Jinwei Suo, Heng Zhang, Qi Zhao, Nan Zhang, Yongxue Zhang, Ying Li, Baohua Song, Juanjuan Yu, Jianguo Cao, Tai Wang, Ji Luo, Lihai Guo, Jun Ma, Xumin Zhang, Yimin She, Lianwei Peng, Weimin Ma, Siyi Guo, Yuchen Miao, Sixue Chen, Zhi Qin, Shaojun Dai

Alkali-salinity exerts severe osmotic, ionic, and high-pH stresses to plants. To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species (ROS) homeostasis, physiological and diverse quantitative proteomics analyses of alkaligrass (Puccinellia tenuiflora) under Na2CO3 stress were conducted. In addition, Western blot, real-time PCR, and transgenic techniques were applied to validate the proteomic results and test the functions of the Na2CO3-responsive proteins. A total of 104 and 102 Na2CO3-responsive proteins were identified in leaves and chloroplasts, respectively. In addition, 84 Na2CO3-responsive phosphoproteins were identified, including 56 new phosphorylation sites in 56 phosphoproteins from chloroplasts, which are crucial for the regulation of photosynthesis, ion transport, signal transduction, and energy homeostasis. A full-length PtFBA encoding an alkaligrass chloroplastic fructose-bisphosphate aldolase (FBA) was overexpressed in wild-type cells of cyanobacterium Synechocystis sp. Strain PCC 6803, leading to enhanced Na2CO3 tolerance. All these results indicate that thermal dissipation, state transition, cyclic electron transport, photorespiration, repair of photosystem (PS) II, PSI activity, and ROS homeostasis were altered in response to Na2CO3 stress, which help to improve our understanding of the Na2CO3-responsive mechanisms in halophytes.
盐碱胁迫导致渗透胁迫、离子胁迫，以及高pH胁迫，是最严重的非生物胁迫之一，限制了植物的生产力和地理分布。叶绿体作为光合作用的细胞器，对盐碱胁迫极为敏感。Na+的过度积累降低了气孔和叶肉细胞CO2的扩散，影响植物的光合作用。同时，过度的激发能导致活性氧（ROS）的产生，造成类囊体膜损伤。然而，目前人们对植物叶绿体响应碱性盐（如Na2CO3和NaHCO3）胁迫的精细分子机制仍不清楚。 禾本科盐生牧草小花碱茅（Puccinellia tenuiflora），是苏打碱型盐碱地的先锋植物，在我国东北和西北地区的盐碱地广泛分布。上海师范大学戴绍军团队利用多种蛋白质组学和磷酸化蛋白质组学策略揭示了小花碱茅（P. tenuiflora）叶绿体响应Na2CO3胁迫过程的光合和ROS清除机制。共鉴定到84种小花碱茅叶绿体中参与Na2CO3应答的磷酸化蛋白质，其中包括56个未被报道过的磷酸化位点，这些磷酸化蛋白质在植物光合作用、离子运输、信号转导和能量平衡等代谢途径中发挥重要作用。同时，利用Western blot、Real-time PCR与分子遗传学策略，对蛋白质组学研究结果进行了初步验证。该研究绘制了盐生牧草叶绿体中应答Na2CO3胁迫的蛋白质丰度与蛋白质磷酸化动态图谱，揭示了维持PSII和PSI之间的能量平衡、PSII损伤修复、循环电子传递，以及ROS稳态等对牧草响应Na2CO3过程中的光合调节至关重要，细胞核和叶绿体编码的蛋白质协同作用参与应答Na2CO3胁迫，蛋白质可逆磷酸化参与调控牧草叶绿体Na2CO3应答过程的多种信号与代谢通路。 该研究结果不仅有助于提高我们对盐生牧草Na2CO3响应分子机制的认识，也为深入研究蛋白质可逆磷酸化在盐生牧草Na2CO3胁迫应答过程中的作用提供了新的线索。

Page 271-288

Original Research

Characterization of Lysine Monomethylome and Methyltransferase in Model Cyanobacterium Synechocystis sp. PCC 6803

Xiaohuang Lin, Mingkun Yang, Xin Liu, Zhongyi Cheng, Feng Ge

Protein lysine methylation is a prevalent post-translational modification (PTM) and plays critical roles in all domains of life. However, its extent and function in photosynthetic organisms are still largely unknown. Cyanobacteria are a large group of prokaryotes that carry out oxygenic photosynthesis and are applied extensively in studies of photosynthetic mechanisms and environmental adaptation. Here we integrated propionylation of monomethylated proteins, enrichment of the modified peptides, and mass spectrometry (MS) analysis to identify monomethylated proteins in Synechocystis sp. PCC 6803 (Synechocystis). Overall, we identified 376 monomethylation sites in 270 proteins, with numerous monomethylated proteins participating in photosynthesis and carbon metabolism. We subsequently demonstrated that CpcM, a previously identified asparagine methyltransferase in Synechocystis, could catalyze lysine monomethylation of the potential aspartate aminotransferase Sll0480 both in vivo and in vitro and regulate the enzyme activity of Sll0480. The loss of CpcM led to decreases in the maximum quantum yield in primary photosystem II (PSII) and the efficiency of energy transfer during the photosynthetic reaction in Synechocystis. We report the first lysine monomethylome in a photosynthetic organism and present a critical database for functional analyses of monomethylation in cyanobacteria. The large number of monomethylated proteins and the identification of CpcM as the lysine methyltransferase in cyanobacteria suggest that reversible methylation may influence the metabolic process and photosynthesis in both cyanobacteria and plants.
研究问题： 蓝细菌中发生赖氨酸甲基化的蛋白有哪些？是否有赖氨酸甲基转移酶？赖氨酸甲基化有何功能？ 研究方法： 在本研究中，我们通过对单甲基化蛋白质进行化学丙酰化，将赖氨酸单甲基化与赖氨酸二甲基化和三甲基化区分开。利用免疫亲和的方法进行单甲基化修饰肽段的富集，最后利用高精度质谱鉴定技术，实现了集胞藻PCC6803赖氨酸单甲基化蛋白的系统鉴定，共包括376个赖氨酸单甲基化位点，分布于270个蛋白质中。GO功能富集和KEGG通路分析提示赖氨酸甲基化对光合作用及能量代谢的调控作用。对蓝细菌全基因序列进行保守结构域比对，预测可能的赖氨酸甲基转移酶。结合基因敲除以及体外甲基化反应验证CpcM是一个新的赖氨酸甲基转移酶。对CpcM敲除株和野生型进行质谱检测找到CpcM的作用底物Sll0480。体外甲基化反应联合质谱检测技术对Sll0480被CpcM甲基化的靶位点进行精准定位。本研究揭示CpcM催化的蛋白质赖氨酸甲基化对转氨酶活性的调控机制，以及对光合作用的潜在影响。 主要结果1： 获得光合生物中首个赖氨酸单甲基化蛋白组数据。 主要结果2： 在模式蓝细菌集胞藻PCC6803中发现首个赖氨酸甲基转移酶CpcM。 主要结果3： CpcM通过催化Sll0480赖氨酸甲基化调控底物蛋白的天冬氨酸转氨酶活性。 主要结果4： 赖氨酸甲基转移酶CpcM的敲除影响了蓝细菌光合作用电子传递。 数据链接： 原始质谱文件及谱图： http://www.peptideatlas.org/PASS/PASS01127

Page 289-304

Original Research

Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles

Liya Zhu, Han Cheng, Guoqing Peng, Shuansuo Wang, Zhiguo Zhang, Erdong Ni, Xiangdong Fu, Chuxiong Zhuang, Zexian Liu, Hai Zhou

Ubiquitination, an essential post-transcriptional modification (PTM), plays a vital role in nearly every biological process, including development and growth. Despite its functions in plant reproductive development, its targets in rice panicles remain unclear. In this study, we used proteome-wide profiling of lysine ubiquitination in rice (O. sativa ssp. indica) young panicles. We created the largest ubiquitinome dataset in rice to date, identifying 1638 lysine ubiquitination sites on 916 unique proteins. We detected three conserved ubiquitination motifs, noting that acidic glutamic acid (E) and aspartic acid (D) were most frequently present around ubiquitinated lysine. Enrichment analysis of Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles. Interestingly, enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptor-like kinases and cytoplasmic tyrosine and serine-threonine kinases. Furthermore, we analyzed the crosstalk between ubiquitination, acetylation, and succinylation, and constructed a potential protein interaction network within our rice ubiquitinome. Moreover, we identified ubiquitinated proteins related to pollen and grain development, indicating that ubiquitination may play a critical role in the physiological functions in young panicles. Taken together, we reported the most comprehensive lysine ubiquitinome in rice so far, and used it to reveal the functional role of lysine ubiquitination in rice young panicles.

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Original Research

Genome Size Evolution Mediated by Gypsy Retrotransposons in Brassicaceae

Shi-Jian Zhang, Lei Liu, Ruolin Yang, Xiangfeng Wang

The dynamic activity of transposable elements (TEs) contributes to the vast diversity of genome size and architecture among plants. Here, we examined the genomic distribution and transposition activity of long terminal repeat retrotransposons (LTR-RTs) in Arabidopsis thaliana (Ath) and three of its relatives, Arabidopsis lyrata (Aly), Eutrema salsugineum (Esa), and Schrenkiella parvula (Spa), in Brassicaceae. Our analyses revealed the distinct evolutionary dynamics of Gypsy retrotransposons, which reflects the different patterns of genome size changes of the four species over the past million years. The rate of Gypsy transposition in Aly is approximately five times more rapid than that of Ath and Esa, suggesting an expanding Aly genome. Gypsy insertions in Esa are strictly confined to pericentromeric heterochromatin and associated with dramatic centromere expansion. In contrast, Gypsy insertions in Spa have been largely suppressed over the last million years, likely as a result of a combination of an inherent molecular mechanism of preferential DNA removal and purifying selection at Gypsy elements. Additionally, species-specific clades of Gypsy elements shaped the distinct genome architectures of Aly and Esa.
转座子的动态活性贡献了植物中基因组大小及架构的巨大差异。该项工作在拟南芥（Ath）及其三个十字花科亲属物种中检查了长末端重复反转位子（long terminal repeat retrotransposons，LTR-RTs）的基因组分布和转座活性。这三个亲属物种为深山拟南芥（Aly）、山嵛菜（Esa）和盐芥（Spa）。该工作的分析揭示了吉普赛（Gypsy）转座子的不同演化动态，反应出这四个物种的基因组大小在过去百万年内变化的不同模式。Aly的Gypsy转座速率比Ath和Eas的大概快5倍，暗示了Aly基因组的扩大。Esa中的Gypsy插入被严格限制在着丝粒周围异染色质并与急剧的着丝粒扩张有关。相比而言，Spa中的Gypsy插入在过去百万年内被大大抑制了，这可能是优选DNA移除这种可遗传分子机制与Gypsy元件负选择共同导致的结果。此外，Gypsy元件的物种特异分支塑造了Aly和Esa不同的基因组架构。该工作的创新之处，是通过对LTR-反转座子的转座活性的分析，特别是针对Gypsy元件超家族的转座活性，可以在短的演化时段内推断植物中基因组大小演化的趋势。

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Original Research

Paleo-polyploidization in Lycophytes

Jinpeng Wang, Jigao Yu, Pengchuan Sun, Chao Li, Xiaoming Song, Tianyu Lei, Yuxian Li, Jiaqing Yuan, Sangrong Sun, Hongling Ding, Xueqian Duan, Shaoqi Shen, Yanshuang Shen, Jing Li, Fanbo Meng, Yangqin Xie, Jianyu Wang, Yue Hou, Jin Zhang, Xianchun Zhang, Xiu-Qing Li, Andrew H. Paterson, Xiyin Wang

Lycophytes and seed plants constitute the typical vascular plants. Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants. Here, genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events, with one occurring approximately 13–15 million years ago (MYA) and another about 125–142 MYA, during the evolution of the genome of Selaginella moellendorffii, a model lycophyte. In addition, comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleo-polyploidization events than seed plants. Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages—lycophytes and seed plants—of vascular plants.
石松类植物（Lycophytes）和种子植物（seed plants）构成了主要维管植物（vascular plants）。尽管古多倍化事件（paleo-polyploidization）被认为对种子植物的快速分化至关重要，但石松类一直以来被认为没有经历古多倍化事件。本文通过同源基因点阵图（homologous gene dot plot）在内的基因组分析，确定了江南卷柏（Selaginella moellendorffii）基因组进化中经历了多次古多倍化事件。其中较近的一次发生在13-15百万年前（MYA），另一次发生在125-142 百万年前。另外，本文通过对重新构建的石松类祖先和被子植物祖先的比较分析表明，石松类植物与种子植物相比，受到了更多次古多倍体化事件的影响。目前的基因组分析结果暗示，古多倍化事件对维管植物谱系（种子植物和石松类植物）的建立具有贡献。

Page 333-340

Letter

Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea

Yuan Liang, Dengxue Lu, Sen Wang, Yuhui Zhao, Shenghan Gao, Rongbing Han, Jun Yu, Weili Zheng, Jianing Geng, Songnian Hu

Agrocybe cylindracea, an edible mushroom, is widely cultivated for its abundance of nutrients and flavor, and many of its metabolites are reported to have beneficial roles, such as medicinal effects on tumors and chronical illnesses. However, the lack of genomic information has hindered further molecular studies on this fungus. Here, we present a genome assembly of A. cylindracea together with comparative genomics and pathway analyses of Agaricales species. The draft, generated from both next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing platforms to overcome high genetic heterozygosity, is composed of a 56.5 Mb sequence and 15,384 predicted genes. This mushroom possesses a complex reproductive system, including tetrapolar heterothallic and secondary homothallic mechanisms, and harbors several hydrolases and peptidases for gradual and effective degradation of various carbon sources. Our pathway analysis reveals complex processes involved in the biosynthesis of polysaccharides and other active substances, including B vitamins, unsaturated fatty acids, and N-acetylglucosamine. RNA-seq data show that A. cylindracea stipes tend to synthesize carbohydrate for carbon sequestration and energy storage, whereas pilei are more active in carbon utilization and unsaturated fatty acid biosynthesis. These results reflect diverse functions of the two anatomical structures of the fruiting body. Our comprehensive genomic and transcriptomic data, as well as preliminary comparative analyses, provide insights into the molecular details of the medicinal effects in terms of active compounds and nutrient components.
柱状田头菇（A. cylindrace），隶属于真菌界，担子菌门，伞菌目，是常见的可食用真菌，在亚洲地区被广泛种植。本项研究利用全基因组测序数据，获得了约56.5Mb较高质量的基因组草图，预测了15,384个蛋白编码基因，阐述了A. cylindracea基因组序列的基本特征、潜在的生殖方式、伞菌目真菌中的进化地位以及营养物质合成的组学基础并构建了A. cylindrace活性物质的代谢通路图。研究发现A. cylindrace基因组中包含丰富的碳水化合物水解酶、蛋白酶以及有效降解植物细胞壁所需多种酶用于降解和利用外源物质提供能量。转录组分析发现A. cylindrace伞柄部分糖类物质合成相关基因及碳水化合物代谢通路上表达更为活跃，而在其伞盖部分则表现出利用碳源合成不饱和脂肪酸等物质的能力。同时基因表达谱反映了代谢途径中一些关键基因的表达特征。

Page 341-351

Application Note

CircPlant: An Integrated Tool for circRNA Detection and Functional Prediction in Plants

Peijing Zhang, Yongjing Liu, Hongjun Chen, Xianwen Meng, Jitong Xue, Kunsong Chen, Ming Chen

The recent discovery of circular RNAs (circRNAs) and characterization of their functional roles have opened a new avenue for understanding the biology of genomes. circRNAs have been implicated to play important roles in a variety of biological processes, but their precise functions remain largely elusive. Currently, a few approaches are available for novel circRNA prediction, but almost all these methods are intended for animal genomes. Considering that the major differences between the organization of plant and mammal genomes cannot be neglected, a plant-specific method is needed to enhance the validity of plant circRNA identification. In this study, we present CircPlant, an integrated tool for the exploration of plant circRNAs, potentially acting as competing endogenous RNAs (ceRNAs), and their potential functions. With the incorporation of several unique plant-specific criteria, CircPlant can accurately detect plant circRNAs from high-throughput RNA-seq data. Based on comparison tests on simulated and real RNA-seq datasets from Arabidopsis thaliana and Oryza sativa, we show that CircPlant outperforms all evaluated competing tools in both accuracy and efficiency. CircPlant is freely available at http://bis.zju.edu.cn/circplant.
环状RNA(circular RNA, circRNA)是一类具有共价闭合环结构的单链RNA分子。作为内源性非编码RNA的一员，circRNA与多种生物学过程相关，可以调控转录、影响可变剪接、沉默miRNA或蛋白质。目前，已有数十种环状RNA识别工具，但这些方法几乎都是为动物环状RNA而开发的。考虑到动植物基因组之间的差异和植物环状RNA的特性，需要植物特异性方法来增强植物circRNA识别的有效性。因此，我们开发了植物环状RNA整合分析工具CircPlant，该工具整合了植物特异性识别标准，不仅可以从高通量RNA-seq数据中准确检测植物circRNA，也适用于环状RNA和miRNA互作预测,ceRNA网络预测和环状RNA功能预测等后续分析。通过拟南芥和水稻的模拟数据和真实RNA-seq数据进行评估，发现CircPlant在模拟数据集中的敏感性和准确性均优于以前的工具，在真实数据中也取得很好的效果。CircPlant可以通过访问。

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