Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana

Background:Messenger RNA polyadenylation is an essential step for the maturation of most eukaryotic mRNAs.Accurate determination of poly(A) sites helps define the 3’-ends of genes, which is important for genome annotation and gene function research. Genomic studies have revealed the presence of poly(A) sites in intergenic regions, which may be attributed to 3’-UTR extensions and novel transcript units. However, there is no systematically evaluation of intergenic poly(A) sites in plants. Results:Approximately 16,000 intergenic poly(A) site clusters (IPAC) in Arabidopsis thaliana were discovered and evaluated at the whole genome level. Based on the distributions of distance from IPACs to nearby sense and antisense genes, these IPACs were classified into three categories. About 70 % of them were from previously unannotated 3’-UTR extensions to known genes, which would extend 6985 transcripts of TAIR10 genome annotation beyond their 3’-ends, with a mean extension of 134 nucleotides. 1317 IPACs were originated from novel intergenic transcripts, 37 of which were likely to be associated with protein coding transcripts. 2957 IPACs corresponded to antisense transcripts for genes on the reverse strand, which might affect 2265 protein coding genes and 39 non-protein-coding genes, including long non-coding RNA genes. The rest of IPACs could be originated from transcriptional read-through or gene mis-annotations. Conclusions:The identified IPACs corresponding to novel transcripts, 3’-UTR extensions, and antisense transcription should be incorporated into current Arabidopsis genome annotation. Comprehensive characterization of IPACs from this study provides insights of alternative polyadenylation and antisense transcription in plants.Funding supports were in part from US National Science Foundation (No. 1541737 to QQL), the Hundred Talent Plans of Fujian Province and Xiamen City (to QQL). This project was also funded by the National Natural Science Foundation of China (Nos. 61201358 and 61174161), the Natural Science Foundation of Fujian Province of China (No. 2012J01154), and the specialized Research Fund for the Doctoral Program of Higher Education of China (Nos. 20120121120038 and 20130121130004), and the Fundamental Research Funds for the Central Universities in China (Xiamen University: Nos. 2013121025, 201412G009, and 2014X0234)

scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data

Motivation: Alternative polyadenylation (APA) plays a key post-transcriptional regulatory role in mRNA stability and functions in eukaryotes. Single cell RNA-seq (scRNA-seq) is a powerful tool to discover cellular heterogeneity at gene expression level. Given 30 enriched strategy in library construction, the most commonly used scRNA-seq protocol—10 Genomics enables us to improve the study resolution of APA to the single cell level. However, currently there is no computational tool available for investigating APA profiles from scRNA-seq data. Results: Here, we present a package scDAPA for detecting and visualizing dynamic APA from scRNA-seq data. Taking bam/sam files and cell cluster labels as inputs, scDAPA detects APA dynamics using a histogram-based method and the Wilcoxon rank-sum test, and visualizes candidate genes with dynamic APA. Benchmarking results demonstrated that scDAPA can effectively identify genes with dynamic APA among different cell groups from scRNA-seq data.This research was supported in part by the Fundamental Research Funds for the Central Universities in China [Xiamen University: 20720170076 and 20720190106], and the National Natural Science Foundation of China [61802323, 31801268 and 61573296]

多种环境条件下的亲本效应均惠及后代：基于动植物数据的元分析研究

在生物界，当上代生存环境恶劣时，是否一定会带给后代一个消极、负面的影响?环境与生态学院李庆顺教授课题组就此展开了大数据元分析研究，综合分析了从上世纪90年代至今的大量相关研究数据,从关键词索引得到的1000余篇论文中，筛选出139篇研究论文，这些论文涉及112个物种，包括不同的亲代环境处理、不同的子世代等。结果发现，对那些世代周期短、活动能力受限的一年生植物和无脊椎动物（如昆虫），无论上一代经历的是优质环境还是恶劣环境，这些经历总能使子代受益。但是，对于脊椎动物如老鼠和人等，只有上代经历优质环境才能使其子代受益。这一“源头”上的机制发现或为今后快速改良农作物，使其更有效应对干旱、升温、虫害等不良影响提供一种思路和方向。The adaptive value of transgenerational effects (the ancestor environmental effects on offspring) in changing environments has received much attention in recent years, but the related empirical evidence remains equivocal. Here, we conducted a meta‐analysis summarising 139 experimental studies in plants and animals with 1170 effect sizes to investigate the generality of transgenerational effects across taxa, traits, and environmental contexts. It was found that transgenerational effects generally enhanced offspring performance in response to both stressful and benign conditions. The strongest effects are in annual plants and invertebrates, whereas vertebrates appear to benefit mostly under benign conditions, and perennial plants show hardly any transgenerational responses at all. These differences among taxonomic/life‐history groups possibly reflect that vertebrates can avoid stressful conditions through their mobility, and longer‐lived plants have alternative strategies. In addition to environmental contexts and taxonomic/life‐history groups, transgenerational effects also varied among traits and developmental stages of ancestors and offspring, but the effects were similarly strong across three generations of offspring. By way of a more comprehensive data set and a different effect size, our results differ from those of a recent meta‐analysis, suggesting that transgenerational effects are widespread, strong and persistent and can substantially impact the responses of plants and animals to changing environments.This study is supported by the National Natural Science Foundation of China (grant No. 31600291 to Y‐YZ) and the Fundamental Research Funds for the Central Universities in China (grant No. 20720170074 to Y‐YZ)

Integration of Developmental and Environmental Signals via a Polyadenylation Factor in Arabidopsis

<div><p>The ability to integrate environmental and developmental signals with physiological responses is critical for plant survival. How this integration is done, particularly through posttranscriptional control of gene expression, is poorly understood. Previously, it was found that the 30 kD subunit of Arabidopsis cleavage and polyadenylation specificity factor (AtCPSF30) is a calmodulin-regulated RNA-binding protein. Here we demonstrated that mutant plants (<i>oxt6</i>) deficient in AtCPSF30 possess a novel range of phenotypes – reduced fertility, reduced lateral root formation, and altered sensitivities to oxidative stress and a number of plant hormones (auxin, cytokinin, gibberellic acid, and ACC). While the wild-type AtCPSF30 (C30G) was able to restore normal growth and responses, a mutant AtCPSF30 protein incapable of interacting with calmodulin (C30GM) could only restore wild-type fertility and responses to oxidative stress and ACC. Thus, the interaction with calmodulin is important for part of AtCPSF30 functions in the plant. Global poly(A) site analysis showed that the C30G and C30GM proteins can restore wild-type poly(A) site choice to the <i>oxt6</i> mutant. Genes associated with hormone metabolism and auxin responses are also affected by the <i>oxt6</i> mutation. Moreover, 19 genes that are linked with calmodulin-dependent CPSF30 functions, were identified through genome-wide expression analysis. These data, in conjunction with previous results from the analysis of the <i>oxt6</i> mutant, indicate that the polyadenylation factor AtCPSF30 is a regulatory hub where different signaling cues are transduced, presumably via differential mRNA 3′ end formation or alternative polyadenylation, into specified phenotypic outcomes. Our results suggest a novel function of a polyadenylation factor in environmental and developmental signal integration.</p></div

Genetic admixture accelerates invasion via provisioning rapid adaptive evolution

互花米草，一种原产于北美东海岸的海滩植物。它天性耐盐耐淹、抗风浪，种子及无性分株可随海浪传播。由于互花米草茎干密集粗壮、地下根茎发达，能够促进泥沙的快速沉降和淤积。1979年，我国从美国的北卡罗来纳、佐治亚和佛罗里达分别引进了高、中、低三个生态型的互花米草，用于保滩护堤、促淤造陆。试种成功后，它们被引种至福建省的罗源湾，之后又陆续推广至其他沿海省份，为抵御台风、保滩护岸起到了一定作用。然而，引种的互花米草在各地迅速繁殖扩张成为入侵物种，威胁当地海岸生态系统、影响湿地滩涂养殖、阻塞船道等，带来了巨大的经济损失。 2014年起，我校环境与生态学院李庆顺教授、张宜辉教授和张原野助理教授的三支科研团队开展联合攻关，力图从分子遗传学、生态学、进化生物学等多学科角度，在互花米草的DNA序列中寻找其扩散的“秘密”。五年多来，研究团队采用DNA指纹技术，对来自入侵地中国沿海七个省份的10个区域及原产地北美12个州的15个区域的250个样本进行了分析。最终发现，这些入侵地植株全部是最初从美国引进的三个生态型的杂交后代，具有显著的杂种优势。这也意味着，互花米草的引种和扩散发生在杂交后。 通过进一步测量以上25个区域来源的植株性状，研究团队发现，三个基因型间的杂交还通过整合两种不同的生长能力即纵向生长能力和横向扩张能力，从而产生了超强的基因型，正是这种新的超强基因型因具有生长和繁殖的优势而被自然选择保留，成为互花米草恶性入侵的主要驱动力。 科研团队的这一项研究发现了恶性入侵植物互花米草侵占我国滨海湿地的遗传进化机制，有利于帮助人们进一步了解互花米草扩散的原因，为从源头上治理互花米草蔓延提供了方向和思路。Genetic admixture, the intraspecific hybridization among divergent introduced sources, can immediately facilitate colonization via hybrid vigor and profoundly enhance invasion via contributing novel genetic variation to adaption. As hybrid vigor is short-lived, provisioning adaptation is anticipated to be the dominant and long-term profit of genetic admixture, but the evidence for this is rare. We employed the 30 years’ geographic-scale invasion of the salt marsh grass, Spartina alterniflora, as an evolutionary experiment and evaluated the consequences of genetic admixture by combining the reciprocal transplant experiment with quantitative and population genetic surveys. Consistent with the documentation, we found that the invasive populations in China had multiple origins from the southern Atlantic coast and the Gulf of Mexico in the US. Interbreeding among these multiple sources generated a “hybrid swarm” that spread throughout the coast of China. In the northern and mid-latitude China, natural selection greatly enhanced fecundity, plant height and shoot regeneration compared to the native populations. Furthermore, genetic admixture appeared to have broken the negative correlation between plant height and shoot regeneration, which was genetically-based in the native range, and have facilitated the evolution of super competitive genotypes in the invasive range. In contrast to the evolved northern and mid-latitude populations, the southern invasive populations showed slight increase of plant height and shoot regeneration compared to the native populations, possibly reflecting the heterotic effect of the intraspecific hybridization. Therefore, our study suggests a critical role of genetic admixture in accelerating the geographic invasion via provisioning rapid adaptive evolution.This research was supported in part by the National Key Research and Development Program of China (Grant No. 2017YFC0506102 to Y-H.Z. and Q.Q.L.), the Fundamental Research Funds for the Central Universities (Grant No. 20720150097 to Y-H.Z.), the National Natural Science Foundation of China (Grant No. 41276078 to Y-H.Z. and No. 31600291 to Y-Y. Z.), and the Extramural Collaborative Program of the Fujian Province China (Grant No. 2016I0013 to Q.Q.L.)