The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum)

Zanthoxylum armatum and Zanthoxylum bungeanum, known as ‘Chinese pepper’, are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species-special metabolites. Here, we report reference-grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole-genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (>82%) and high chromosome number (2n = 4x = 132). Further analysis of the high-quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes.     

基于人地关系视角的鄱阳湖水陆交错带范围划分

水陆交错带是典型的过渡性地理空间,是地理学研究的关键样带,承载着特殊且复杂的人地关系。根据鄱阳湖过水性、吞吐型、季节性特点,考虑行政区划完整性与尺度效应,基于高分辨率遥感影像和长时间序列水位变化数据,利用非监督分类、目视解译、调查验证等方法,从自然和行政区划两个维度划分了鄱阳湖水陆交错带的地域范围,阐述了其自然、经济和社会等基本特征,分析了其理论基础、现实意义及科学内涵。研究表明：(1)鄱阳湖水陆交错带最大自然范围约为2508.08 km~2,行政范围涉及11个县(市、区)78个乡镇单元,包含行政村974个;(2)其景观要素变化多样,经济发展主要以生态农业、生态旅游业为主,人口分布呈现带状特征,与交错带范围高度吻合;(3)自然基础、尺度效应和内涵特征是其范围划分的理论基础,探究其人与环境相互作用的过程、机理与规律是重要现实意义;(4)未来可以从景观格局变化、人地关系分解、社会生活变迁等方面开展进一步研究,以揭示该区域特殊人地关系变化。     

不同施肥与灌水量对槟榔土壤氨挥发的影响

利用通气法田间原位试验,研究了不同施肥模式、灌溉量对槟榔土壤氨挥发速率和挥发量的影响。结果表明：槟榔恢复期和出花期追肥灌水后,不同施肥处理均在第3天出现氨挥发速率峰值（0.50-3.42 kg.hm-2.d-1）,而后迅速下降并进入低挥发阶段。出花期氨挥发速率峰值（1.50-4.42 kg.hm-2.d-1）比恢复期氨挥发速率峰值明显高。灌水量小(300 m3. hm-2)的氨挥发率和总量比灌水量大(600 m3. hm-2)的明显减小。在同一氮水平下,有机质含量较低的氨挥发率较高。在同一有机质含量条件,氨挥发率随着N肥含量增加而升高。与单施N肥处理相比,有机肥与N肥配施可明显减少氨挥发速率和总量,可减少氮损失。     

三峡库区消落带4种适生植物根际与非根际土壤养分与酶活性特征研究

三峡库区消落带植被修复过程中,物种的更替对库区土壤的地球化学循环产生潜在影响。以三峡库区忠县石宝寨汝溪河消落带植被修复示范基地165-170 m海拔段人工种植狗牙根、牛鞭草、落羽杉以及立柳根际与非根际土为试验对象,探究其根际与非根际土壤的养分含量及酶活性差异,以阐明不同物种的生长适应性及其根际养分利用策略,比较不同物种对库区土壤的营养改良作用。结果表明：（1）三峡库区消落带4种适生植物根系活动导致根际与非根际土壤养分因子以及土壤酶活性产生差异,不同物种的栽植均在一定程度上使库区土壤营养条件得以改善;（2）碳、氮两种元素在4种适生植物根际土壤中发生不同程度的富集,但磷素与钾素在不同物种根际与非根际土壤之间的变化不一致;（3）蔗糖酶、脲酶以及酸性磷酸酶在4种适生植物根际土中均表现出一定程度的根际正效应（R/S>1）,且狗牙根对3种土壤酶的根际活化效果最为明显,其根际效应分别高达2.39、1.89和2.7;（4）在植物根系的调控下,根际土中有机质与氮素、磷素以及钾素的相关性更为显著,而非根际土壤中,仅钾素与有效氮、有效磷呈显著负相关,其余各土壤养分因子之间均无显著相关性;（5）与落羽杉和立柳两木本植物相比,狗牙根与牛鞭草两草本植物根际具有更为合理的养分调节模式,对库区土壤的改良效果更好。     

极端干旱区多枝柽柳幼苗对人工水分干扰的形态及生理响应

在塔里木河下游断流河道人工生态输水的大背景下,多枝柽柳(Tamarix ramosissima )作为当地优势物种,其更新恢复研究对下游荒漠河岸林的恢复尤为重要。通过研究多枝柽柳幼苗形态、水分和光合生理对不同灌溉处理的响应,分析不同人工水分干扰模式对柽柳幼苗生长发育的影响。实验设计了侧渗分层(LSI)和地表灌溉(AGI)两种给水方式,以及高灌(W1,50 L/株)、中灌(W2,25 L/株)、低灌(W3,12.5 L/株)3 个给水水平,并在整个生长季定期监测幼苗的形态参数变化、生物量、水势和光合速率。结果显示:(1)侧渗分层灌溉方式对幼苗基径、株高、冠幅以及前期生长速率都有促进作用;(2)在侧渗分层灌溉高灌下,幼苗地下及总生物量都显著高于地表灌溉(P < 0.05),且地表灌溉下根冠比(R/S:Root shoot ratio)明显高于侧渗分层灌溉;(3)侧渗分层灌溉下,幼苗茎水势高于地表漫灌,且在中灌和低灌下达到显著水平(P < 0.05),表明侧渗分层灌溉下幼苗的水分吸收效率更高;(4)在侧渗分层高灌及中灌下,实际光化学光量子产量值高于地表灌溉处理,并在高灌时差异极显著(P < 0.01)。研究表明,侧渗分层灌溉方式对多枝柽柳幼苗早期生长及水分和光合生理都具有显著促进作用。     

基于水稻染色体片段代换系的耐盐发芽QTL分析

为了检测水稻种子的耐盐相关数量性状位点,也为耐盐遗传机理的研究提供理论基础,本实验以Koshihikari(受体)和Nona Bokra(供体)为亲本构建的全基因组单片段代换系(154个)作为研究群体,采用培养皿培养,在水稻种子的萌发期进行浓度为1％的盐胁迫,以种子的发芽情况为指标,统计发芽率数据,利用分子标记技术,定...     

Comparative analysis of vertebrate <Emphasis Type="Italic">PEPT1</Emphasis> and <Emphasis Type="Italic">PEPT2</Emphasis> genes

The plasma membrane transport proteins belong to SoLute Carrier 15 (SLC15) family and two members of this family have been characterized extensively in higher vertebrates, namely PEPT1 and PEPT2. Despite many efforts have made to define a pharmacophore model for efficient binding and transporting of substrates, there is not a comprehensive study performed to elucidate the evolutionary mechanisms among the SLC15 family members and to statistically evaluate sequence conservation and functional divergence between members. In this study, we compared and contrasted the rates and patterns of molecular evolution of 2 PEPT genes. Phylogenetic tree assembly with all available vertebrate PEPTs suggests that the PEPTs originated by duplications and diverged from a common protein at the base of the eukaryotic tree. Topological structure demonstrates both members share the similar hydrophobic domains (TMDs), which have been constrained by purifying selection. Although both genes show qualitatively similar patterns, their rates of evolution differ significantly due to an increased rate of synonymous substitutions in the structural domains in one copy, suggesting substantial differences in functional constraint on each gene. Site-specific profiles were established by posterior probability analysis revealing significantly divergent regions mainly locate at the hydrophobic region between predicted transmembrane domains 9 and 10 of the proteins. Thus, these results provide the evidence that several amino acid residues with reduced selective constraints are largely responsible for functional divergence between the paralogous PEPTs. These findings may provide a starting point for further experimental verifications.     

结合三代测序与二代测序技术揭示蜜蜂球囊菌孢子转录组的复杂性

【目的】蜜蜂球囊菌(Ascosphaera apis)是一种专性侵染蜜蜂幼虫的致死性真菌病原。本研究旨在利用PacBio单分子实时(singlemoleculereal-time,SMRT)测序技术对蜜蜂球囊菌孢子(AaS)中基因的可变剪切(alternative splicing,AS)和可变多聚腺苷酸化(alternative polyadenylation,APA)以及长链非编码RNA (long non-coding RNA,lncRNA)进行鉴定和分析,进而揭示蜜蜂球囊菌孢子中转录组的复杂性。【方法】采用Suppa软件对蜜蜂球囊菌孢子中基因的AS事件进行鉴定。通过RT-PCR对不同类型的AS事件进行验证。采用TAPIS pipeline对蜜蜂球囊菌孢子基因的APA位点进行鉴定。利用MEME软件分析孢子全长转录本的poly(A)剪接位点上游50bp的序列特征并鉴定motif。联用CPC和CNCI软件和比对Swiss-prot数据库的方法预测lncRNA,取三者的交集作为高可信度的lncRNA集合。进一步比较lncRNA和mRNA的转录本长度,外显子数量与长度,内含子长度,GC含...