Strategies for adaptation of Suaeda physophora, Haloxylon ammodendron and Haloxylon persicum to a saline environment during seed-germination stage

BACKGROUND AND AIMS: Germination is very important for plant establishment in arid regions. The strategies taken by halophytes during the seed germination stage to adapt to saline environments in an arid zone were investigated in Suaeda physophora (euhalophyte), Haloxylon ammodendron (xero-halophyte) and Haloxylon persicum (xerophyte). METHODS: Seeds of S. physophora, H. ammodendron and H. persicum were exposed to a range of iso-osmotic NaCl and PEG solutions. Seed germination in, and recovery germination from, high NaCl were recorded. The effects of iso-osmotic NaCl and PEG on seed water uptake and changes in ion content were measured. In addition, the structure of seeds and Na+ distribution in the seed coat and embryos of dry seeds were investigated. KEY RESULTS: The relative increase in fresh weight of germinating seeds was markedly reduced in -2.24 MPa PEG compared with that in -2.24 MPa NaCl, while the opposite trend was found in concentration of K+ during the initial 9 h for all species. Haloxylon ammodendron and S. physophora had a higher recovery germination from -3.13 MPa NaCl compared with H. persicum. Seeds of all species had no endosperm. More Na+ was compartmentalized in the seed coats of the two halophytic species compared with that in the xerophyte H. persicum. CONCLUSIONS: The effect of NaCl on seed germination was due to both osmotic stress and ion toxicity for the three species. High soil salinity and a high content of Na+ in seeds may induce more seeds to remain ungerminated in S. physophora and H. ammodendron. Morphological structure and adaptation to salinity during seed germination may determine the geographical distribution of H. ammodendron and S. physophora in certain saline regions.     

塔克拉玛干沙漠腹地梭梭(Haloxylon ammodendron)蒸腾耗水规律

塔里木沙漠公路防护林生长于极端干旱的塔克拉玛干沙漠中,防护林植物的蒸腾耗水和灌溉管理是防护林可持续的核心问题.利用植物茎流计连续测定了塔里木沙漠公路塔中段防护林植物梭梭的茎干液流、蒸腾耗水量.结果表明:梭梭茎干液流具有明显昼夜节律性,液流的高峰值出现在白天10:00～15:00,最小值出现在0:00～03:00,夜间也保持较小的液流;茎干液流受环境因子影响而波动,太阳辐射、气温和风速与茎干液流有较明显的正相关关系,相对湿度和茎干液流呈负相关关系;滴灌条件下,防护林带内土壤含水量充足且在各个月份变化不大,土壤含水量对茎干液流影响不大;依据清晨和午后水势变化,梭梭体内水分在夜间得到了较好的恢复;在一个生长季内,3株直径为2.0、2.8、3.4cm的梭梭总的耗水量分别为295、436、616kg,日平均耗水量分别为1.48、2.18、3.08kg;现行灌溉模式提供了充足的水分供应,梭梭的水分状况良好;在充足水分条件下,梭梭有较大的蒸腾耗水量,干旱的环境条件和较为充足的水分供应是梭梭耗水量大的主要原因;依据梭梭的水分状况,当前水分管理为防护林提供了较充足的水分.     

Chromosome-level genome assembly of Welwitschia mirabilis,a unique Namib Desert species

Welwitschia mirabilis, which is endemic to the Namib Desert, is the only living species within the family Welwitschiaceae. This species has an extremely long lifespan of up to 2,000 years and bears a single pair of opposite leaves that persist whilst alive. However, the underlying genetic mechanisms and evolution of the species remain poorly elucidated. Here, we report on a chromosome-level genome assembly for W. mirabilis, with a 6.30-Gb genome sequence and contig N50 of 27.50 Mb. In total, 39,019 protein-coding genes were predicted from the genome. Two brassinosteroid-related genes (BRI1 and CYCD3), key regulators of cell division and elongation, were strongly selected in W. mirabilis and may contribute to their long ever-growing leaves. Furthermore, 29 gene families in the mitogen-activated protein kinase signalling pathway showed significant expansion, which may contribute to the desert adaptations of the plant. Three positively selected genes (EHMT1, EIF4E, SOD2) may be involved in the mechanisms leading to long lifespan. Based on molecular clock dating and fossil calibrations, the divergence time of W. mirabilis and Gnetum montanum was estimated at ~123.5 million years ago. Reconstruction of population dynamics from genome data coincided well with the aridification of the Namib Desert. The genome sequence detailed in the current study provides insight into the evolution of W. mirabilis and should be an important resource for further study on gnetophyte and gymnosperm evolution.     

荒漠区固沙植物梭梭(Haloxylon ammodendron)耗水特征

利用SF-300热脉冲树干液流仪,连续观测了生长季节荒漠区固沙植物梭梭树干液流速率,研究了荒漠区固沙植物梭梭林木的耗水量及其与气象因子的关系。结果表明：在生长季节,梭梭树干液流速率昼夜变化小;不同的生长日,梭梭树干液流速率介于（5．9±0．7）～（14．5±3．6）gcm^-2h^-1;观测期间,梭梭平均日耗水量为（0．3±0．2）mm,生长季节单株木耗水量达49．4mm。树干液流速率对气象因子均有一定程度的响应,且在不同时间的影响程度不同。日耗水量与林冠投影面积、基径、基径的平方乘以树高的积、边材厚度和边材面积呈线性关系。     

Current challenges in de novo plant genome sequencing and assembly

Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community.     

民勤绿洲人工梭梭林退化现状、特征与恢复对策

民勤全县共有人工梭梭林近3．5万hm^2,占人工林总面积的51．5％,在民勤固沙林中占主导地位。但目前除水库与环河周围外,人工梭梭林均出现不同程度的退化现象,并表现为建群种梭梭光合强度减弱、群落盖度降低、梭梭种群优势度下降、林地土壤含水率下降、组成群落的物种多样性减少、地表土壤结皮破坏、风蚀作用增强等特征。梭梭林的退化,直接威胁到民勤绿洲的生存与发展,其恢复与重建成为当前一项十分重要而紧迫的任务,为此提出控制梭梭林密度、人工集雨、布设粘土或新型材料沙障、引进与培育抗旱新品种、特殊区域应用喷灌技术补水、补充水源不断恢复民勤地区的地下水位等措施,以期达到恢复与维持梭梭群落稳定发展的目的。     

荒漠植物梭梭和沙拐枣光合作用、蒸腾作用及水分利用效率特征

运用开放式气体交换LI-6400便携式光合作用测定系统,研究了梭梭(Haloxylonammodendron)和沙拐枣(Calligonummongolicum)的净光合速率(Pn)、蒸腾速率(E)及水分利用效率(WUE)特征。结果表明:梭梭和沙拐枣在湿润状况下的Pn日变化呈单峰型,梭梭低于沙拐枣,日平均分别为19.60±0.12μmol·m-2·s-1和24.06±0.50μmol·m-2·s-1;E也是梭梭低于沙拐枣,日平均分别为5.53±0.08mmol·m-2·s-1和8.21±0.26mmol·m-2·s-1;WUE则不同,日平均梭梭高于沙拐枣,分别为3.28±0.05mmolCO2·mol-1H2O和2.84±0.06mmolCO2·mol-1H2O。WUE年均值也是梭梭高于沙拐枣,二者最高值都出现在9月,次高值出现在7月,WUE的高低变化与年降水量的高低分布一致。在湿润和干燥两种状况下,梭梭和沙拐枣Pn对光强的响应表明,水分条件好时Pn明显增大,光能利用率提高。从湿润状况时的净光合速率、光饱和点和CO2补偿点,以及干燥状况时也具有低CO2补偿点,确定梭梭和沙拐枣具有C4光合途径。     

Chromosome-level de novo genome assembly of two conifer-parasitic wasps,Megastigmus duclouxiana and Megastigmus sabinae,reveals genomic imprints of adaptation to hosts

Conifers make up about one third of global forests but are threatened by seed parasitoid wasp species. Many of these wasps belong to the genus Megastigmus, yet little is known about their genomic background. In this study, we provide chromosome-level genome assemblies for two oligophagous conifer parasitoid species of Megastigmus, which represent the first two chromosome-level genomes of the genus. The assembled genomes of Megastigmus duclouxiana and M. sabinae are 878.48 Mb (scaffold N50 of 215.60 Mb) and 812.98 Mb (scaffold N50 of 139.16 Mb), respectively, which are larger than the genome size of most hymenopterans due to the expansion of transposable elements. Expanded gene families highlight the difference in sensory-related genes between the two species, reflecting the difference in their hosts. We further found that these two species have fewer family members but more single-gene duplications than polyphagous congeners in the gene families of ATP-binding cassette transporter (ABC), cytochrome P450 (P450) and olfactory receptors (OR). These findings shed light on the pattern of adaptation to a narrow spectrum of hosts in oligophagous parasitoids. Our findings suggest potential drivers underlying genome evolution and parasitism adaptation, and provide valuable resources for understanding the ecology, genetics and evolution of Megastigmus, as well as for the research and biological control of global conifer forest pests.     

High-quality genome assembly of an important biodiesel plant,Euphorbia lathyris L

Caper spurge, Euphorbia lathyris L., is an important energy crop and medicinal crop. Here, we generated a high-quality, chromosome-level genome assembly of caper spurge using Oxford Nanopore sequencing, Illumina sequencing, and Hi-C technology. The final genome assembly was ∼988.9 Mb in size, 99.8% of which could be grouped into 10 pseudochromosomes, with contig and scaffold N50 values of 32.6 and 95.7 Mb, respectively. A total of 651.4 Mb repetitive sequences and 36,342 protein-coding genes were predicted in the genome assembly. Comparative genomic analysis showed that caper spurge and castor bean clustered together. We found that no independent whole-genome duplication event had occurred in caper spurge after its split from the castor bean, and recent substantial amplification of long terminal repeat retrotransposons has contributed significantly to its genome expansion. Furthermore, based on gene homology searching, we identified a number of candidate genes involved in the biosynthesis of fatty acids and triacylglycerols. The reference genome presented here will be highly useful for the further study of the genetics, genomics, and breeding of this high-value crop, as well as for evolutionary studies of spurge family and angiosperms.     

光照、温度和盐分对梭梭种子萌发的影响

梭梭是我国西北荒漠中分布的多年生植物,属中亚荒漠植被成分。其种子萌发的最适温度为10℃,亚适宜温度为15～20℃。从20℃起,温度越高,萌发比率越低。种子无论在光下和暗中都能萌发,萌发率无显著性差异。浓度低于0.2mol/L的NaCl溶液对萌发的影响不大;但从0.8mol/L起,萌发率随着浓度增高而降低,直至为零。将在盐溶液中处理9d的种子转移至蒸馏水后,原来较高浓度下的种子具有较高的萌发恢复率。不同浓度下的种子的萌发率和萌发恢复率要比蒸馏水中的低,表明NaCl处理后的部分种子永久地失去萌发力。     

采用RAPD和ISSR标记研究古尔班通古特沙漠东南缘梭梭种群的遗传结构

梭梭(Haloxylon ammodendron(CA Mey.)Bunge)是一种沙漠旱生优势树种,具有重要的生态和经济价值,然而,我们对梭梭种群的遗传多样性和遗传结构所知甚少.本文采用RAPD和ISSR标记对来自古尔班通古特沙漠东南缘的4个天然梭梭种群的遗传多样性和遗传结构进行了检测.5个RAPD引物和8个ISSR引物分别扩增出61和195条带,多态性位点比率分别为83.6%和89.7%,Shannon信息指数分别为0.333和0.367,RAPD和ISSR分析均表明梭梭种群的遗传多样性水平较高.利用分子方差分析(AMOVA)研究梭梭种群的遗传结构,结果表明,大部分遗传变异存在于种群内,通过RAPD分析发现138.2%的遗传变异发生在种群内;通过ISSR分析发现89.4%的遗传变异发生在种群内;而种群间的遗传分化很小.通过RAPD标记没有检测到种群间的遗传分化,ISSR分析表明10.6%的遗传变异发生在种群内.我们推测梭梭种群较高的遗传多样性水平可能源于对异质、高胁迫环境的长期适应,但还需要进一步的研究加以证实.种群间遗传分异低的主要原因是种群间存在强大的基因流.     

Chromosome‐level genome assembly for the horned‐gall aphid provides insights into interactions between gall‐making insect and its host plant

The aphid Schlechtendalia chinensis is an economically important insect that can induce horned galls, which are valuable for the medicinal and chemical industries. Up to now, more than twenty aphid genomes have been reported. Most of the sequenced genomes are derived from free‐living aphids. Here, we generated a high‐quality genome assembly from a galling aphid. The final genome assembly is 271.52 Mb, representing one of the smallest sequenced genomes of aphids. The genome assembly is based on contig and scaffold N50 values of the genome sequence are 3.77 Mb and 20.41 Mb, respectively. Nine‐seven percent of the assembled sequences was anchored onto 13 chromosomes. Based on BUSCO analysis, the assembly involved 96.9% of conserved arthropod and 98.5% of the conserved Hemiptera single‐copy orthologous genes. A total of 14,089 protein‐coding genes were predicted. Phylogenetic analysis revealed that S. chinensis diverged from the common ancestor of Eriosoma lanigerum approximately 57 million years ago (MYA). In addition, 35 genes encoding salivary gland proteins showed differentially when S. chinensis forms a gall, suggesting they have potential roles in gall formation and plant defense suppression. Taken together, this high‐quality S. chinensis genome assembly and annotation provide a solid genetic foundation for future research to reveal the mechanism of gall formation and to explore the interaction between aphids and their host plants.     

灌溉植被梭梭、白刺光合蒸腾特性及影响因素研究

通过灌溉植被梭梭、白刺光合生理特性测定结果显示:梭梭、白刺光合、蒸腾日变化均呈单峰曲线,上午主要进行光合作用,10:00达到峰值,下午蒸腾作用较强,14:00～16∶00达到高峰期;灌溉植被光合速率随灌水量的增加而增大,灌溉梭梭平均光合速率相对免灌对照增加量为1.8～4.2μmolCO2·m-2·s-1,灌溉白刺相对增加量为1.5～2.3μmolCO2·m-2·s-1,梭梭光合增加量较高;灌溉梭梭蒸腾速率高于对照,增量为2.4～6.8mmolH2O·m-2·s-1,灌溉白刺蒸腾速率低于对照,减量为6.2～12.0mmolH2O·m-2·s-1;相关分析表明:光量子密度、胞间CO2浓度是影响梭梭、白刺光合作用的主要因子,大气温度、水汽压是影响其蒸腾作用的因子,叶片温度对灌溉植被梭梭、白刺的光合和蒸腾速率变化反应特别敏感,是影响其生理进程的重要因素之一.     

Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation

Rhododendrons are woody plants, famous throughout the world as having high horticultural value. However, many wild species are currently threatened with extinction. Here, we report for the first time a high-quality, chromosome-level genome of Rhododendron griersonianum, which has contributed to approximately 10% of all horticultural rhododendron varieties but which in its wild form has been evaluated as critically endangered. The final genome assembly, which has a contig N50 size of approximately 34 M and a total length of 677 M, is the highest-quality genome sequenced within the genus to date, in part due to its low heterozygosity (0.18%). Identified repeats constitute approximately 57% of the genome, and 38 280 protein-coding genes were predicted with high support. We further resequenced 31 individuals of R. griersonianum as well as 30 individuals of its widespread relative R. delavayi, and performed additional conservation genomic analysis. The results showed that R. griersonianum had lower genetic diversity (θ = 2.58e−3; π = 1.94e−3) when compared not only to R. delavayi (θ = 11.61e−3, π = 12.97e−3), but also to most other woody plants. Furthermore, three severe genetic bottlenecks were detected using both the Stairway plot and fastsimcoal2 analysis, which are thought to have occurred in the late Middle Pleistocene and the Last Glacial Maximum (LGM) period. After these bottlenecks, R. griersonianum recovered and maintained a constant effective population size (>25 000) until now. Intriguingly, R. griersonianum has accumulated significantly more deleterious mutations in the homozygous state than R. delavayi, and several deleterious mutations (e.g., in genes involved in the response to heat stress) are likely to have harmed the adaptation of this plant to its surroundings. This high-quality, chromosome-level genome and the population genomic analysis of the critically endangered R. griersonianum will provide an invaluable resource as well as insights for future study in this species to facilitate conservation and in the genus Rhododendron in general.     

民勤绿洲荒漠过渡带植物白刺和梭梭光合特性

研究了民勤绿洲荒漠过渡带两种优势植物白刺(Nitrariatangutorum)和梭梭(Haloxylonammodendron)气体交换特征参数和叶绿素荧光参数的日变化,结果表明:梭梭同化枝日均净光合速率(Pn)、蒸腾速率(E)、水分利用效率(WUE)和早晨PSII最大光化学效率(Fv/Fm)明显低于白刺叶片;同时它们在中午都呈现明显的光合“午休”现象。通过气孔限制值(Ls)、胞间二氧化碳浓度(Ci)和叶绿素荧光参数(Fv/Fm)变化趋势分析表明:梭梭同化枝净光合速率的下降在9:00~12:00主要是由于气孔关闭引起的,而在12:00~15:00主要是非气孔因素光抑制的影响;而白刺叶片光合速率的下降主要是气孔关闭引起的。同时,梭梭在一天中其同化枝的温度(Tleaf)高于大气温度尤其在中午差值更大,而白刺叶片的温度却低于大气温度,因此说明梭梭同化枝在中午不仅遭受着干旱和强光的胁迫而且面临严酷的高温胁迫。总之,在绿洲荒漠过渡带生境中白刺比梭梭具有更好的适应性,这可能是民勤绿洲荒漠过渡带人工梭梭林衰退的重要原因之一。     

Genetic variation within and among populations of a dominant desert tree Haloxylon ammodendron (Amaranthaceae) in China

BACKGROUND AND AIMS: China is one of the countries most severely affected by desertification. Haloxylon ammodendron (Amaranthaceae) is an ecologically important component of the desert ecosystem and is one of the main tree species used for restoration, yet we know little about its genetic structure. METHODS: Genetic variation within and between nine populations of H. ammodendron from two regions of China was investigated using ISSR (inter-simple sequence repeat) markers. KEY RESULTS: Eight primers used in this study amplified 219 reproducible bands of which 184 (84 %) were polymorphic. Analysis of molecular variance (AMOVA) revealed high genetic variation within populations (97.63 %) and low genetic differentiation between regions (0.62 %) and among populations (1.75 %). CONCLUSIONS: It is suggested that the present genetic structure could have arisen by high levels of gene flow. The gene flow among populations observed here is probably mainly attributable to pollen movement. The genetic structure also has important implications in ecological restoration practice.     

西北沙区梭梭根系深色有隔内生真菌等微生物时空分布及对根际土壤环境的响应

为揭示西北沙区不同时空尺度梭梭Haloxylon ammodendron根系深色有隔内生真菌（dark septate endophyte,DSE）分布规律及其环境驱动机制,分别于2019年7月、9月和12月在安西极旱荒漠国家级自然保护区和民勤连古城国家级自然保护区采集根系和土壤样品,根据真菌形态学特征、组织化学等方法,研究了梭梭根系DSE真菌定殖规律、定殖特征及其与土壤环境因子间的相互关系。结果表明,DSE真菌在自然生境梭梭根系广泛定殖,形成具有时空异质性的典型暗色有隔菌丝和微菌核结构。梭梭根系DSE真菌定殖受季节和空间分布影响,其中总定殖率在生长旺季7月最高（85.6%）,且菌丝隔间距显著大于9、12月;安西样地菌丝定殖率（71.5%）和总定殖率（85.6%）显著高于民勤样地（40.7%,60.0%）,但民勤样地微菌核直径显著高于安西样地。相关性分析表明,DSE定殖率及形态特征受土壤理化性质影响,温度、有效磷是影响DSE真菌定殖率的主要土壤因子,湿度和碱解氮是影响DSE真菌定殖形态的主要土壤因子。相比空白土壤,梭梭根际革兰氏阳性细菌含量、土壤脲酶活性以及安西样地有效磷含量均更高,预示其对荒漠土壤具有改善作用。本研究对梭梭DSE真菌时空分布和影响因素的系统性调查有助于为荒漠化治理和生态恢复提供依据。     

Old can be new again: HAPPY whole genome sequencing, mapping and assembly

During the last three decades, both genome mapping and sequencing methods have advanced significantly to provide a foundation for scientists to understand genome structures and functions in many species. Generally speaking, genome mapping relies on genome sequencing to provide basic materials, such as DNA probes and markers for their localizations, thus constructing the maps. On the other hand, genome sequencing often requires a high-resolution map as a skeleton for whole genome assembly. However, both genome mapping and sequencing have never come together in one pipeline. After reviewing mapping and next-generation sequencing methods, we would like to share our thoughts with the genome community on how to combine the HAPPY mapping technique with the new-generation sequencing, thus integrating two systems into one pipeline, called HAPPY pipeline. The pipeline starts with preparation of a HAPPY panel, followed by multiple displacement amplification for producing a relatively large quantity of DNA. Instead of conventional marker genotyping, the amplified panel DNA samples are subject to new-generation sequencing with barcode method, which allows us to determine the presence/absence of a sequence contig as a traditional marker in the HAPPY panel. Statistical analysis will then be performed to infer how close or how far away from each other these contigs are within a genome and order the whole genome sequence assembly as well. We believe that such a universal approach will play an important role in genome sequencing, mapping, and assembly of many species; thus advancing genome science and its applications in biomedicine and agriculture.