一株稀有海洋真菌Stachybotrys longispora FG216的De Novo测序及基因组学分析

【背景】长孢葡萄穗霉菌(Stachybotrys longispora) FG216是一株稀有海洋真菌,其次生代谢产物FGFC1具有纤溶活性。进行S. longispora FG216的基因组序列分析,将充实和促进海洋微生物功能基因和次生代谢产物合成生物学的基础研究和应用研究。【目的】解析S. longispora FG216的基因组序列,分析基因组生物功能和同源相似性关系,分析次生代谢产物纤溶活性化合物FGFC1的相关基因。【方法】基于Illumina HiSeq高通量测序平台对S. longispora FG216菌株进行De Novo测序,使用SSPACE、Augustus等软件进行组装、编码基因预测、基因功能注释、物种共线性分析以及预测FGFC1次生代谢产物合成基因簇。【结果】S. longispora FG216的基因组测序总长度为45622830bp,共得到605个Scaffold,GC含量为51.31%,注释预测得到13329个编码基因和169个非编码RNA。基因组测序数据提交至国家微生物科学数据中心(编号为NMDC60016264),其中13 053、8 422、8 460、7 714和2 847个基因分别能够在NR、KEGG、KOG、GO和CAZy数据库匹配到注释信息。比较基因组学分析发现,Stachybotrys具有保守性,核心基因占基因家族总数目的71.44%,S. longispora FG216与S. chlorohalonata IBT 40285的相似性最高;同时,预测得到101个次生代谢产物合成基因簇,其中18个基因簇与已知的化合物相匹配。通过antiSMASH预测,Cluster57是编码合成FGFC1母核结构异吲哚啉酮的基因簇,与S.chlorohalonataIBT40285中的基因簇相似度为40%。【结论】海洋稀有真菌S.longisporaFG216的基因组信息已上传至国家微生物科学数据中心公开使用,为Stachybotrys种属的研究提供了重要的参考意义,同时发现了S. longispora FG216次生代谢产物纤溶活性化合物FGFC1母核部分编码基因是Cluster 57。     

Fungal dual-domain LysM effectors undergo chitin-induced intermolecular,and not intramolecular,dimerization

Chitin is a homopolymer of β-(1,4)-linked N-acetyl-D-glucosamine (GlcNAc) and a major structural component of fungal cell walls. In plants, chitin acts as a microbe-associated molecular pattern (MAMP) that is recognized by lysin motif (LysM)-containing plant cell surface-localized pattern recognition receptors (PRRs) that activate a plethora of downstream immune responses. To deregulate chitin-induced plant immunity and successfully establish infection, many fungal pathogens secrete LysM domain-containing effector proteins during host colonization. The LysM effector Ecp6 from the tomato (Solanum lycopersicum) leaf mold fungus Cladosporium fulvum can outcompete plant PRRs for chitin binding because two of its three LysM domains cooperate to form a composite groove with ultra-high (pM) chitin-binding affinity. However, most functionally characterized LysM effectors contain only two LysMs, including Magnaporthe oryzae MoSlp1, Verticillium dahliae Vd2LysM, and Colletotrichum higginsianum ChElp1 and ChElp2. Here, we performed modeling, structural, and functional analyses to investigate whether such dual-domain LysM effectors can also form ultra-high chitin-binding affinity grooves through intramolecular LysM dimerization. However, our study suggests that intramolecular LysM dimerization does not occur. Rather, our data support the occurrence of intermolecular LysM dimerization for these effectors, associated with a substantially lower chitin binding affinity than monitored for Ecp6. Interestingly, the intermolecular LysM dimerization allows for the formation of polymeric complexes in the presence of chitin. Possibly, such polymers may precipitate at infection sites to eliminate chitin oligomers, and thus suppress the activation of chitin-induced plant immunity.

Fungal LysM effectors composed of two LysM domains bind chitin via intermolecular LysM dimerization, leading to polymers that may precipitate to eliminate chitin from infection sites to prevent the activation of host immune receptors.     

Positional behavior and canopy use of black snub-nosed monkeys Rhinopithecus strykeri in the Gaoligong Mountains,Yunnan, China

Studies on positional behavior and canopy use are essential for understanding how arboreal animals adapt their morphological characteristics and behaviors to the challenges of their environment. This study explores canopy and substrate use along with positional behavior in adult black snub-nosed monkeys Rhinopithecus strykeri, an endemic, critically endangered primate species in Gaoligong Mountains, southwest China. Using continuous focal animal sampling, we collected data over a 52-month period and found that R. strykeri is highly arboreal primarily using the high layers of the forest canopy (15–30 m), along with the terminal zone of tree crowns (52.9%), medium substrates (41.5%), and oblique substrates (56.8%). We also found sex differences in canopy and substrate use. Females use the terminal zones (56.7% versus 40.4%), small/medium (77.7% versus 60.1%), and oblique (59.9% versus 46.5%) substrates significantly more than males. On the other hand, males spend more time on large/very large (39.9% versus 22.3%) and horizontal (49.7% versus 35.2%) substrates. Whereas both sexes mainly sit (84.7%), and stand quadrupedally (9.1%), males stand quadrupedally (11.5% versus 8.3%), and bipedally (2.9% versus 0.8%) more often than females. Clamber, quadrupedalism, and leap/drop are the main locomotor modes for both sexes. Rhinopithecus strykeri populations never enter canopies of degenerated secondary forest and mainly use terminal branches in the middle and upper layers of canopies in intact mid-montane moist evergreen broadleaf forest and hemlock coniferous broadleaf mixed forests across their habitat.     

城市尺度的城乡建设用地潜力及空间格局匹配评价——以南昌市为例

随着经济快速发展和城镇化进程不断加快,土地开发强度日益增大,导致生态环境不断恶化,分析城乡建设用地承载能力及空间格局匹配情况,对解决土地利用不合理、生态破坏等问题具有重要意义。以江西省南昌市为例,首先从生态安全、自然条件、社会经济等方面构建指标体系,采用层次分析法和限制系数评价模型,进行城乡建设用地开发适宜性评价,然后测算城乡建设用地承载力、可承载城乡建设用地丰度;最后与现状城乡建设用地进行空间匹配度分析,并探讨可承载临界值、丰度与空间匹配度的相关性。结果表明:南昌市城乡建设用地最适宜区、较适宜区、较不适宜区和不适宜区面积分别为1466.19、1346.01、353.69 km²和3770.70 km²;研究区城乡建设用地可承载临界值和可承载潜力分别为41.25%和24.05%,各县(区)值差异较大,各县(区)可承载临界值和可承载潜力范围分别为19.43%—98.71%和5.65%—49.83%,可承载城乡建设用地丰度情况良好,各县(区)值介于0.19—1.50之间;研究区各县(区)空间匹配度范围为67.41%—99.25%;相关分析显示,空...     

GenoBaits Soy40K: a highly flexible and low-cost SNP array for soybean studies

<正>Dear Editor,Soybean(Glycine max [L.] Merr.) provides more than half of the oilseeds and more than a quarter of protein worldwide. It is estimated that the production of soybean has to be doubled by 2050 to meet the needs of the rapidly increasing consumption of soybean seeds along with a continuously increasing population(Ray et al., 2013). As such, development of a genotyping platform with high throughput, high efficiency and high precision but low-cost is urgently needed to accelerate...     

Chromosome-level genome of Tibetan naked carp (Gymnocypris przewalskii) provides insights into Tibetan highland adaptation

Gymnocypris przewalskii, a cyprinid fish endemic to the Qinghai-Tibetan Plateau, has evolved unique morphological, physiological and genetic characteristics to adapt to the highland environment. Herein, we assembled a high-quality G. przewalskii tetraploid genome with a size of 2.03 Gb and scaffold N50 of 44.93 Mb, which was anchored onto 46 chromosomes. The comparative analysis suggested that gene families related to highland adaptation were significantly expanded in G. przewalskii. According to the G. przewalskii genome, we evaluated the phylogenetic relationship of 13 schizothoracine fishes, and inferred that the demographic history of G. przewalskii was strongly associated with geographic and eco-environmental alterations. We noticed that G. przewalskii experienced whole-genome duplication, and genes preserved post duplication were functionally associated with adaptation to high salinity and alkalinity. In conclusion, a chromosome-scale G. przewalskii genome provides an important genomic resource for teleost fish, and will particularly promote our understanding of the molecular evolution and speciation of fish in the highland environment.