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.     

Sex pheromone components of the rice leaffolder,Cnaphalocrocis medinalis (Lepidoptera: Crambidae), in Indonesia

Field tests of three synthetic sex pheromone blends (Japanese blend: Z11–18:Ald (55 μg), Z13–18:Ald (500 μg), Z11–18:OH (120 μg) and Z13–18:OH (180 μg), Indian blend: Z11–16:Ac (50 μg) and Z13–18:Ac (500 μg) and Philippine blend: Z11–16:Ac (500 μg) and Z13–18:Ac (10 μg) based on geographic variations in sex pheromones) of the rice leaffolder moth, Cnaphalocrocis medinalis Guenée (Lepidoptera: Crambidae), were conducted at Yogyakarta (Java), and at Sempidi and Penatih (Bali), Indonesia. Only the Japanese blend attracted significant numbers of male C. medinalis, while neither the Indian nor the Philippine blend showed any attractiveness to the males. In the GC–MS analysis of a crude extract from pheromone glands of female C. medinalis collected at Sanur, Bali. Indonesia, Z11–18:Ald, Z13–18:Ald, Z11–18:OH and Z13–18:OH were detected at a ratio of 10:100:26:37, and the total amount was approximately 0.8 ng/female. Neither Z11–16:Ac nor Z13–18:Ac were detected. These results suggest that C. medinalis that respond to the Japanese blend are widely distributed from Eastern Asia through Southeast Asia.     

Effect of multiple mating on the reproductive performance of the rice leaffolder moth,Cnaphalocrocis medinalis (Lepidoptera: Crambidae)

To clarify whether multiple mating of females and males affects the reproductive performance of the rice leaffolder moth, Cnaphalocrocis medinalis (Guenée), we examined the effect of the number of matings (once, twice, or three times) for females (female treatment) and males (male treatment) on the incidence of moth mating, number of eggs laid, egg hatchability, and adult longevity. We also compared the effect of multiple mating imposed on males or females separately with the effect of that imposed on both sexes simultaneously (both sexes treatment). The incidence of mating of females and males that mated three times (3-mated females and males) was significantly lower than for females and males that mated twice or once (2-mated or 1-mated females and males). The incidence of mating of 1-mated moths (both sexes) was significantly higher than for 2-mated or 3-mated moths (both sexes). Two-mated or 3-mated females laid significantly more eggs with significantly higher hatchability than 1-mated females. Females that mated with 1-mated males (second male mating) or 2-mated males (third male mating) laid significantly fewer eggs than those that mated with virgin males (first male mating). Females laid significantly more eggs after the second and third matings for moths of both sexes than after the first mating for moths of both sexes. The mechanisms of improvement and decline of female reproductive performance when multiple mating was imposed on males or females are also discussed in relation to the reproductive biology of C. medinalis.     

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.     

The effect of leaffolder Cnaphalocrocis medinalis (Guenee) [Lepidoptera: Pyralidae] injury on the plant physiology and yield loss in rice

Influence of leaffolder feeding on chlorophyll, PS II activity and plant–water relations, effect of larval density on leaf damage and time course studies on larval feeding behaviour on altered physiological changes in TN1 rice culture were studied. Quantification of yield losses in the field caused by leaffolder was also assessed. Leaffolder damage resulted in 57% reduction in chlorophyll content, 23% reduction in PS II activity and 23% reduction in relative water content in comparison with control. Rice leaffolder larva folds the leaf and scrapes the green tissue from within the fold resulting in scorching and drying of the leaves. Larval density had differentially influenced effective leaf area of rice crop. Larval densities of more than 3 larvae per hill at maximum tillering stage resulted up to 20% unfilled grains, 28–57% reduction in PS II activity and 23% reduction in relative water content in comparison with the control. At flowering stage, flag leaf area damage of above 25% resulted in more than 50% unfilled grains over control, indicating direct effect of yield reduction in rice. Thus, a cumulative effect of loss in chlorophyll, reduced photosynthate availability and altered water relations caused by the leaffolder injury to flag leaf lead to greater yield loss in rice.     

Geographical variation in female sex pheromones of the rice leaffolder moth, Cnaphalocrocis medinalis: identification of pheromone components in Japan

Sex pheromone components of the Japanese rice leaffolder moth, Cnaphalocrocis medinalis Guenée (Lepidoptera: Pyralidae) were identified from ovipositor extracts of virgin females as (Z)-11-octadecenal, (Z)-13-octadecenal, (Z)-11-octadecen-1-ol and (Z)-13-octadecen-1-ol at a ratio of 11:100:24:36 by GC-EAD, GC, GC-MS. The total amount was estimated to be ca.0.9 ng/female. Field bioassays in Kagoshima, Japan, showed that the two aldehydes are essential for male attraction and the alcohols may have a synergistic effect on the aldehydes. A rubber septum containing 0.9 mg of the four components at the natural ratio was shown to be an effective lure for monitoring this pest in Japan. The above four components are quite different from the sex pheromone components reported previously for the same species of either Philippine or Indian origin; components were shown to be (Z)-11-hexadecenyl acetate and (Z)-13-octadecenyl acetate at a ratio of 98:2 in the Philippine blend and 1:10 in the Indian blend. Furthermore, in the field tests in Japan, neither the Philippine blend nor the Indian blend showed any attractive activity, while the Japanese blend attracted significant numbers of male moths. These results suggest that there are remarkable geographical variations in the sex pheromone composition of this species or there are several distinct species using different sex pheromone blends.     

Chromosome-level Asian elephant genome assembly and comparative genomics of long-lived mammals reveal the common substitutions for cancer resistance

The naked mole rat (Heterocephalus glaber), bats (e.g., genus Myotis), and elephants (family Elephantidae) are known as long-lived mammals and are assumed to be excellent cancer antagonists. However, whether there are common genetic changes underpinning cancer resistance in these long-lived species is yet to be fully established. Here, we newly generated a high-quality chromosome-level Asian elephant (Elephas maximus) genome and identified that the expanded gene families in elephants are involved in Ras-associated and base excision repair pathways. Moreover, we performed comparative genomic analyses of 12 mammals and examined genes with signatures of positive selection in elephants, naked mole rat, and greater horseshoe bat. Residues at positively selected sites of CDR2L and ALDH6A1 in these long-lived mammals enhanced the inhibition of tumor cell migration compared to those in short-lived relatives. Overall, our study provides a new genome resource and a preliminary survey of common genetic changes in long-lived mammals.     

水稻品种对稻纵卷叶螟抗性的物理及生化机制

稻纵卷叶螟Cnaphalocrocis medinalis连年大发生,为在其治理中培育和推广抗虫品种,本文应用扫描电镜和生化测定研究了5个常用水稻栽培品种扬辐粳8号、扬稻6号、扬粳9538、淮稻9号和宁梗1号叶片中的硅含量、硅颗粒大小、蜡质含量等物理指标和一些生化指标与抗虫性的关系,并比较了稻纵卷叶螟幼虫危害不同水稻品种后其体内生化反应的差异。结果表明抗虫品种宁梗1号、淮稻9号叶片表面的硅含量显著高于感虫品种,硅颗粒大小在品种间无显著差异。宁粳1号叶片蜡质含量显著高于其他品种。由此表明叶片表面硅和蜡质含量与抗性有关。稻纵卷叶螟幼虫取食后,抗虫品种体内的过氧化物酶（POD）、超氧化物岐化酶（SOD）活性显著高于感虫品种,但丙二醛(MDA)含量低于感虫品种。稻纵卷叶螟幼虫取食不同品种后,其体内一些酶的活性明显不同,取食抗虫品种的幼虫体内POD和谷胱甘肽-S-转移酶(GST)活性显著高于取食其他品种的幼虫,SOD活性显著低于取食感虫品种的幼虫, 表明抗虫品种对稻纵卷叶螟幼虫有毒害作用。     

稻纵卷叶螟对性信息素和花香的嗅觉行为反应及在其种群监测中的应用

[目的]明确稻纵卷叶螟Cnaphalocrocis medinalis生理状态对性信息素和花香气味的嗅觉行为反应的影响,以及在田间性信息素和花香气味诱蛾量的动态.[方法]于2020年在广西、湖南、浙江、四川5个试验点,通过田间网捕、花香气味和性信息素诱捕稻纵卷叶螟成虫,结合解剖卵巢和精巢,比较性信息素和花香诱捕的基本迁...     

Chromosome-level genome assembly of a xerophytic plant,Haloxylon ammodendron

Haloxylon ammodendron is a xerophytic perennial shrub or small tree that has a high ecological value in anti-desertification due to its high tolerance to drought and salt stress. Here, we report a high-quality, chromosome-level genome assembly of H. ammodendron by integrating PacBio’s high-fidelity sequencing and Hi-C technology. The assembled genome size was 685.4 Mb, of which 99.6% was assigned to nine pseudochromosomes with a contig N50 value of 23.6 Mb. Evolutionary analysis showed that both the recent substantial amplification of long terminal repeat retrotransposons and tandem gene duplication may have contributed to its genome size expansion and arid adaptation. An ample amount of low-GC genes was closely related to functions that may contribute to the desert adaptation of H. ammodendron. Gene family clustering together with gene expression analysis identified differentially expressed genes that may play important roles in the direct response of H. ammodendron to water-deficit stress. We also identified several genes possibly related to the degraded scaly leaves and well-developed root system of H. ammodendron. The reference-level genome assembly presented here will provide a valuable genomic resource for studying the genome evolution of xerophytic plants, as well as for further genetic breeding studies of H. ammodendron.     

锐劲特在水稻主要害虫总体防治中的应用研究

系列试验证明：锐劲特是水稻害虫多靶标防治中较好的防治药剂,5％锐劲特SC600mL/hm^2对白背飞虱的防效同25％噻嗪酮WP675g/hm^2加80％杀虫单WP750g/hm^2基本一致;对褐飞虱的防效,其速率性及持效性显著居优;对2代二化防治具有较好的效果,杀虫及保穗效果均明显高于杀虫单,差异显著,对稻纵卷叶螟、低龄稻苞虫的防治效果分别为77．52％,97．62％;用量为750mL/hm^2时,对高龄稻苞虫的防治效果为89．00％,可达一药多治的防治效果。     

Structural and functional analysis of rice genome

Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4-6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (> 10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at >50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macroand micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.     

转Bt基因水稻对稻纵卷叶螟幼虫体内三种保护酶活性的影响

用转Cry1Ab/Cry1Ac基因水稻的叶片饲喂稻纵卷叶螟Cnaphalocrocis medinalis (Guenée)幼虫,采用酶活力测定方法研究了转基因水稻对稻纵卷叶螟幼虫体内3种保护酶（SOD,CAT和POD）活性的影响。结果表明：取食转基因水稻叶片4 h后,幼虫体内SOD酶活性比对照提高了91.5%,与对照有显著差异;36 h后活性达到最大值,但与对照差异不显著。取食转基因水稻叶片24 h后,幼虫体内CAT酶活性达到最大值且高于对照,但与对照差异不显著;48 h后酶活性受到显著抑制,与对照差异显著。取食转基因水稻叶片12 h后,幼虫体内POD酶活性达到最大值,与对照差异不显著;48 h后酶活性逐渐下降达到最小值,比对照下降68.05%。实验同时测定了幼虫体内及其粪便中Bt毒蛋白含量的变化,结果表明取食转基因水稻叶片12 h后,随着大量取食进入体内的毒蛋白随粪便排出,幼虫体内的毒蛋白含量一直低于粪便中的含量,且在24 h时两者差异达到最大。由于Bt毒蛋白在幼虫体内的积累,扰乱了稻纵卷叶螟幼虫体内SOD,CAT和POD 3种保护酶的动态平衡,使虫体内自由基的清除遇到障碍,从而对其产生毒害作用。     

几种药剂及施药方式对稻纵卷叶螟的防治效果

对稻纵卷叶螟Cnaphalocrocis medinalis Guen e高龄幼虫防治药剂31%氟虫腈.三唑磷ME和当地几种常用药剂及不同施药方法对防治效果影响进行试验。结果表明:(1)毒死蜱(48%乐斯本EC)有较好速效性,药后1 d可达理想防效,三唑磷与氟出腈、氟铃脲复配的药剂(31%氟虫腈.三唑磷ME、21%氟虫腈.三唑磷EC、15%氟铃脲.三唑磷EC)药后3d才能达到理想防效;(2)药后3d,各处理均达到理想防效,防效依次为31%氟虫腈.三唑磷ME1.5L/hm2>31%氟虫腈.三唑磷ME1.05L/hm2>21%氟虫腈.三唑磷EC1.5L/hm2>48%毒死蜱EC1.5L/hm2>15%氟虫腈.三唑磷EC1.5L/hm2>15%阿维菌素.毒死蜱EC1.5L/hm2;(3)分虫龄防效统计,药后3d供试药剂对1龄以下(施药时虫龄,后同)幼虫防效均在91%以上,对2~3龄幼虫,31%氟虫腈.三唑磷ME保持90%以上的防效,其它处理防效明显下降,对4龄以上高龄幼虫,31%氟虫腈.三唑磷1.5L/hm2细喷雾处理防效仍达95.6%,其它处理防效很低。(4)细喷雾可提高31%氟虫腈.三唑磷ME对稻纵卷叶螟的防治效果,尤其是对高龄幼虫,与工农16型1.8mm孔径喷片的常规喷雾相比,1.2mm孔径喷片细喷雾处理药后3 d防效提高5.5%,东方红18型弥雾处理防效提高7.8%,其中,弥雾处理对1~2龄幼虫防效提高4.7%,对4~5龄幼虫防效提高了20.8%。     

Comparison of three transgenic Bt rice lines for insecticidal protein expression and resistance against a target pest,Chilo suppressalis (Lepidoptera: Crambidae)

Two transgenic rice lines (T2A‐1 and T1C‐19b) expressing cry2A and cry1C genes, respectively, were developed in China, targeting lepidopteran pests including Chilo suppressalis (Walker) (Lepidoptera: Crambidae). The seasonal expression of Cry proteins in different tissues of the rice lines and their resistance to C. suppressalis were assessed in comparison to a Bt rice line expressing a cry1Ab/Ac fusion gene, Huahui 1, which has been granted a biosafety certificate. In general, levels of Cry proteins were T2A‐1 > Huahui 1 > T1C‐19b among rice lines, and leaf > stem > root among rice tissues. The expression patterns of Cry protein in the rice line plants were similar: higher level at early stages than at later stages with an exception that high Cry1C level in T1C‐19b stems at the maturing stage. The bioassay results revealed that the three transgenic rice lines exhibited significantly high resistance against C. suppressalis larvae throughout the rice growing season. According to Cry protein levels in rice tissues, the raw and corrected mortalities of C. suppressalis caused by each Bt rice line were the highest in the seedling and declined through the jointing stage with an exception for T1C‐19b providing an excellent performance at the maturing stage. By comparison, T1C‐19b exhibited more stable and greater resistance to C. suppressalis larvae than T2A‐1, being close to Huahui 1. The results suggest cry1C is an ideal Bt gene for plant transformation for lepidopteran pest control, and T1C‐19b is a promising Bt rice line for commercial use for tolerating lepidopteran rice pests.     

The chromosome-scale assembly of the Canary Islands endemic spider Dysdera silvatica (Arachnida,Araneae) sheds light on the origin and genome structure of chemoreceptor gene families in chelicerates

Here, we present the chromosome-level genome assembly of Dysdera silvatica Schmidt, 1981, a nocturnal ground-dwelling spider endemic from the Canary Islands. The genus Dysdera has undergone a remarkable diversification in this archipelago mostly associated with shifts in the level of trophic specialization, becoming an excellent model to study the genomic drivers of adaptive radiations. The new assembly (1.37 Gb; scaffold N50 of 174.2 Mb), was performed using the chromosome conformation capture scaffolding technique, represents a continuity improvement of more than 4500 times with respect to the previous version. The seven largest scaffolds or pseudochromosomes, which cover 87% of the total assembly size, probably correspond with the seven chromosomes of the karyotype of this species, including a characteristic large X chromosome. To illustrate the value of this new resource we performed a comprehensive analysis of the two major arthropod chemoreceptor gene families (i.e., gustatory and ionotropic receptors). We identified 545 chemoreceptor sequences distributed across all pseudochromosomes, with a notable underrepresentation in the X chromosome. At least 54% of them localize in 83 genomic clusters with a significantly lower evolutionary distances between them than the average of the family, suggesting a recent origin of many of them. This chromosome-level assembly is the first high-quality genome representative of the Synspermiata clade, and just the third among spiders, representing a new valuable resource to gain insights into the structure and organization of chelicerate genomes, including the role that structural variants, repetitive elements and large gene families played in the extraordinary biology of spiders.     

Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness

Nymphoides indica, an aquatic plant, is an invasive species that causes both ecological and economic damage in North America and elsewhere. However, the lack of genomic data of N. indica limits the in-depth analysis of this invasive species. Here, we report a chromosome-level genome assembly of nine pseudochromosomes of N. indica with a total size of ∼ 520 Mb. More than half of the N. indica genome consists of transposable elements (TEs), and a higher density of TEs around genes may play a significant role in response to an ever-changing environment by regulating the nearby gene. Additionally, our analysis revealed that N. indica only experienced a gamma (γ) whole-genome triplication event. Functional enrichment of the N. indica-specific and expanded gene families highlighted genes involved in the responses to hypoxia and plant–pathogen interactions, which may strengthen the ability to adapt to external challenges and improve ecological fitness. Furthermore, we identified 160 members of the nucleotide-binding site and leucine-rich repeat gene family, which may be linked to the defence response. Collectively, the high-quality N. indica genome reported here opens a novel avenue to understand the evolution and rapid invasion of Nymphoides spp.