蚜虫基因组及功能基因组研究进展

蚜虫作为刺吸式昆虫和植物病毒的传播者,已经成为严重威胁农业生产发展的重要害虫之一。近几年随着分子生物学的发展,尤其是基因组测序技术的进步,蚜虫基因组学和功能基因组学取得了重大突破,使我们对蚜虫特殊的生物学特征有了深层次的认识。本文就蚜虫与内共生菌关系、表型可塑性、发育和生殖、系统进化、解毒酶基因家族以及唾液腺方面在基因组和功能基因组水平上的研究进展进行了综述。     

Legume comparative genomics: progress in phylogenetics and phylogenomics

The legumes are the focus of numerous rapidly expanding genomic projects, all of which involve members of one part of the Leguminosae, the subfamily Papilionoideae. This subfamily is monophyletic, and recent studies concur on a series of clades within it that are well supported and have received informal names. These include the Cladrastis clade, the genistoids (including Lupinus), the mirbelioids, the dalbergioids (including Arachis), the millettioids (including Glycine and Phaseolus), and the hologalegina (galegoid) legumes, which comprise the robinioids (including Lotus) and the inverted repeat loss (IRL) clade (including Medicago and Pisum). The canavanine-accumulating legumes appear to fall into a single clade, consistent with the idea that the production of this toxic amino acid evolved only once. Recent advances in analytical techniques for dating phylogenies support an 'early explosion hypothesis', suggesting that much of the morphological diversity of the legume family evolved rapidly around 50-60 million years ago. Within the papilionoids, the divergence between Glycine and Medicago is estimated to have taken place around 54 million years ago. There is strong evidence for a palaeoduplication event that affected both Glycine (a millettioid) and Medicago (from the IRL clade). As more genomic data are forthcoming for Arachis, it will be possible to test whether this event extends to the dalbergioids.     

Rice functional genomics research: progress and implications for crop genetic improvement

Rice is a staple food crop and has become a reference of monocot plant for functional genomic research. With the availability of high quality rice genome sequence, there has been rapid accumulation of functional genomic resources, including: large mutant libraries by T-DNA insertion, transposon tagging, and chemical mutagenesis; global expression profiles of the genes in the entire life cycle of rice growth and development; full-length cDNAs for both indica and japonica rice; sequences from resequencing large numbers of diverse germplasm accessions. Such resource development has greatly accelerated gene cloning. By the end of 2010, over 600 genes had been cloned using various methods. Many of the genes control agriculturally useful traits such as yield, grain quality, resistances to biotic and abiotic stresses, and nutrient-use efficiency, thus have potential utility in crop genetic improvement. This review was aimed to provide a comprehensive summary of such progress. We also presented our perspective for future studies.     

Biobanks for genomics and genomics for biobanks

Biobanks include biological samples and attached databases. Human biobanks occur in research, technological development and medical activities. Population genomics is highly dependent on the availability of large biobanks. Ethical issues must be considered: protecting the rights of those people whose samples or data are in biobanks (information, autonomy, confidentiality, protection of private life), assuring the non-commercial use of human body elements and the optimal use of samples and data. They balance other issues, such as protecting the rights of researchers and companies, allowing long-term use of biobanks while detailed information on future uses is not available. At the level of populations, the traditional form of informed consent is challenged. Other dimensions relate to the rights of a group as such, in addition to individual rights. Conditions of return of results and/or benefit to a population need to be defined. With 'large-scale biobanking' a marked trend in genomics, new societal dimensions appear, regarding communication, debate, regulation, societal control and valorization of such large biobanks. Exploring how genomics can help health sector biobanks to become more rationally constituted and exploited is an interesting perspective. For example, evaluating how genomic approaches can help in optimizing haematopoietic stem cell donor registries using new markers and high-throughput techniques to increase immunogenetic variability in such registries is a challenge currently being addressed. Ethical issues in such contexts are important, as not only individual decisions or projects are concerned, but also national policies in the international arena and organization of democratic debate about science, medicine and society.     

A review of catfish genomics: progress and perspectives

Catfish is one of the lower teleosts whose genome research is important for evolutionary genomics. As the major aquaculture species in the USA, its genome research also has practical and economical implications. Much progress has been made in recent years, including the development of large numbers of molecular markers, the construction of framework genetic linkage maps, the identification of putative markers involved in performance traits, and the development of genomic resources. Repetitive elements have been identified and characterized in the catfish genome that should facilitate physical analysis of the catfish genome. A large number of genes or full-length cDNAs have been analysed using genomic approaches, providing information on gene structure, gene evolution and gene expression in relation to functions. Catfish genome research has come to a stage when physical mapping through BAC contig construction is greatly demanded, in order to develop regional markers for QTL analysis and for large-scale comparative mapping. The current effort in large-scale EST analysis and type I marker mapping should further enhance research efficiency through comparative mapping. Candidate gene identification is being accelerated through the use of cDNA microarrays.     

Sequence-based cancer genomics: progress,lessons and opportunities

Technologies that provide a genome-wide view offer an unprecedented opportunity to scrutinize the molecular biology of the cancer cell. The information that is derived from these technologies is well suited to the development of public databases of alterations in the cancer genome and its expression. Here, we describe the synergistic efforts of research programmes in Brazil, the United Kingdom and the United States towards building integrated databases that are widely accessible to the research community, to enable basic and applied applications in cancer research.     

Recent progress in livestock genomics and potential impact on breeding programs

Most of the major livestock breeding organizations in the world are actively involved in using the emerging tools for genome analysis to obtain a better understanding of the molecular architecture of their favourite production traits. This is bound to generate a considerable amount of novel biological information that will provide a competitive advantage to those that have access to it. At present, the preferred avenue to exploit this information is via marker-assisted selection (MAS), and several breeding organisations are starting to implement MAS in breeding programs. However, it seems unlikely that the exploitation of genomics information will be limited to MAS in the future. Even though it is difficult to anticipate the ultimate impact of genomics on animal production, it would be very surprising if it were not to revolutionize this industry as it is already revolutionizing the biomedical and plant breeding industries.     

From Pasteur to genomics: progress and challenges in infectious diseases

Over the past decade, microbiology and infectious disease research have undergone the most profound revolution since the times of Pasteur. Genomic sequencing has revealed the much-awaited blueprint of most pathogens. Screening blood for the nucleic acids of infectious agents has blunted the spread of pathogens by transfusion, the field of antiviral therapeutics has exploded and technologies for the development of novel and safer vaccines have become available. The quantum jump in our ability to detect, prevent and treat infectious diseases resulting from improved technologies and genomics was moderated during this period by the greatest emergence of new infectious agents ever recorded and a worrisome increase in resistance to existing therapies. Dozens of new infectious diseases are expected to emerge in the coming decades. Controlling these diseases will require a better understanding of the worldwide threat and economic burden of infectious diseases and a global agenda.     

Bursaphelenchus xylophilus: opportunities in comparative genomics and molecular host-parasite interactions

Most Bursaphelenchus species are fungal feeding nematodes that colonize dead or dying trees. However, Bursaphelenchus xylophilus, the pine wood nematode, is also a pathogen of trees and is the causal agent of pine wilt disease. B. xylophilus is native to North America and here it causes little damage to trees. Where it is introduced to new regions it causes huge damage. The most severely affected areas are found in the Far East but more recently B. xylophilus has been introduced into Portugal and the potential for damage here is also high. As incidence and severity of pine wilt disease are linked to temperature we suggest that climate change is likely to exacerbate the problems caused by B. xylophilus and, in addition, will extend (northwards in Europe) the range in which pine wilt disease can occur. Here we review what is currently known about the interactions of B. xylophilus with its hosts, including recent developments in our understanding of the molecular biology of pathogenicity in the nematode. We also examine the potential developments that could be made by more widespread use of genomics tools to understand interactions between B. xylophilus, bacterial pathogens that have been implicated in disease and host trees.     

Predator-mediated habitat use: some consequences for species interactions

Synopsis Behavioral responses to predators can have a major impact on a fishes' diet and habitat choice. Studies with the bluegill sunfish, Lepomis macrochirus, demonstrate that bluegills undergo pronounced shifts in diet and habitat use as they grow in response to changes in their vulnerability to predators. Other species of fish exhibit similar habitat shifts with body size, presumably also in response to changing predation risks and/or foraging gains. An important but little appreciated consequence of this type of predator-mediated habitat use is that predation risk, by structuring size and/or age-specific resource use, may also indirectly affect species interactions. This paper discusses some of the ways in which behavioral responses to predators may affect intra- and interspecific competition in fish. Observational and experimental studies with sunfish (Centrarchidae) provide most of the examples. These studies suggest that the nonlethal effects of predators may be as important as the actual killing of prey.     

Temperature regimes and aphid density interactions differentially influence VOC emissions in Arabidopsis

The effects of volatile emissions from plants exposed to individual abiotic and biotic stresses are well documented. However, the influence of multiple stresses on plant photosynthesis and defense responses, resulting in a variety of volatile profiles has received little attention. In this study, we investigated how temperature regimes in the presence and absence of the sucking insect Myzus persicae affected volatile organic compound (VOC) emissions in Arabidopsis over three time periods (0–24, 24–48, and 48–72 h). Headspace solid-phase microextraction coupled with gas chromatography–mass spectrometry was used to evaluate Arabidopsis VOCs. The results showed that under laboratory conditions, eight volatile classes [alcohols (mainly 2-ethyl-hexan-1-ol), ketone (6-methyl hept-5-en-2-one), esters (mainly (Z)-3-hexenyl acetate), aldehydes (mainly phenylacetaldehyde), isothiocyanates (mainly 4-methylpentyl isothiocyanate), terpenes (mainly (E,E)-α-farnesene), nitrile (5-(methylthio) pentanenitrile), and sulfide (dimethyl trisulfide)] were observed on plants exposed to stress combinations, whereas emissions of six volatile classes were observed during temperature stress treatments alone (with the exception of nitriles and sulfides). Aphid density at high temperature combinations resulted in significantly higher isothiocyanate, ester, nitrile, and sulfide proportions. The results of the present study provide an insight into the effects of temperature–aphid interactions on plant volatile emissions.     

The shock of the new: progress in schizophrenia genomics

A growing list of common and rare genetic risk variants are being implicated in schizophrenia susceptibility. As with other complex genetic disorders most of the variance in genetic risk is still to be attributed. What can be learned from progress to date? The available data challenges how we conceptualize schizophrenia and suggests strong aetiological links with other psychiatric and developmental disorders. With the identification of rare copy number risk variants implicating specific genes (e.g. VIPR2 and NRXN1) it is increasingly possible to investigate molecular aetiology in patient subgroups to establish whether schizophrenia represents one or many different disease processes. This review summarizes recent research progress and suggests how the tools of modern genomics and neuroscience can be applied to best understand this devastating disorder.     

Research progress on banana functional genomics involved in fruit quality

Banana is one of the most important tropical fruits and main economical resource for tropical people. Banana quality is always becoming a focus for people to follow with interest. Here, we reviewed recent research progresses on isolation and identification of banana genes involved in fruit quality such as ripening, softening, glycometabolism, and scent, which will help us explore their functions and facilitate banana quality improvement.     

香蕉品质相关功能基因组学的研究进展

香蕉是重要的热带水果之一,是热区人民脱贫致富的主要经济来源。香蕉品质一直是人们关注的焦点。文章综述了近年来香蕉果实品质如成熟、软化、糖代谢及香气相关功能基因分离和鉴定等方面的最新研究进展,将有助于从源头上对香蕉进行创新性的探索与研究,支撑香蕉品质改良和新品种培育。     

Behavioral interactions between three birch aphid species and Adalia bipunctata larvae

First and fourth instars of three birch aphid species were exposed to first and fourth instars of Adalia bipunctata (L.), the most common aphid predator on silver birch, Betula pendula Roth, in northern California. Defensive behavior differed by aphid species. Euceraphis betulae (Koch) (Eb), the most successful escapee, was highly mobile and frequently walked away from coccinellid larvae. Betulaphis brevipilosa Börner (Bb), a flat, sessile species, was the least successful aphid at actively escaping from A. bipunctata larvae, but could passively escape detection when coccinellid larvae walked over nymphs and did not perceive them. Active escape behavior was much safer for aphids than passive avoidance of detection. Both instars of Eb and fourth instars of Callipterinella calliptera (Hartig) (Cc) escaped from coccinellid larvae more frequently when approached from the front, apparently using vision for pre-contact detection of A. bipunctata. These aphids avoided physical contact with larger predators more often than with smaller predators. Level of predation by A. bipunctata on these three aphid species is dependent upon types of aphid defense.

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Résumé Des larves de premier et troisième stades de 3 espèces de pucerons du bouleau: Betulaphis brevipilosa, Callipterinella calliptera et Euceraphis betulae ont été exposées aux attaques des larves du premier et du quatrième stades d'Adalia bipunctata, prédateur le plus fréquent de pucerons sur Betula pendula en Californie du Nord. Le comportement défensif dépend beaucoup de l'espèce de puceron. E. betulae, qui s'échappe avec le plus de succès, est très mobile et s'écarte fréquemment des larves agressives de coccinelles. B. brevipilosa, espèce plate, sessile, a le moins de succès dans la protection active contre les attaques des larves de A. bipunctata, mais elle peut échapper passivement à la détection des larves de coccinelles qui ne peuvent pas les discerner lorsqu'elles circulent parmi les larves de pucerons. E. betulae (aux deux stades) et C. calliptera (au quatrième) échappent le plus aux larves de coccinelles qui attaquent de front, ce qui laisse supposer que la vision permet de détecter A. bipunctata avant le contact. Le succès des larves de coccinelles varie selon les stades du puceron et de la coccinelle. Les possibilités d'obtention de niveaux de prédation élevés de ces 3 pucerons par A. bipunctata dépend du type de protection du puceron.