共查询到20条相似文献，搜索用时 0 毫秒
1.
Hernandez P Martis M Dorado G Pfeifer M Gálvez S Schaaf S Jouve N Šimková H Valárik M Doležel J Mayer KF 《The Plant journal : for cell and molecular biology》2012,69(3):377-386
Wheat is the third most important crop for human nutrition in the world. The availability of high-resolution genetic and physical maps and ultimately a complete genome sequence holds great promise for breeding improved varieties to cope with increasing food demand under the conditions of changing global climate. However, the large size of the bread wheat (Triticum aestivum) genome (approximately 17 Gb/1C) and the triplication of genic sequence resulting from its hexaploid status have impeded genome sequencing of this important crop species. Here we describe the use of mitotic chromosome flow sorting to separately purify and then shotgun-sequence a pair of telocentric chromosomes that together form chromosome 4A (856 Mb/1C) of wheat. The isolation of this much reduced template and the consequent avoidance of the problem of sequence duplication, in conjunction with synteny-based comparisons with other grass genomes, have facilitated construction of an ordered gene map of chromosome 4A, embracing ≥85% of its total gene content, and have enabled precise localization of the various translocation and inversion breakpoints on chromosome 4A that differentiate it from its progenitor chromosome in the A genome diploid donor. The gene map of chromosome 4A, together with the emerging sequences of homoeologous wheat chromosome groups 4, 5 and 7, represent unique resources that will allow us to obtain new insights into the evolutionary dynamics between homoeologous chromosomes and syntenic chromosomal regions. 相似文献
2.
Bala A. Akpinar Stuart J. Lucas Jan Vrána Jaroslav Doležel Hikmet Budak 《Plant biotechnology journal》2015,13(6):740-752
Flow cytometric sorting of individual chromosomes and chromosome‐based sequencing reduces the complexity of large, repetitive Triticeae genomes. We flow‐sorted chromosome 5D of Aegilops tauschii, the D genome donor of bread wheat and sequenced it by Roche 454 GS FLX platform to approximately 2.2x coverage. Repetitive sequences represent 81.09% of the survey sequences of this chromosome, and Class I retroelements are the prominent type, with a particular abundance of LTR/Gypsy superfamily. Nonrepetitive sequences were assembled to cover 17.76% of the total chromosome regions. Up to 6188 nonrepetitive gene loci were predicted to be encoded by the 5D chromosome. The numbers and chromosomal distribution patterns of tRNA genes suggest abundance in tRNALys and tRNAMet species, while the nonrepetitive assembly reveals tRNAAla species as the most abundant type. A comparative analysis of the genomic sequences of bread wheat and Aegilops chromosome 5D indicates conservation of gene content. Orthologous unique genes, matching Aegilops 5D sequences, numbered 3730 in barley, 5063 in Brachypodium, 4872 in sorghum and 4209 in rice. In this study, we provide a chromosome‐specific view into the structure and organization of the 5D chromosome of Ae. tauschii, the D genome ancestor of bread wheat. This study contributes to our understanding of the chromosome‐level evolution of the wheat genome and presents a valuable resource in wheat genomics due to the recent hybridization of Ae. tauschii genome with its tetraploid ancestor. 相似文献
3.
Ke Chen Haona Yang Yajun Peng Ducai Liu Jingyuan Zhang Zhenghong Zhao Lamei Wu Tao Lin Lianyang Bai Lifeng Wang 《Plant biotechnology journal》2023,21(8):1642-1658
Polyploidy confers a selective advantage under stress conditions; however, whether polyploidization mediates enhanced herbicide adaptation remains largely unknown. Tetraploid Leptochloa chinensis is a notorious weed in the rice ecosystem, causing severe yield loss in rice. In China, L. chinensis has only one sister species, the diploid L. panicea, whose damage is rarely reported. To gain insights into the effects of polyploidization on herbicide adaptation, we first assembled a high-quality genome of L. panicea and identified genome structure variations with L. chinensis. Moreover, we identified herbicide-resistance genes specifically expanded in L. chinensis, which may confer a greater herbicide adaptability in L. chinensis. Analysis of gene retention and loss showed that five herbicide target-site genes and several herbicide nontarget-site resistance gene families were retained during polyploidization. Notably, we identified three pairs of polyploidization-retained genes including LcABCC8, LcCYP76C1 and LcCYP76C4 that may enhance herbicide resistance. More importantly, we found that both copies of LcCYP76C4 were under herbicide selection during the spread of L. chinensis in China. Furthermore, we identified another gene potentially involved in herbicide resistance, LcCYP709B2, which is also retained during polyploidization and under selection. This study provides insights into the genomic basis of the enhanced herbicide adaptability of Leptochloa weeds during polyploidization and provides guidance for the precise and efficient control of polyploidy weeds. 相似文献
4.
Weihua Ma Le Xu Hongxia Hua Mengyao Chen Mengjian Guo Kang He Jing Zhao Fei Li 《Molecular ecology resources》2021,21(1):226-237
The brown planthopper Nilaparvata lugens, white‐backed planthopper Sogatella furcifera, and small brown planthopper Laodelphax striatellus are three major insect pests of rice. They are genetically close; however, they differ in several ecological traits such as host range, migration capacity, and in their sex chromosomes. Though the draft genome of these three planthoppers have been previously released, the quality of genome assemblies need to be improved. The absence of chromosome‐level genome resources has hindered in‐depth research of these three species. Here, we performed a de novo genome assembly for N. lugens to increase its genome assembly quality with PacBio and Illumina platforms, increasing the contig N50 to 589.46 Kb. Then, with the new N. lugens genome and previously reported S. furcifera and L. striatellus genome assemblies, we generated chromosome‐level scaffold assemblies of these three planthopper species using HiC scaffolding technique. The scaffold N50s significantly increased to 77.63 Mb, 43.36 Mb and 29.24 Mb for N. lugens, S. furcifera and L. striatellus, respectively. To identify sex chromosomes of these three planthopper species, we carried out genome re‐sequencing of males and females and successfully determined the X and Y chromosomes for N. lugens, and X chromosome for S. furcifera and L. striatellus. The gene content of the sex chromosomes showed high diversity among these three planthoppers suggesting the rapid evolution of sex‐linked genes, and all chromosomes showed high synteny. The chromosome‐level genome assemblies of three planthoppers would provide a valuable resource for a broad range of future research in molecular ecology, and subsequently benefits development of modern pest control strategies. 相似文献
5.
6.
Chu‐Yu Ye Ting Li Hengfu Yin David J. Weston Gerald A. Tuskan Timothy J. Tschaplinski Xiaohan Yang 《The Plant journal : for cell and molecular biology》2013,73(5):788-797
There are a large number of ‘non‐family’ (NF) genes that do not cluster into families with three or more members per genome. While gene families have been extensively studied, a systematic analysis of NF genes has not been reported. We performed comparative studies on NF genes in 14 plant species. Based on the clustering of protein sequences, we identified ~94 000 NF genes across these species that were divided into five evolutionary groups: Viridiplantae wide, angiosperm specific, monocot specific, dicot specific, and those that were species specific. Our analysis revealed that the NF genes resulted largely from less frequent gene duplications and/or a higher rate of gene loss after segmental duplication relative to genes in both low‐copy‐number families (LF; 3–10 copies per genome) and high‐copy‐number families (HF; >10 copies). Furthermore, we identified functions enriched in the NF gene set as compared with the HF genes. We found that NF genes were involved in essential biological processes shared by all plant lineages (e.g. photosynthesis and translation), as well as gene regulation and stress responses associated with phylogenetic diversification. In particular, our analysis of an Arabidopsis protein–protein interaction network revealed that hub proteins with the top 10% most connections were over‐represented in the NF set relative to the HF set. This research highlights the roles that NF genes may play in evolutionary and functional genomics research. 相似文献
7.
The success in complete sequencing of small genomes and development of new technologies that markedly speed up the cloning and sequencing processes open the way to intense development of plant genomics and complete sequencing of DNA of some species. It is assumed that success in plant genomics will result in revolutionary changes in biotechnology and plant breeding. However, the enormous size of genomes (tens of billions of base pairs), their extraordinary abundance of repetitive sequences, and allopolyploidy (the presence in a nucleus of several related but not identical genomes) force us to think that only few basic plant species will undergo complete sequencing, whereas genome investigations in other species will follow the principles of comparative genomics. By the present time, sequencing of the Arabidopsis genome (125 Mbp) is completed and that of the rice genome (about 430 Mbp) is close to its end. Studying the genomes of other plants, including economically valuable ones, already began on the basis of these works. The peculiarities of plant genomes make extraordinarily important our detailed knowledge on plant chromosomes which, in its turn, calls for expansion of research in this direction and development of new chromosome technologies, including the DNA-sparing methods of high-resolution banding. 相似文献
8.
10.
水稻所在的稻属(Oryza)共有24个左右的物种。由于野生稻含有大量的优良农艺性状基因, 在水稻遗传学研究中日益受到重视。随着国际稻属基因组计划的开展, 越来越多的稻属基因组序列被测定, 稻属成为进行比较、功能和进化基因组学研究的模式系统。近期开展的一系列研究对稻属不同基因组区段以及全基因组序列的比较分析, 揭示了稻属在基因组大小、基因移动、多倍体进化、常染色质到异染色质的转化以及着丝粒区域的进化等方面的分子机制。转座子的活性以及转座子因非均等重组或非法重组而造成的删除, 对稻属基因组的扩增和收缩具有重要作用。DNA双链断裂修复介导的基因移动, 特别是非同源末端连接, 是稻属基因组非共线性基因形成的主要来源。稻属基因组从常染色质到异染色质的转换过程, 伴随着转座子的大量扩增、基因片段的区段性和串联重复以及从基因组其他位置不断捕获异染色质基因。对稻属不同物种间基因拷贝数、特异基因和重要农艺性状基因的进化等研究, 可揭示稻属不同物种间表型和适应性差异的分子基础, 将加速水稻的育种和改良。 相似文献
11.
昆虫种类繁多,它与生态系统中的生物多样性,以及人类的日常生活和生产密切相关。自2000年黑腹果蝇Drosophila melanogaster全基因组测序完成以来,至今已先后开展了88种昆虫全基因组测序工作,这标志着昆虫学研究进入了基因组时代。本文综述了近年来昆虫基因组测序进展,以及基于基因组的昆虫学研究方法及应用等两方面的研究成果。同时,着重介绍了昆虫全基因组测序进程,昆虫基因组在个体生物学、多物种间及种群,及系统生物学研究中的应用等方面的内容。最后,还探讨了基因组时代昆虫学研究所面临的挑战。 相似文献
12.
马基因组研究进展 总被引：3，自引：0，他引：3
各种生物都具有其独特的遗传信息, 深入了解生物体的形成过程以及各种生命活动都离不开基因组的研究成果。由于在世界范围内马具有良好的健康情况记录和详细的系谱记录, 使得马成为生命科学研究中极具价值的模式动物。尽管起步较晚, 但在过去的几年中, 马基因组图谱经历了前所未有的发展。文章主要对近年来马基因组遗传图谱、物理图谱、基因组比较作图以及功能基因组学等研究进展进行了综述, 这些图谱也正是世界各地研究人员用以探寻与马的各种性状(包括全部的健康状况、抗病性能、生殖生育能力、运动性能以及诸如毛色这样的表型特征等)相关基因的重要工具。相信这些研究成果将为马匹疾病预防、诊断和治疗提供新的思路与方法, 并将为马遗传育种提供更好的选配依据。 相似文献
13.
Jasper R. L. Depotter Xiaoqian Shi‐Kunne Hlne Missonnier Tingli Liu Luigi Faino Grardy C. M. van den Berg Thomas A. Wood Baolong Zhang Alban Jacques Michael F. Seidl Bart P. H. J. Thomma 《Molecular ecology》2019,28(15):3482-3495
Plant pathogens continuously evolve to evade host immune responses. During host colonization, many fungal pathogens secrete effectors to perturb such responses, but these in turn may become recognized by host immune receptors. To facilitate the evolution of effector repertoires, such as the elimination of recognized effectors, effector genes often reside in genomic regions that display increased plasticity, a phenomenon that is captured in the two‐speed genome hypothesis. The genome of the vascular wilt fungus Verticillium dahliae displays regions with extensive presence/absence polymorphisms, so‐called lineage‐specific regions, that are enriched in in planta‐induced putative effector genes. As expected, comparative genomics reveals differential degrees of sequence divergence between lineage‐specific regions and the core genome. Unanticipated, lineage‐specific regions display markedly higher sequence conservation in coding as well as noncoding regions than the core genome. We provide evidence that disqualifies horizontal transfer to explain the observed sequence conservation and conclude that sequence divergence occurs at a slower pace in lineage‐specific regions of the V. dahliae genome. We hypothesize that differences in chromatin organisation may explain lower nucleotide substitution rates in the plastic, lineage‐specific regions of V. dahliae. 相似文献
14.
David W Burt 《Briefings in Functional Genomics and Prot》2004,3(1):60-67
In this paper, the current status of chicken genomics is reviewed. This is timely given the current intense activity centred on sequencing the complete genome of this model species. The genome project is based on a decade of map building by genetic linkage and cytogenetic methods, which are now being replaced by high-resolution radiation hybrid and bacterial artificial chromosome (BAC) contig maps. Markers for map building have generally depended on labour-intensive screening procedures, but in recent years this has changed with the availability of almost 500,000 chicken expressed sequence tags (ESTs). These resources and tools will be critical in the coming months when the chicken genome sequence is being assembled (eg cross-checked with other maps) and annotated (eg gene structures based on ESTs). The future for chicken genome and biological research is an exciting one, through the integration of these resources. For example, through the proposed chicken Ensembl database, it will be possible to solve challenging scientific questions by exploiting the power of a chicken model. One area of interest is the study of developmental mechanisms and the discovery of regulatory networks throughout the genome. Another is the study of the molecular nature of quantitative genetic variation. No other animal species have been phenotyped and selected so intensively as agricultural animals and thus there is much to be learned in basic and medical biology from this research. 相似文献
15.
Marcelo Dimase Sebe Brown Graham P. Head Paula A. Price Wade Walker Wenbo Yu Fangneng Huang 《Insect Science》2021,28(4):1147-1158
A seed blend refuge has been implemented in the U.S. Corn Belt for Bt maize resistance management. The fall armyworm, Spodoptera frugiperda (J.E. Smith), is a target pest of Bt maize in the Americas. The larvae of this pest are mobile, which may affect the efficacy of seed blend refuges. In this study, field and greenhouse trials were conducted to determine the performance of Bt-susceptible (aabb) and -heterozygous dual-gene-resistant (AaBb) genotypes of S. frugiperda in seed blends of non-Bt and pyramided Bt maize. Three field trials evaluated larval survival, larval growth, and plant injury with aabb in seed blends of Bt maize expressing Cry1A.105/Cry2Ab2/Vip3A with 0–30% non-Bt seeds. Greenhouse tests investigated the performance of aabb and AaBb in seed blends of Cry1A.105/Cry2Ab2 with 0–30% non-Bt seeds. In pure non-Bt maize plots, after 9–13 d of neonates being released on the plants, 0.39 and 0.65 larvae/plant survived with leaf injury ratings of 4.7 and 5.9 (Davis's 1–9 scale) in the field and greenhouse, respectively. In contrast, live larvae and plant injury were virtually not observed on Bt plants across all planting patterns. Larval occurrence and plant injury by aabb on non-Bt plants were similar between seed blends and pure non-Bt plantings, suggesting that the blended refuges could provide an equivalent susceptible population as structured refuge under the test conditions. In the greenhouse, the two insect genotypes in seed blends performed similarly, indicating that the seed blends did not provide more favorable conditions for AaBb over aabb. The information generated from this study should be useful in managing S. frugiperda and evaluating if send blends could be suitable refuge options for Bt resistance management in the regions where the insect is a primary target pest. 相似文献
16.
17.
Michele Gevinski Otolakoski Bianca Zampieron Bagio Brenda Gallina Viegas Crislaine Sartori Suzana Milan Jaqueline Huzar-Novakowiski 《The Annals of applied biology》2023,183(3):254-261
Silicon can increase the natural defence of plants against stresses including herbivorous insects. Silicon dioxide (SiO2) is one of the forms of silicon, and despite its wide use in the industrial sector, its use in agriculture is still poorly adopted. The aim of this study was to evaluate the effectiveness of foliar application of SiO2 in inducing defence against Spodoptera frugiperda in soybean. The experiments were conducted in a completely randomised design with four treatments (0%, 1%, 2.5%, and 5% of SiO2). The effect on cannibalism, biological parameters (mortality, duration of the larval stage, duration of the pupal stage and pupal weight) and wear on the mandible of S. frugiperda were evaluated. The foliar silicon content was also determined. The supply of SiO2 prolonged the duration of the larval and pupal stages of the S. frugiperda by 0.56 and 0.17 days for each 1% of SiO2 applied, respectively. The use of SiO2 at 5% increased the mortality rate of caterpillars in the larval stage by approximately 25%. There was no effect of SiO2 application on cannibalism and weight of S. frugiperda pupae. There was wear on the caterpillars' jaws in the third and fourth instar at the highest SiO2 concentration. The application of SiO2 promoted greater accumulation of silicon in soybean leaves. It is concluded that the foliar application of SiO2 affects the biological performance of S. frugiperda through the induction of defence in the soybean crop and presents itself as a promising strategy in integrated pest management programmes. 相似文献
18.
19.
20.
Hongran Li Jicheng Wang Yan Peng Chenliang Guo Wanmei Qu Nan Yang Yongzhe Zhu Inhong Jeong Xianchun Li Murad Ghanim Yutao Xiao Youjun Zhang Dong Chu 《Diversity & distributions》2023,29(9):1172-1189