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Zuccolo A Bowers JE Estill JC Xiong Z Luo M Sebastian A Goicoechea JL Collura K Yu Y Jiao Y Duarte J Tang H Ayyampalayam S Rounsley S Kudrna D Paterson AH Pires JC Chanderbali A Soltis DE Chamala S Barbazuk B Soltis PS Albert VA Ma H Mandoli D Banks J Carlson JE Tomkins J dePamphilis CW Wing RA Leebens-Mack J 《Genome biology》2011,12(5):R48-14
Background
Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.Results
Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.Conclusions
When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution. 相似文献3.
正Plants, as primary producers, have been playing an indispensable role in other organisms’ survival and the balance of whole ecosystem on Earth. Especially, they provide the main source of energy, food, and medicine for human beings, some of which are derived from the primary or secondary metabolites 相似文献
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拟南芥转录因子GRAS 家族基因群响应渗透和干旱胁迫的初步探索 总被引:2,自引:0,他引:2
GRAS家族是一类植物特有的转录调控因子, 已有报道表明该家族基因在植物生长发育和光信号转导过程中具有重要作用。目前在拟南芥(Arabidopsis thaliana)基因组中已鉴定了33个GRAS家族基因。利用功能基因组学和生物信息学手段,通过基因芯片数据挖掘和基因功能预测, 对拟南芥GRAS家族基因在渗透和干旱胁迫过程中的应答模式进行了初步探索, 提出了一类响应渗透胁迫和干旱胁迫的拟南芥GRAS家族基因。以SCL13为例, 利用基因芯片相关性和GO分析, 对其在渗透胁迫信号转导过程中可能的调控机制进行了预测和分析。这一研究将为阐明GRAS家族基因参与水分胁迫的分子机制提供新的思路, 同时也为植物抗逆分子育种提供候选基因。 相似文献
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Xiao Jun Liu Bao Yao Yingyin Guo Zifeng Jia Haiyan Kong Lingrang Zhang Aimin Ma Wujun Ni Zhongfu Xu Shengbao Lu Fei Jiao Yuannian Yang Wuyun Lin Xuelei Sun Silong Lu Zefu Gao Lifeng Zhao Guangyao Cao Shuanghe Chen Qian Zhang Kunpu Wang Mengcheng Wang Meng Hu Zhaorong Guo Weilong Li Guoqiang Ma Xin Li Junming Han Fangpu Fu Xiangdong Ma Zhengqiang Wang Daowen Zhang Xueyong Ling Hong-Qing Xia Guangmin Tong Yiping Liu Zhiyong He Zhonghu Jia Jizeng Chong Kang 《中国科学:生命科学英文版》2022,65(9):1718-1775
Science China Life Sciences - Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world’s population. Over the past several decades, advances in genomics have led to... 相似文献
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GRAS家族是一类植物特有的转录调控因子,已有报道表明该家族基因在植物生长发育和光信号转导过程中具有重要作用.目前在拟南芥(Arabidopsis thaliana)基因组中已鉴定了33个GRAS家族基因.利用功能基因组学和生物信息学手段,通过基因芯片数据挖掘和基因功能预测,对拟南芥GRAS家族基因在渗透和干旱胁迫过程中的应答模式进行了初步探索,提出了一类响应渗透胁迫和干旱胁迫的拟南芥GRAS家族基因.以SCL13为例,利用基因芯片相关性和GO分析,对其在渗透胁迫信号转导过程中可能的调控机制进行了预测和分析.这一研究将为阐明GRAS家族基因参与水分胁迫的分子机制提供新的思路,同时也为植物抗逆分子育种提供候选基因. 相似文献
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Yuannian Jiao Andrew H. Paterson 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》2014,369(1648)
The occurrence of polyploidy in land plant evolution has led to an acceleration of genome modifications relative to other crown eukaryotes and is correlated with key innovations in plant evolution. Extensive genome resources provide for relating genomic changes to the origins of novel morphological and physiological features of plants. Ancestral gene contents for key nodes of the plant family tree are inferred. Pervasive polyploidy in angiosperms appears likely to be the major factor generating novel angiosperm genes and expanding some gene families. However, most gene families lose most duplicated copies in a quasi-neutral process, and a few families are actively selected for single-copy status. One of the great challenges of evolutionary genomics is to link genome modifications to speciation, diversification and the morphological and/or physiological innovations that collectively compose biodiversity. Rapid accumulation of genomic data and its ongoing investigation may greatly improve the resolution at which evolutionary approaches can contribute to the identification of specific genes responsible for particular innovations. The resulting, more ‘particulate’ understanding of plant evolution, may elevate to a new level fundamental knowledge of botanical diversity, including economically important traits in the crop plants that sustain humanity. 相似文献
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Haiying Liang Saravanaraj Ayyampalayam Norman Wickett Abdelali Barakat Yi Xu Lena Landherr Paula E. Ralph Yuannian Jiao Tao Xu Scott E. Schlarbaum Hong Ma James H. Leebens-Mack Claude W. dePamphilis 《Tree Genetics & Genomes》2011,7(5):941-954
Liriodendron tulipifera L., a member of Magnoliaceae in the order Magnoliales, has been used extensively as a reference species in studies on plant evolution. However, genomic resources for this tree species are limited. We constructed cDNA libraries from ten different types of tissues: premeiotic flower buds, postmeiotic flower buds, open flowers, developing fruit, terminal buds, leaves, cambium, xylem, roots, and seedlings. EST sequences were generated either by 454 GS FLX or Sanger methods. Assembly of almost 2.4 million sequencing reads from all libraries resulted in 137,923 unigenes (132,905 contigs and 4,599 singletons). About 50% of the unigenes had significant matches to publically available plant protein sequences, representing a wide variety of putative functions. Approximately 30,000 simple sequence repeats were identified. More than 97% of the cell wall formation genes in the Cell Wall Navigator and the MAIZEWALL databases are represented. The cinnamyl alcohol dehydrogenase (CAD) homologs identified in the L. tulipifera EST dataset showed different expression levels in the ten tissue types included in this study. In particular, the LtuCAD1 was found to partially recover the stiffness of the floral stems in the Arabidopsis thaliana CAD4 and CAD5 double mutant plants, of the LtuCAD1 in lignin biosynthesis. L. tulipifera genes have greater sequence similarity to homologs from other woody angiosperm species than to non-woody model plants. This large-scale genomic resour"HistryDatesce will be instrumental for gene discovery, cDNA microarray production, and marker-assisted breeding in L. tulipifera, and strengthen this species' role in comparative studies. 相似文献
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Satoko Yoshida Seungill Kim Eric K. Wafula Jaakko Tanskanen Yong-Min Kim Loren Honaas Zhenzhen Yang Thomas Spallek Caitlin E. Conn Yasunori Ichihashi Kyeongchae Cheong Songkui Cui Joshua P. Der Heidrun Gundlach Yuannian Jiao Chiaki Hori Juliane K. Ishida Hiroyuki Kasahara Ken Shirasu 《Current biology : CB》2019,29(18):3041-3052.e4