Floral gene resources from basal angiosperms for comparative genomics research.
Floral gene resources from basal angiosperms for comparative genomics research.
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DOI：
10.1186/1471-2229-5-5
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发表时间：
2005-03-30
影响因子：
5.3
通讯作者：
Leebens-Mack JH
中科院分区：
文献类型：
--
作者：
Albert VA;Soltis DE;Carlson JE;Farmerie WG;Wall PK;Ilut DC;Solow TM;Mueller LA;Landherr LL;Hu Y;Buzgo M;Kim S;Yoo MJ;Frohlich MW;Perl-Treves R;Schlarbaum SE;Bliss BJ;Zhang X;Tanksley SD;Oppenheimer DG;Soltis PS;Ma H;DePamphilis CW;Leebens-Mack JH
花卉基因组计划的启动是为了填补研究最为广泛的植物模式系统之间的基因组差距。拟南芥和水稻虽然现在已完全测序，并在进行深入的比较基因组研究，但它们在进化上至少相隔1.25亿年，无法单独提供关于开花植物基因组动态的结构和功能方面的全面视角。在此我们讨论科学界可利用的新的基因组资源，包括一系列系统发育上较为基础的被子植物的cDNA文库和表达序列标签（EST）序列，这些植物是专门挑选出来的，用以填补模式植物之间的进化差距，并为了解最早的开花植物的基因含量和基因组结构提供见解。
到目前为止（截至2004年12月1日），对系统发育上重要的真双子叶植物、非禾本科单子叶植物和裸子植物谱系代表的cDNA进行随机测序，已经产生了70514个EST和48170个组装的单基因。基于拟南芥/水稻全蛋白质组比较，将EST序列有效地分类到假定的基因家族中，这使得能够容易地识别用于完成测序的cDNA克隆。初步来看，（i）已测序的花卉基因中功能类别的比例似乎能代表整个拟南芥转录组，（ii）许多已知的花卉基因同源物已被获取，（iii）EST的系统发育分析为与被子植物起源和多样化相关的基因家族进化过程提供了新的见解。
初步比较说明了EST数据集在发现基本花卉转录组方面的实用性。这些最初的发现也提供了机会来解决一些显著的进化基因组问题，包括被子植物和裸子植物生殖器官转录组的重叠、全基因组复制历史、谱系特异性基因复制和功能分化，以及适应性分子进化的分析。由于花卉转录组中并非所有基因都与开花相关，这些EST资源对于研究其他功能（如光合作用、信号转导和代谢途径）的植物科学家也会有吸引力。
The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST) sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants. Random sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04) generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i) proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii) many known floral gene homologues have been captured, and (iii) phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms. Initial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and functional divergence, and analyses of adaptive molecular evolution. Since not all genes in the floral transcriptome will be associated with flowering, these EST resources will also be of interest to plant scientists working on other functions, such as photosynthesis, signal transduction, and metabolic pathways.
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DOI：
10.1111/j.1096-0031.1996.tb00196.x
发表时间：
1994-09-01
期刊：
CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY
影响因子：
--
作者：
FARRIS, JS;KALLERSJO, M;BULT, C
通讯作者：
BULT, C
影响因子：
1.9
作者：
CHASE, MW;SOLTIS, DE;ALBERT, VA
通讯作者：
ALBERT, VA
影响因子：
7
作者：
Castelli, V;Aury, JM;Salanoubat, M
通讯作者：
Salanoubat, M
影响因子：
5.2
作者：
Dhanaraj, AL;Slovin, JP;Rowland, LJ
通讯作者：
Rowland, LJ
影响因子：
4.3
作者：
Ando, S;Sato, Y;Sakai, S
通讯作者：
Sakai, S