生物谷报道:主要用来酿酒的葡萄是一种古老的农作物,有证据显示它在新石器时代和铜器时代早期就存在了。虽然人们对种植培养过程如何影响收获的葡萄的治疗已经有了较多的了解,但是对葡萄本身的了解却并不算充分。发表在本周PLoS ONE杂志上的一篇文章公布了高质量的葡萄(Pinot Noir grape)的基因组序列草图。
这种葡萄的基因组分散在19队染色体中,并且其长度大约有5.046亿个碱基对。由意大利科学家进行的这项研究使用一种鸟枪测序方法对葡萄基因组进行了测序。与此同时,葡萄叶绿体基因在也完成了测序。
葡萄是基因在相对较小的一种农作物,其大小与水稻和杨树相似,比小麦和玉米则要小的多。然而,测序这个基因组则因为染色体对之间的杂合性程度高而变得很复杂。事实上,与之前公布的两个基因在存在很大的变异性。
而且,研究组在确定出的29585个基因中的87%的基因中发现了超过两百万个单核苷酸多肽性(SNP)——这使得测序过程变得非常困难。
这个研究组还能提供有关葡萄进化的重要线索。许多植物基因组都是由较小的祖先基因组经过至少一次复制得来的。葡萄是否也是这种情况还存在争议,但是这项新研究则清楚地证实19个染色体中的10个是由复制得来。
研究人员称,Pinot Noir基因组降能够未培育能抗病且不会影响红酒质量的葡萄新品种提供了一个无价的工具。
此前,两项公布在《BMC 基因组学》杂志上的两篇新研究论文提供了一系列有关果实成熟的新遗传信息,而果实的成熟对商业价值非常重要。葡萄的基因表达分析揭示出两个与葡萄的绿色阶段和变红阶段相对应的不同的分子和功能阶段。研究人员公布了首个生物化学证据证实,在颜色过渡期发生着活性氧的累积。
意大利IASMA研究中心的Stefania Pilati和同事分析了正在成熟的加州红葡萄,以确定出果实成熟基因并研究季节对该过程的影响。他们发现,超过1400个成熟特异性基因的表达在三个不同的生长季节中发生相似的波动,其中一小类基因则受到气候条件的强烈影响。
在绿果阶段,大量的与激素信号和转录调节有关的基因被调节——这意味着大规模的细胞代谢过程被重排。生长素、乙烯和光起到关键作用。在之后的成熟期,细胞壁组织和生物发生、糖类和次级代谢和压力应答相关基因则开始起作用。此时,光合作用受到强烈抑制。这些转录事件与果实软化和糖、颜色和香味化合物的积累过程相一致,而这些都决定着最终葡萄的品质。在两个阶段的转折点上,研究人员发现一种与H2O2有关的氧化力和抗氧化酶网络的一种广泛的调整。
与此同时,来自美国内华达州大学和波士顿大学医学院的Laurent G. Deluc和同事对V. vinifera Cavernet Sauvignon进行了进一步的研究,他们分析了葡萄果实发育的7个不同的阶段。该研究组确定出,在一系列相关过程中起关键作用的基因的mRNA在整个发育过程中发生了显著的变化。相关过程包括有机和氨基酸代谢、光合作用、碳循化和抗病性。
原始出处:
PLoS ONE
Received: October 5, 2007; Accepted: November 21, 2007; Published: December 19, 2007
A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety
Riccardo Velasco1*#, Andrey Zharkikh2#, Michela Troggio1#, Dustin A. Cartwright1,2, Alessandro Cestaro1, Dmitry Pruss2, Massimo Pindo1, Lisa M. FitzGerald2, Silvia Vezzulli1, Julia Reid2, Giulia Malacarne1, Diana Iliev2, Giuseppina Coppola1, Bryan Wardell2, Diego Micheletti1, Teresita Macalma2, Marco Facci1, Jeff T. Mitchell2, Michele Perazzolli1, Glenn Eldredge2, Pamela Gatto1, Rozan Oyzerski2, Marco Moretto1, Natalia Gutin2, Marco Stefanini1, Yang Chen2, Cinzia Segala1, Christine Davenport2, Lorenzo Demattè1, Amy Mraz5, Juri Battilana1, Keith Stormo5, Fabrizio Costa1, Quanzhou Tao5, Azeddine Si-Ammour1, Tim Harkins4, Angie Lackey4, Clotilde Perbost3, Bruce Taillon3, Alessandra Stella6, Victor Solovyev9, Jeffrey A. Fawcett7, Lieven Sterck7, Klaas Vandepoele7, Stella M. Grando1, Stefano Toppo8, Claudio Moser1, Jerry Lanchbury2, Robert Bogden5, Mark Skolnick2, Vittorio Sgaramella6, Satish K. Bhatnagar2, Paolo Fontana1, Alexander Gutin2, Yves Van de Peer7, Francesco Salamini6, Roberto Viola1
1 IASMA Research Center, San Michele all'Adige, Trento, Italy, 2 Myriad Genetics Inc, Salt Lake City, Utah, United States of America, 3 454 Life Sciences Corporation, Branford, Connecticut, United States of America, 4 Roche Diagnostics Corporation, Roche Applied Science, Indianapolis, Indiana, United States of America, 5 Amplicon Express Inc., Pullman, Washington, United States of America, 6 Technology Park Lodi, Lodi, Italy, 7 Department of Plant Systems Biology, VIB, Gent University, Gent, Belgium, 8 Department of Biological Chemistry, Padova University, Padova, Italy, 9 Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, United Kingdom
Abstract
Background
Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented.
Principal Findings
We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before).
Conclusions
Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape.
Table 1. Number and sizes of assembled sequences in Mb.