Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: analysis of chromosome 2.
Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: analysis of chromosome 2.
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DOI：
10.1186/s12863-014-0152-1
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发表时间：
2014-12-29
期刊：
影响因子：
2.9
通讯作者：
Ollitrault P
中科院分区：
文献类型：
--
作者：
Curk F;Ancillo G;Garcia-Lor A;Luro F;Perrier X;Jacquemoud-Collet JP;Navarro L;Ollitrault P
最重要的经济柑橘物种起源于自然种间杂交的四个祖先类群（柑橘reticulata，柑橘maxima，柑橘medica，和柑橘micrantha）和有限的随后的种间重组作为无融合生殖和营养繁殖的结果。这种网状进化加上营养繁殖的结果在镶嵌基因组与大染色体片段的基本类群在频繁的种间杂合性。这些物种的现代育种受到其复杂的杂合基因组结构的阻碍，这些结构决定了物种表型，并被有性杂交打破。然而，大量的多样性存在于柑橘基因库中，并且育种以允许包括期望的性状是至关重要的。然而，有效地调动柑橘生物多样性的创新育种计划需要以前的理解柑橘的起源和基因组结构。沿着整个基因组的多个基因片段的单倍型分析是揭示当前物种的混合基因组结构和解析基因库的进化历史的有力手段。在这项研究中，平行测序与454方法破译现代柑橘物种的杂交结构的效率进行了评估，通过分析染色体2上的16个基因片段。使用Fluidigm阵列系统建立了454个扩增子文库，用于48个基因型和来自2号染色体的16个基因片段。从每个登录的读段建立单倍型，并使用每个基因片段的单倍型数据进行系统发育分析。454读段的长度和现代柑橘的祖先类群之间的分化水平允许16个基因片段中的12个有效的单倍型系统发育分配。现代种和栽培种的混合基因组结构分析表明：（i）C.最大的渐渗在现代tenoins，（ii）与以前的假设相一致，关于次要物种的起源，和（iii）提供了一个新的图片2号染色体的进化。454测序是一个有效的策略，建立单倍型与显着的系统发育分配在柑橘，提供了一个新的图片的混合结构的第2染色体上的48个柑橘基因型。本文的在线版本（doi：10.1186/s12863-014-0152-1）包含补充材料，可供授权用户使用。
The most economically important Citrus species originated by natural interspecific hybridization between four ancestral taxa (Citrus reticulata, Citrus maxima, Citrus medica, and Citrus micrantha) and from limited subsequent interspecific recombination as a result of apomixis and vegetative propagation. Such reticulate evolution coupled with vegetative propagation results in mosaic genomes with large chromosome fragments from the basic taxa in frequent interspecific heterozygosity. Modern breeding of these species is hampered by their complex heterozygous genomic structures that determine species phenotype and are broken by sexual hybridisation. Nevertheless, a large amount of diversity is present in the citrus gene pool, and breeding to allow inclusion of desirable traits is of paramount importance. However, the efficient mobilization of citrus biodiversity in innovative breeding schemes requires previous understanding of Citrus origins and genomic structures. Haplotyping of multiple gene fragments along the whole genome is a powerful approach to reveal the admixture genomic structure of current species and to resolve the evolutionary history of the gene pools. In this study, the efficiency of parallel sequencing with 454 methodology to decipher the hybrid structure of modern citrus species was assessed by analysis of 16 gene fragments on chromosome 2. 454 amplicon libraries were established using the Fluidigm array system for 48 genotypes and 16 gene fragments from chromosome 2. Haplotypes were established from the reads of each accession and phylogenetic analyses were performed using the haplotypic data for each gene fragment. The length of 454 reads and the level of differentiation between the ancestral taxa of modern citrus allowed efficient haplotype phylogenetic assignations for 12 of the 16 gene fragments. The analysis of the mixed genomic structure of modern species and cultivars (i) revealed C. maxima introgressions in modern mandarins, (ii) was consistent with previous hypotheses regarding the origin of secondary species, and (iii) provided a new picture of the evolution of chromosome 2. 454 sequencing was an efficient strategy to establish haplotypes with significant phylogenetic assignations in Citrus, providing a new picture of the mixed structure on chromosome 2 in 48 citrus genotypes. The online version of this article (doi:10.1186/s12863-014-0152-1) contains supplementary material, which is available to authorized users.
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