An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)
An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)
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DOI：
10.1534/g3.118.200840
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发表时间：
2019-05-01
影响因子：
2.6
通讯作者：
Ingvarsson, Par K.
中科院分区：
文献类型：
--
作者：
Bernhardsson, Carolina;Vidalis, Amaryllis;Ingvarsson, Par K.
挪威云杉(Picea abies(L.)喀斯特。)是一种具有重要经济价值和生态价值的针叶树种。与大多数针叶树一样，冷杉的基因组非常大(类似于20GBP)，并包含高比例的重复DNA。目前的冷杉基因组组装(v1.0)覆盖了大约60%的基因组总大小，但高度碎片化，由1000万个支架组成。基因组注释包含66,632个至少部分有效的基因模型()，然而，组装的碎片化性质意味着目前几乎没有关于这些基因如何在12条染色体上物理分布的信息。通过创建超高密度的遗传连锁图谱，我们将支架锚定并排序成连锁群，这补充了组装重叠群中可用的精细信息。我们的超高密度单倍体共识遗传图谱由来自14,336个支架的21,056个标记组成，这些支架包含17,079个基因模型(占验证基因模型的25.6%)，我们已经锚定到12个连锁群。我们利用来自三个独立成分图谱的数据，以及与之前发表的云杉图谱的比较，来评估连锁群的准确性和标记排序。我们证明，共识图谱覆盖的大约3.8%的锚定支架和1.6%的基因模型可能存在组装错误，因为它们包含的遗传标记映射到连锁组内或连锁组之间的不同区域。我们通过使用无关个体的独立数据集来评估基因组范围内遗传多样性的变异，使用锚定于连锁群的基因组区域，进一步评估了遗传图谱对于针叶树研究社区的实用性。结果表明，我们的图谱足够密集，可以对冷杉基因组进行详细的进化分析。
Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (similar to 20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.