Low coverage genome sequencing is rapid and cost-effective for recovering complete mitochondrial genomes for crustacean phylogenomics. The recovery of high-copy-number nuclear genes, including histone H3, 18S and 28S ribosomal RNAs, is also possible using this approach based on our research with freshwater crayfishes (Astacidea). We explored the potential of genome skimming (GS) to recover additional nuclear genes from shallow sequencing projects using decapod crustaceans. Using an in silico-baited approach, we recovered three additional core histone genes (H2A, H2B, and H4) from our low-coverage decapod dataset (99 species, 69 genera, 38 families, 10 infraorders). Phylogenetic analyses using various combinations of mitochondrial and nuclear genes for the entire decapod dataset and a subset of 40 species of crayfishes showed that the evolutionary rates for different classes of genes varied widely. A very high level of congruence was nevertheless found between trees from the six nuclear genes and those derived from the mitogenome sequences for freshwater crayfish. These findings indicate that nuclear genes recovered from the same genome skimming datasets designed to obtain mitogenomes can be used to support more robust and comprehensive phylogenetic analyses. Further, a search for additional intron-less nuclear genes identified several high-copy-number genes across the decapod dataset, and recovery of NaK, PEPCK, and GAPDH gene fragments is possible at slightly elevated coverage, suggesting the potential and utility of GS in recovering even more nuclear genetic information for phylogenetic studies from these inexpensive and increasingly abundant datasets.

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更多来自更少：基因组略读动物系统基因组学的核标记，使用十足目甲壳类动物的案例研究

低覆盖基因组测序对于为甲壳类动物系统基因组学恢复完整的线粒体基因组而言是快速且具有成本效益的。基于我们对淡水小龙虾 (Astacidea) 的研究，使用这种方法也可以恢复高拷贝数核基因，包括组蛋白 H3、18S 和 28S 核糖体 RNA。我们探索了基因组略读 (GS) 从使用十足目甲壳类动物的浅层测序项目中恢复额外核基因的潜力。使用计算机诱饵方法，我们从我们的低覆盖率十足目动物数据集（99 个物种、69 个属、38 个科、10 个下目）中恢复了三个额外的核心组蛋白基因（H2A、H2B 和 H4）。使用线粒体和核基因的各种组合对整个十足类数据集和 40 种小龙虾的子集进行系统发育分析表明，不同类别基因的进化速率差异很大。然而，在来自六个核基因的树与来自淡水小龙虾有丝分裂基因组序列的树之间发现了非常高水平的一致性。这些发现表明，从旨在获得有丝分裂基因组的相同基因组略读数据集中恢复的核基因可用于支持更稳健和全面的系统发育分析。此外，对其他无内含子核基因的搜索在十足类动物数据集中发现了几个高拷贝数基因，并且在稍微提高覆盖率的情况下恢复 NaK、PEPCK 和 GAPDH 基因片段是可能的，