瘿螨是一类植食性螨类，属世界分布。目前全世界已描述发表的瘿螨高达4400余种，是蜱螨亚纲中最大的类群。与其他螨类相比，瘿螨具有特殊的形态特征和生物学习性，例如，个体微小，平均体长约为200微米；体型为梭型或蠕虫型，仅有两对足，全身刚毛退化严重；对寄主高度专化，约80%的种类被报道仅寄生于一种寄主植物之上。目前，瘿螨总科属于蜱螨亚纲、真螨总目、绒螨目。

关于瘿螨的研究已经持续了一个多世纪。由于瘿螨相较于其他螨类具有较少的形态特征（如刚毛的缺失和后足的退化等），基于形态学特征而构建的瘿螨分类系统缺少足够的系统发育信号，形态祖征和衍征的确立受主观影响太强。因此，瘿螨总科的分类地位经历过多次变动。近年来，随着分子生物学的发展，基于DNA短片段的分子标记技术为瘿螨分类研究提供了新的方向。然而在基于线粒体基因与核基因的研究中，瘿螨总科在蜱螨亚纲中的位置仍不够明晰。本研究利用含有更多遗传信息的系统发育基因组学分析，为澄清瘿螨总科在蜱螨亚纲中的位置提供了新的证据。主要研究结果如下：

（1）获得了32种瘿螨的全基因组。在这32个瘿螨基因组中，有15个基因组的大小在50Mb以下，并未发现contig数量与基因组大小存在联系。在基于节肢动物数据库的BUSCO评估中，几乎所有的基因组具有60%以上的BUSCO评分值，即与节肢动物有较高的同源性。本研究设计了针对瘿螨提取UCE位点的探针集Eri-v2，能够有效地从瘿螨中提取1988个保守位点，同时此探针集也适用于节肢动物中的其他物种。本研究中所获得UCE位点的总长度为1,062,012bp，平均长度为534bp。在碱基构成上，AT含量要比GC含量略高。系统发育信息位点在UCE位点中的占比约为50%，且数量随着位点长度的增加而增加。

（2）对所测定的32个瘿螨全基因组与其他124个所选螯肢动物的基因组或转录组数据进行UCE位点提取与系统发育分析，恢复了拟蝎目、蝎目、剑尾目、盲蛛目、避日蛛目，真螨总目、寄螨总目、瘿螨总科的单系性，并确定了瘿螨总科与真螨总目的姐妹群关系。在基于不同数据量与低LB异质化得分构成的数据集所构建的系统发育树中，瘿螨总科都与真螨总目在具有高支持度的情况下构成姐妹群关系。在基于MPSI得分所构建的不同位点数量的分析中，随着系统发育信息的引入，瘿螨总科与真螨总目的姐妹群关系一直稳定的保持在高支持度水平下。在关于长枝吸引效应的分析结果中，当将部分已知会导致长枝吸引的类群（拟蝎、海鲎、盲蛛、微型鞭尾蝎、泛甲壳动物等）去除后，寄螨总目与真螨总目的姐妹群得到了恢复，同时瘿螨总科也与真螨总目中的绒螨目和疥螨目构成姐妹群关系。

（3）本研究使用从全基因组中提取的UCE位点的核苷酸序列通过MCMCTree对所选类群的分化时间进行了估计。结果表明：蛛形纲的分化年龄为志留纪422Ma；真螨总目中绒螨目与疥螨目的分化时间为石炭纪末期299Ma，寄螨总目中中气门目和蜱目的分化时间为石炭纪330Ma；瘿螨总科在石炭纪中期324Ma左右与真螨总目中的其他类群分化，而在瘿螨总科之中，大部分的类群的分化时间在白垩纪。

本文选取124个螯肢动物中已公开发表的基因组或转录组序列，并对32个瘿螨样本进行了基因组的测序和组装。选取多种数据集通过最大似然法与贝叶斯分析方法对瘿螨在高级阶元中的系统发育关系进行了重新构建，进而系统的阐明了瘿螨总科在蜱螨亚纲中的系统发育地位和各类群的分化时间。本研究首次使用基因组数据对瘿螨进行分析，为之后的瘿螨分类研究提供了一种可行的组学层面的遗传信息获取方法以及一个新方向。

As a diverse and widely distributed plant-eating mite, eriophyoid mites are widely present worldwide. At present, more than 4400 species of eriophyoid mites have been described and published, therefore Eriophyoidea has become the most diverse group in the Acari. Compared with other mites, eriophyoid mites have special morphological characteristics such as the tiny body size, the average body length of about 200μm, the fusiform or vermiform body shape, the two pairs of leg, and the severe degeneration of the setae in the body. Eriophyoid mites are highly host-specialized, 80% of them are reported to parasitize in only one host plant. According to the latest classification system, the superfamily Eriophyoidea belong to subclass Acari, superorder Acariformes, order Trobidiformes.
The research on eriophyoid mites has lasted for more than a century, but the research has mainly focused on the morphology description. Compared with other mites, eriophyoid mites lack many morphological characteristics (such as the loss of setae and the degeneration of rear legs), therefore the classification system based on morphological identification lacks sufficient identification information, and the phylogenetic position of Eriophyoidea has experienced many changes. Recently, with the development of molecular biology, molecular marker technology based on short DNA fragments provides a new direction for the classification of eriophyoid mites. However, the position of eriophyoid mites in Acari has not been determined in the study based on mitochondrial genomes or nuclear genes. In this study, we inferred the HIGHER-LEVEL phylogeny of Acari using phylogenetic genomic analysis and provided new evidence for the phylogenetic position of Eriophyoidea.
(1) A total of 32 eriophyoid mites’ genomes were obtained. Among these genomes, 15 of them are less than 50Mb, and no significant relationship was found between contig number and genome size. Almost all genomes have high BUSCO scores during the BUSCO evaluation using arthropods dataset. We also designed an Eriophyoidea specialized probe set Eri-v2 for extracting UCE locus, and successfully extracted nearly 2,000 UCE loci. Moreover, this probe set is also suitable for other species in arthropods. The total length of UCE loci obtained in this study was 1,062,012bp, and the average length of each locus is 534bp. As for base composition, the content of AT is slightly higher than that of GC. The proportion of phylogenetic information loci in UCE locus is about 50%, and the number increases with the increase of locus length.
(2) Using 32 eriophyoid mites genomes we sequenced and 124 other genome or transcriptome data downloaded from National Center for Biotechnology Information, we applied phylogenetic analysis with maximum likelihood and Bayesian analysis based on UCE loci we extracted, and restored the monophyly of Scorpiones, Pseudoscorpiones, Xiphosura, Opiliones, Solifugae, Acariformes, Parasitiformes, Eriophyoidae, as well as the sister relationship between Eriophyoidae and Acariformes. In the phylogenetic tree reconstructed based on the data sets composed of different matrix completeness and low LB heterogeneity scores, Eriophyoidae is always a sister group to Acariformes with high support. Across MPSI data sets, Eriophyoidea was consistently found within Acariformes. The placement of Eriophyoidea as sister group to Acariformes was robust after the removal of several taxa known to cause long-branch attraction, such as Pseudoscropiones, Xiphosura, and Opiliones, alone with the sister relationship of Acariformes and Parasitiformes.
(3) Divergence times of the Acari were estimated with MCMCTree using UCE loci extracted from genomes as nucleotide sequences in this study. The results show that the differentiation age of Arachnida is 422Ma in Silurian, the differentiation time of Trombidiformes and Sarcoptiformes is 288Ma in late Carboniferous, and Mesostigmata and Ixodida diverged in Carboniferous (330Ma). Eriophyoidae differentiated from other groups in Acariformes at about 324Ma in the middle Carboniferous, and most eriophyoid mites diverged in Cretaceous.
We selected 124 published genome and transcriptome sequences of Chelicerata, and sequenced 32 eriophyoid mite genomes. The phylogenetic relationship of Eriophyoidae in HIGHER-LEVEL was reconstructed using a variety of data sets with maximum likelihood and Bayesian analysis. The phylogenetic relationship of Acari and the differentiation time of various clade were systematically clarified. We inferred the higher-level phylogeny of eriophyoid mites from genomic sequences and propose that Eriophyoidea was a sister group to superorder Acariformes. For the first time, genomic data were used in analyzing phylogenetic relationship of Eriophyoidae. We present a new approach to retain genomic data and shed new light on the classification of eriophyoid mites.