The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera

Abstract

A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun 2 sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.

Early evolution of Cupedidae revealed by a mid‐Cretaceous reticulated beetle from Myanmar (Coleoptera: Archostemata)

“…However, our Bayesian analysis (using the discrete Marcov k model) of the same dataset strongly supported the monophyly of the two families (C. Cai, unpublished data). The molecular-based phylogenetic studies are promising for elucidating the interrelationships in Archostemata, but published results appear limited by insufficient taxon and gene sampling, and the effects of missing data (Bocak et al, 2014;McKenna et al, 2015;Kusy et al, 2018;Linard et al, 2018). One of the challenges we face is that Crowsoniella relicta Pace (Crowsoniellidae) has not been sequenced because so far only three specimens are known.…”

“…Compared with their extant based on morphological characters and molecular data have yielded inconsistent topologies (e.g. Hörnschemeyer, 2009;Lawrence et al, 2011;McKenna et al, 2015;Linard et al, 2018). It is noteworthy that some authors adopted a broader concept of Cupedidae, regarding the family Ommatidae as a subfamily within Cupedidae sensu lato (e.g.…”

The complete mitochondrial genome sequence and phylogenetic analysis of Lycocerus asperipennis (Coleoptera, Cantharidae)

“…The neighbour-joining tree was constructed by MEGA 7.0 with 1,500 bootstrap replicates, based on Kimure-2 parameter model, using 14 species of Elateroidea (Li et al 2007;Sheffield et al 2009;Jiao et al 2013;Amaral et al 2016;Gerritsen et al 2016;Linard et al 2016Linard et al , 2018; Uribe and Guti errez-Rodr ıguez 2016) and 1 species of Dryopidae and Buprestidae respectively (Hong et al 2009). The phylogenetic inference was done based on 13PCGs.…”

The complete mitogenome of Lycostomus sp. (Elateroidea: Lycidae)

“…CONTACT Hao-Yu Liu liuhy@aliyun.com; Yu-Xia Yang yxyang@hbu.edu.cn The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding 071002, Hebei Province, China 2016), Melanotus villosus (Linard et al 2016), Anostirus castaneus, Adrastus rachifer, and Lampyris noctiluca (Linard et al 2018), Aquatica leii (Jiao et al 2013), Limonius californicus (Gerritsen et al 2016), Cerophtidae sp., Dryops ernesti and Chrysochroa fulgidissima (Hong et al 2009). The aligned data were concatenated with Sequence Matrix v.1.7.8 (Vaidya et al 2011).…”