Testing ultra-conserved elements for phylogenetic inference across Bivalvia (Mollusca)

Bivalves are among the Mollusca groups that have rapidly joined the phylogenomic movement. While transcriptomes provide dense gene coverage, recent advances in ultraconserved elements (UCEs) have expanded the scope of genomic research. This paper presents the development and validation of a UCE probe set for Bivalvia, consisting of 19,588 baits, and capturing a total of 1,513 UCE loci. In the in vitro validation, the UCEs were extracted from 94 samples including species collected in the last 25 years, DNA already extracted in 2008, and museum species up to 1872. Phylogenetic analyses of both all bivalves and specifically the family Donacidae show the usefulness of this UCE probe set in resolving relationships between species and genera within a bivalve family, and how it allowed the inclusion of old museum samples that were not amplified in the previous Sanger-based study.

双壳类（Bivalvia）是软体动物门（Mollusca）中快速加入系统基因组学研究浪潮的类群之一。转录组虽可提供高密度的基因覆盖，但近年来超保守元件（ultraconserved elements, UCEs）的技术进展拓展了基因组研究的范畴。本文报道了一套针对双壳纲的UCE探针组的开发与验证工作：该探针组包含19588个捕获探针，可靶向捕获共计1513个UCE位点。在体外验证实验中，研究人员从94份样本中提取了UCEs，这些样本涵盖近25年采集的物种、2008年已完成提取的DNA样本，以及可追溯至1872年的馆藏标本。针对全体双壳类以及斧蛤科（Donacidae）的系统发育分析结果显示，这套UCE探针组能够有效解析双壳纲内物种与属间的演化关系，同时可实现此前基于Sanger测序的研究中未能成功扩增的老旧馆藏样本的测序分析。