Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research

Abstract

The Angiosperms353 gene set (AGS) consists of a set of 353 universal low-copy nuclear genes that were selected by examining more than 600 angiosperm species. These genes can be used for phylogenetic studies and population genetics at multiple taxonomic scales. However, current pipelines are not able to recover Angiosperms353 genes efficiently and accurately from high-throughput sequences. Here, we developed Easy353, a reference-guided assembly tool to recover the AGS from high-throughput sequencing (HTS) data (including genome skimming, RNA-seq, and target enrichment). Easy353 is an open-source user-friendly assembler for diverse types of high-throughput data. It has a graphical user interface and a command-line interface that is compatible with all widely-used computer systems. Evaluations based on both simulated and empirical data suggest that Easy353 yields low rates of assembly errors.

Plant DNA barcode library for native flowering plants in the arid region of northwestern China

“…Recently, the use of a large number of single−/low‐copy nuclear genes to reconstruct phylogenetic relationships and clarify complex relationships that have been unresolved using several plastid fragments, ITS and plastome approaches has been increasingly recommended (Liu et al, 2022; Ren et al, 2021; Zhang, Zeng, et al, 2012; Zhao et al, 2021). With the reduction of sequencing costs and the availability of many newly developed bioinformatics pipelines (e.g., Easy353: Zhang et al, 2022; HybPiper: Johnson et al, 2016), obtaining a large number of single‐copy nuclear genes has become more feasible, as demonstrated by deep genome skimming data for Vitaceae (Liu, Ma, et al, 2021 ) and Malus s.l . (Liu et al, 2022).…”

Oreocharis oriolus, a new species of Gesneriaceae in a sclerophyllous oak community from Yunnan, Southwest China

“…A total of 62 species of Oreocharis was used as ingroup and five species from two genera (four specie of Agalmyla Blume (1826: 766) and one species of Metapetrocosmea Wang (1981: 38)) as outgroup ( Lv et al, 2022). The nr ITS and trnL‐F sequences of Oreocharis forrestii (a morphologically closely related species of O. oriolus ) were extracted from the transcriptome (GenBank accession: SRR12339718) of this species published by Kong et al (2022) using Easy353 v1.5.0 (Zhang et al, 2022) with default parameters, owing to its unavailability of leaf materials. The sequences of O. oriolus were newly generated as follows.…”

Single-Copy Orthologs (SCOs) improve species discrimination: A case study in subgusJensoa(Cymbidium)

“…However, HybPiper v2 released recently, its performance needs to reevaluate. Another similar software, Easy353 (Zhang et al, 2022), is also worth investigating. At the step of alignment refining, Spruceup outperforms other popular software, like Gblocks (Castresana, 2000), trimAl (Capella-Gutiérrez et al, 2009), MACSE (Ranwez et al, 2018).…”