Target capture and genome skimming for plant diversity studies

• Published in: Applications in plant sciences Vol. 11; no. 4; pp. e11537 - n/a
• Main Authors: Pezzini, Flávia Fonseca, Ferrari, Giada, Forrest, Laura L., Hart, Michelle L., Nishii, Kanae, Kidner, Catherine A.
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.07.2023; John Wiley and Sons Inc; Wiley
• Subjects: barcoding; bioinformatics; Chromosomes; coalescent analysis; Deoxyribonucleic acid; Design; DNA; Evolution; Flowers & plants; genome; Genomes; Genomics; herbaria; Next-generation sequencing; non‐model plants; Nucleotide sequence; Plant mitochondria; Plant sciences; Review; Ribosomal DNA; short‐read sequencing; species diversity; Whole genome sequencing; United States > US; barcoding; short‐read sequencing; herbaria; non‐model plants; coalescent analysis
• ISSN: 2168-0450; 2168-0450
• DOI: 10.1002/aps3.11537

Recent technological advances in long‐read high‐throughput sequencing and assembly methods have facilitated the generation of annotated chromosome‐scale whole‐genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high‐molecular‐weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast‐freeze newly collected living samples to conserve high‐quality DNA can be complicated when plants are only found in remote areas. Therefore, short‐read reduced‐genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non‐model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best‐informed choice regarding reduced genome representation for evolutionary studies of non‐model plants in cases where whole‐genome sequencing remains impractical.