Development of a Target Enrichment Probe Set for Conifer (REMcon)

doi:10.3390/biology13060361

KIB OpenIR

	Development of a Target Enrichment Probe Set for Conifer (REMcon)
	Khan, Raees; Biffin, Ed; van Dijk, Kor-jent; Hill, Robert S.; Liu, Jie; Waycott, Michelle
	2024
发表期刊	BIOLOGY-BASEL
卷号	13 期号:6 页码:361
摘要	Simple Summary Conifers are vital for both ecological and economic reasons, offering valuable insights into land plant evolution. Molecular phylogenetics plays a significant role in studying evolution, but research on conifers using large-scale data from multiple nuclear genes has been limited. Target enrichment sequencing has emerged as a crucial method in phylogenomic studies. However, a specific bait set for conifers is missing. The REMcon probe set targets around 100 single-copy nuclear loci for family- and species-level phylogenetic studies of conifers. High target recovery and read coverage were observed for the REMcon when tested on 69 species, including conifers and other gymnosperm taxa. Phylogenetic analysis based on the DNA sequences generated from REMcon recovered the existing understanding of conifer relationships. The REMcon bait set will be beneficial in generating large-scale nuclear data consistently for any conifer lineage.Abstract Conifers are an ecologically and economically important seed plant group that can provide significant insights into the evolution of land plants. Molecular phylogenetics has developed as an important approach in evolutionary studies, although there have been relatively few studies of conifers that employ large-scale data sourced from multiple nuclear genes. Target enrichment sequencing (target capture, exon capture, or Hyb-Seq) has developed as a key approach in modern phylogenomic studies. However, until now, there has been no bait set that specifically targets the entire conifer clade. REMcon is a target sequence capture probe set intended for family- and species-level phylogenetic studies of conifers that target c. 100 single-copy nuclear loci. We tested the REMcon probe set using 69 species, including 44 conifer genera across six families and four other gymnosperm taxa, to evaluate the efficiency of target capture to efficiently generate comparable DNA sequence data across conifers. The recovery of target loci was high, with, on average, 94% of the targeted regions recovered across samples with high read coverage. A phylogenetic analysis of these data produced a well-supported topology that is consistent with the current understanding of relationships among conifers. The REMcon bait set will be useful in generating relatively large-scale nuclear data sets consistently for any conifer lineage.
DOI	10.3390/biology13060361
WOS记录号	WOS:001254539800001
引用统计	被引频次：3[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75816
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Khan, Raees,Biffin, Ed,van Dijk, Kor-jent,et al. Development of a Target Enrichment Probe Set for Conifer (REMcon)[J]. BIOLOGY-BASEL,2024,13(6):361.
APA	Khan, Raees,Biffin, Ed,van Dijk, Kor-jent,Hill, Robert S.,Liu, Jie,&Waycott, Michelle.(2024).Development of a Target Enrichment Probe Set for Conifer (REMcon).BIOLOGY-BASEL,13(6),361.
MLA	Khan, Raees,et al."Development of a Target Enrichment Probe Set for Conifer (REMcon)".BIOLOGY-BASEL 13.6(2024):361.

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