Increasing Taxa Sampling Provides New Insights on the Phylogenetic Relationship Between Eriobotrya and Rhaphiolepis

Dong, Zhanghong; Qu, Shaohong; Landrein, Sven; Yu, Wenbin; Jing, Xin; Zhao, Wenzhi; Song, Yu; Tan, Yun‐Hong; Xin, Peiyao

doi:10.3389/fgene.2022.831206

Cited by 8 publications

(5 citation statements)

References 52 publications

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“…Many studies have attempted to resolve the relationships within Araliaceae using molecular markers of ITS or plastid-region data, but the relationship of Araliaceae was still unclear [ 1 – 3 , 5 , 7 – 9 , 11 ]. In addition, studies show that increased sampling of taxa can greatly improve overall phylogenetic accuracy [ 56 – 58 ]. Our study and Valcárcel et al [ 14 ] had found that using the whole plastomes, with an appropriate sampling, can greatly aid the relationship between the deep pedigrees of the Araliaceae.…”

Section: Discussionmentioning

confidence: 99%

The complete plastid genome of the endangered shrub Brassaiopsis angustifolia (Araliaceae): Comparative genetic and phylogenetic analysis

et al. 2022

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Brassaiopsis angustifolia K.M. Feng belongs to the family Araliaceae, and is an endangered shrub species in southwest China. Despite the importance of this species, the plastid genome has not been sequenced and analyzed. In this study, the complete plastid genome of B. angustifolia was sequenced, analyzed, and compared to the eight species in the Araliaceae family. Our study reveals that the complete plastid genome of B. angustifolia is 156,534 bp long, with an overall GC content of 37.9%. The chloroplast genome (cp) encodes 133 genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. All protein-coding genes consisted of 21,582 codons. Among the nine species of Araliaceae, simple sequence repeats (SSRs) and five large repeat sequences were identified with total numbers ranging from 37 to 46 and 66 to 78, respectively. Five highly divergent regions were successfully identified that could be used as potential genetic markers of Brassaiopsis and Asian Palmate group. Phylogenetic analysis of 47 plastomes, representing 19 genera of Araliaceae and two related families, was performed to reconstruct highly supported relationships for the Araliaceae, which highlight four well-supported clades of the Hydrocotyle group, Greater Raukaua group, Aralia-Panax group, and Asian Palmate group. The genus Brassaiopsis can be divided into four groups using internal transcribed spacer (ITS) data. The results indicate that plastome and ITS data can contribute to investigations of the taxonomy, and phylogeny of B. angustifolia. This study provides a theoretical basis for species identification and future biological research on resources of the genus Brassaiopsis.

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Section: Discussionmentioning

confidence: 99%

The complete plastid genome of the endangered shrub Brassaiopsis angustifolia (Araliaceae): Comparative genetic and phylogenetic analysis

et al. 2022

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“…In addition, differences in biparental and maternal inheritance could have caused the divergent results of the ITS and cpDNA evolutionary trees ( Wu, 2018 ). Of course, sampling bias may also lead to phylogenetic errors, and increasing the sampling size can effectively improve the overall phylogenetic accuracy ( Murphy et al., 2001 ; Zwickl and Hillis, 2002 ; Dong et al., 2022a ). Although the results are different, it has been recognized that the cp genome can well analyze the phylogeny of Lauraceae, and the whole cp genome is more effective than the fragment ( Tian et al., 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae)

et al. 2023

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The genus Neocinnamomum is considered to be one of the most enigmatic groups in Lauraceae, mainly distributed in tropical and subtropical regions of Southeast Asia. The genus contains valuable oilseed and medicinal tree species. However, there are few studies on the genus Neocinnamomum at present, and its interspecific relationship is still unclear. In order to explore the genetic structure and evolutionary characteristics of the Neocinnamomum chloroplast genome and to resolve the species relationships within the genus, comparative genomic and phylogenetic analyses were performed on the whole chloroplast genome sequences of 51 samples representing seven Neocinnamomum taxa. The whole Neocinnamomum chloroplast genome size ranged from 150,753-150,956 bp, with a GC content of 38.8%-38.9%. A total of 128 genes were annotated within the Neocinnamomum chloroplast genome, including 84 protein coding genes, 8 rRNA genes, and 36 tRNA genes. Between 71-82 SSRs were detected, among which A/T base repeats were the most common. The chloroplast genome contained a total of 31 preferred codons. Three highly variable regions, trnN-GUU-ndhF, petA-psbJ, and ccsA-ndhD, were identified with Pi values > 0.004. Based on the whole chloroplast genome phylogenetic tree, the phylogenetic relationships among the seven Neocinnamomum taxa were determined. N. delavayi and N. fargesii were the most closely related species, and N. lecomtei was identified as the most basal taxon. In this study, the characteristics and sequence variation of the chloroplast genomes of seven Neocinnamomum taxa were revealed, and the genetic relationship among the species was clarified. The results of this study will provide a reference for subsequent molecular marker development and phylogenetic research of Neocinnamomum.

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“…ined., proposed to conserve the name Eriobotrya against Rhaphiolepis for maintaining nomenclatural stability for this important species. Interestingly, subsequent studies by Dong et al (2022b) supported the monophyly of Eriobotrya and its separation from Rhaphiolepis using nrDNA and ITS data with larger-scale sampling. Apparently, the strongly supported but conflicting relationships were caused by the cytonuclear discordance, and the phylogenetic instability has led to conflicting treatments of Eriobotrya.…”

Section: Infrafamilial or Lower Taxonomic Scale Examplesmentioning

confidence: 96%

Phylogenomics and the flowering plant tree of life

Guo

Luo

Gao

et al. 2022

JIPB

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The advances accelerated by next‐generation sequencing and long‐read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole‐genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole‐genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.

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Increasing Taxa Sampling Provides New Insights on the Phylogenetic Relationship Between Eriobotrya and Rhaphiolepis

Cited by 8 publications

References 52 publications

The complete plastid genome of the endangered shrub Brassaiopsis angustifolia (Araliaceae): Comparative genetic and phylogenetic analysis

The complete plastid genome of the endangered shrub Brassaiopsis angustifolia (Araliaceae): Comparative genetic and phylogenetic analysis

Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae)

Phylogenomics and the flowering plant tree of life

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