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

Comparative genomics and phylogenetic analysis of chloroplast genomes of Asian Caryodaphnopsis taxa (Lauraceae)

The genus Caryodaphnopsis, a member of the Lauraceae family, is characterized by seeds that are rich in oil, as well as highly exploitable fruits and wood. The Asian taxa within this genus exhibit complex morphological variations, posing challenges to their accurate classification and impeding their effective use and development as a resource. In this study, we sequenced the chloroplast genomes of 31 individuals representing nine Asian taxa within the Caryodaphnopsis genus. Our primary objectives were to reveal structural variations in these chloroplast genomes through comparative analyses and to infer the species' phylogenetic relationships. Our findings revealed that all chloroplast genomes had a tetrad structure, ranged in length from 148,828 to 154,946 bp, and harbored 128-131 genes. Notably, contraction of the IR region led to the absence of some genes in eight taxa. A comprehensive analysis identified 1267 long repetitive sequences and 2176 SSRs, 286 SNPs, and 135 indels across the 31 chloroplast genomes. The Ka/Ks ratio analysis indicated potential positive selection on the matK, rpl22, and rpoC2 genes. Furthermore, we identified six variable regions as promising barcode regions. Phylogenetic analysis grouped the nine Asian taxa into six branches, with C. henryi forming the basal group from which three distinct complexes emerged. This study contributes significantly to the current understanding of the evolutionary dynamics and phylogenetic relationships within the genus Caryodaphnopsis. Furthermore, the identified molecular markers hold potential for molecular barcoding applications in population genetics, providing valuable tools for future research and conservation efforts within this diverse genus.

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

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.

Phylogenomics and the flowering plant tree of life

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.

Eriobotryacrassifolia (Rosaceae), a new species from Yunnan Province, China

The new species Eriobotryacrassifolia, collected from Yunnan Province, China, is characterised and illustrated. A phylogeny based on chloroplast genomes supported its closest affinity with E.tengyuehensis, while a phylogeny based on 197 single-copy nuclear genes supported its closest affinity with E.fragrans and E.deflexa. Morphologically, however, it resembles E.angustissima. Nevertheless, it can be easily distinguished from E.angustissima by its abaxially retroflexed and sharply serrate leaf margins, densely rusty tomentose inflorescences, and oblong or elliptic leaves.

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

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.