New insights into the plastome evolution of Lauraceae using herbariomics

Abstract

Background The family Lauraceae possesses ca. 50 genera and 2,500–3,000 species that are distributed in the pantropics. Only half of the genera of the family were represented in previously published plastome phylogenies because of the difficulty of obtaining research materials. Plastomes of Hypodaphnideae and the Mezilaurus group, two lineages with unusual phylogenetic positions, have not been previously reported and thus limit our full understanding on the plastome evolution of the family. Herbariomics, promoted by next generation sequencing technology, can make full use of herbarium specimens, and provides opportunities to fill the sampling gap. Results In this study, we sequenced five new plastomes (including four genera which are reported for the first time, viz. Chlorocardium, Hypodaphnis, Licaria and Sextonia) from herbarium specimens using genome skimming to conduct a comprehensive analysis of plastome evolution of Lauraceae as a means of sampling representatives of all major clades of the family. We identified and recognized six types of plastomes and revealed that at least two independent loss events at the IR-LSC boundary and an independent expansion of SSC occurred in the plastome evolution of the family. Hypodaphnis possesses the ancestral type of Lauraceae with trnI-CAU, rpl23 and rpl2 duplicated in the IR regions (Type-I). The Mezilaurus group shares the same plastome structure with the core Lauraceae group in the loss of trnI-CAU, rpl23 and rpl2 in the IRa region (Type-III). Two new types were identified in the Ocotea group: (1) the insertion of trnI-CAU between trnL-UAG and ccsA in the SSC region of Licaria capitata and Ocotea bracteosa (Type-IV), and (2) trnI-CAU and pseudogenizated rpl23 inserted in the same region of Nectandra angustifolia (Type-V). Our phylogeny suggests that Lauraceae are divided into nine major clades largely in accordance with the plastome types. The Hypodaphnideae are the earliest diverged lineage supported by both robust phylogeny and the ancestral plastome type. The monophyletic Mezilaurus group is sister to the core Lauraceae. Conclusions By using herbariomics, we built a more complete picture of plastome evolution and phylogeny of the family, thus providing a convincing case for further use of herbariomics in phylogenetic studies of the Lauraceae.

The Complete Plastid Genome Sequences of the Belian (Eusideroxylon zwageri): Comparative Analysis and Phylogenetic Relationships with Other Magnoliids

“…In this study, the phylogenetic relationships among 2 Belian plastomes and 42 plastomes from 10 families of Magnoliids were reconstructed based on the chloroplast genomes. The topology of Lauraceae clades is similar to that of previous studies, especially the location of Belian, which is located at the base of Lauraceae [2,18,21,23]. Therefore, there is morphological and molecular evidence that the sequence (GenBank accession No.…”

“…Liu et al (2021) constructed the largest plastid genome dataset of Lauraceae, combining Belian and 190 plastome genomes from 131 species of 25 genera, and generated a phylogenetic tree using ML and NJ methods [22]. Similarly, Yang et al (2023) constructed two phylogenetic trees using the complete chloroplast sequence of Belian, along with other Lauraceae species by ML and BI methods [23]. In both studies, Belian was consistently placed within the Cryptocaryeae tribe, which comprises species from the genera Beilschmiedia, Cryptocarya, Endiandra, Eusideroxylon, Potameia, Sinopora, and Syndiclis.…”

Complete mitochondrial genome of Angelica dahurica and its implications on evolutionary analysis of complex mitochondrial genome architecture in Apiaceae

“…Moreover, a comprehensive comparative genomic analysis contrasts A. dahurica with its closely related species, particularly S. divaricata (NC058846.1). Phylogenetic analysis of a genus is an important means of homology analysis, such as plastid, mitochondrial and geographical distribution analysis of the entire genus Lauraceae ( Liu et al., 2022 ; Tan et al., 2023 ; Yang et al., 2023a ; Yang et al., 2023b ). In this comparison, we discovered ten fragments exceeding 5000 bp in length, indicative of long segments with high homology to S. divaricata , thus reinforcing their close phylogenetic relationship.…”

Phylogeny and Taxonomic Revision of the Genus Melanosciadium (Apiaceae), Based on Plastid Genomes and Morphological Evidence

“…The plastid genome has many features, such as monolepsis, small subfractions, multiple replications, and moderate nucleotide substitution rates [ 37 , 38 , 39 , 40 , 41 ]. Despite the highly variable characteristics of the plastid genome, it has the potential to obtain a robust phylogenetic tree [ 19 , 21 , 42 , 43 , 44 , 45 ]. With the advancement of next-generation sequencing and bioinformatics technologies, obtaining plastid genome data is now more affordable and faster than ever before.…”