Evidence from Phylogenomics and Morphology Provide Insights into the Phylogeny, Plastome Evolution, and Taxonomy of Kitagawia

Abstract

Kitagawia Pimenov is one of the segregate genera of Peucedanum sensu lato within the Apiaceae. The phylogenetic position and morphological delimitation of Kitagawia have been controversial. In this study, we used plastid genome (plastome) and nuclear ribosomal DNA (nrDNA) sequences to reconstruct the phylogeny of Kitagawia, along with comparative plastome and morphological analyses between Kitagawia and related taxa. The phylogenetic results identified that all examined Kitagawia species were divided into Subclade I and Subclade II within the tribe Selineae, and they were all distant from the representative members of Peucedanum sensu stricto. The plastomes of Kitagawia and related taxa showed visible differences in the LSC/IRa junction (JLA) and several hypervariable regions, which separated Subclade I and Subclade II from other taxa. Fruit anatomical and micromorphological characteristics, as well as general morphological characteristics, distinguished the four Kitagawia species within Subclade I from Subclade II and other related genera. This study supported the separation of Kitagawia from Peucedanum sensu lato, confirmed that Kitagawia belongs to Selineae, and two species (K. praeruptora and K. formosana) within Subclade II should be placed in a new genus. We believe that the “core” Kitagawia should be limited to Subclade I, and this genus can be distinguished by the association of a series of morphological characteristics. Overall, our study provides new insights into the phylogeny, plastome evolution, and taxonomy of Kitagawia.

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

“…It exists in all species’s genomes and is influenced by many factors, such as mutation pressure, natural selection, gene composition and gene length [ 55 ]. In the present study, all codons with RSCU > 1.00 were strongly biased towards A/U at the third codon position in seventeen Sanicula plastomes, which was consistent with the observation in most angiosperms [ 56 ], as well as in Apiaceae [ 30 – 32 , 35 – 39 ]. Perhaps the high AT content in plastome is the major reason for the bias towards A/U for codons ending in A/U [ 39 ].…”

“…Similarly, this structure was also detected in other plastomes of angiosperm plants [ 46 – 48 ]. Although gene loss is a common evolutionary event that frequently occurs in other genera of Apiaceae, such as the ycf 15 gene was lost in genus Peucedanum [ 31 ] and the trn T-GGU gene was lost in genus Peucedanum and Kitagawia [ 31 , 35 ], it was not discovered in genus Sanicula . In addition, the gene arrangement and GC content of the seventeen plastomes displayed high similarity.…”

“…IR contraction and expansion is a common phenomenon in the Apiaceae plastomes [ 20 , 30 – 32 , 35 – 40 ]. This phenomenon was also observed in Sanicula plastomes.…”

“…Therefore, we supported the hypothesis that the genome size variation was caused by IR contraction and expansion. Furthermore, we also examined the inverted repeats types described in the Apiaceae [ 20 , 30 – 32 , 35 – 40 ] and found that the situation observed in the genus Sanicula was also detected in the other genera of Apiaceae, such as in Hansenia Turcz., Haplosphaera Hand.-Mazz., Sinodielsia H. Wolff [ 37 ].…”

“…For these obvious advantages, the plastome has become a powerful tool to generate highly supported and resolved phylogenies and to explore more efficient specific DNA barcodes [ 25 , 27 , 28 , 31 – 33 ]. In recent years, with the rapid development of next-generation sequencing technology and bioinformatics technology, a large number of sequence data of plastomes has become more accessible at a much lower cost [ 34 ], and it has been extensively and successfully applied to solve the plants phylogenies, especially for those taxonomically difficult taxa within the family Apiaceae [ 30 – 32 , 35 – 40 ].…”