Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications

Abstract

Ligusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.

A comparative plastomic analysis ofZiziphus jujubavar.spinosa(Bunge) Hu ex H. F. Chow and implication of the origin of Chinese jujube

“…4 ). Higher divergence in SC and lower divergence in IR regions were revealed, implying general conservatism of IR regions compared to other parts, which was consistent with characteristics of other angiosperm species’ plastomes ( Yuan et al . 2021 ).…”

“…SSRs were identified with thresholds of 10, 6, 5, 5, 5 and 5 repeat units for mono-, di-, tri-, tetra-, penta- and hexa-nucleotides, respectively. Forward, reverse, complement and palindromic repeats were examined via REPuter ( Kurtz and Schleiermacher 1999 ) with parameter settings as follows: hamming distance was 3, minimum and maximum sizes of repeats were 30 and 500 bp, and redundant repeats were manually removed ( Yuan et al . 2021 ).…”

Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution

“…Here, a higher divergence of the SC regions and a lower divergence of the IR were discovered, suggesting that the IR is more conservative than in other regions, with the same characteristics of most angiosperms 62 . This occurrence is caused by copy correction of IRs and the removal of harmful mutations via gene conversion 63 .…”

Plastid Phylogenomic Analysis of Tordylieae Tribe (Apiaceae, Apioideae)

“…In Apiaceae plastomes, gene order and genome structure are significantly conserved [ 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ]. However, while for land plant’s plastomes (from early non-vascular plants to angiosperms), a general trend of IR enlarging can be seen [ 1 , 29 ], in the Apioideae subfamily of Apiaceae, a contrary tendency of IR shrinking is observed [ 26 , 30 ].…”