Abstract
In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.
Highlights
The family Rutaceae contains flowering plants belonging to the order Sapindales
The objectives of this study were to (1) sequence the two samples of T. asiatica species collected from Kenya, and compare their structural features with T. asiatica from Asia available in the NCBI database, (2) determine the phylogenetic placement of T. asiatica samples from Africa in the phylogenetic tree, (3) determine the origin of the genus Toddalia and its dispersal areas, and (4) determine the impacts of climate change on Toddalia species
In comparing these Toddalia species with the reference genome (T. asiatica) in the NCBI database, they showed similarities in terms of their composition and genomic structure. Both Toddalia species were represented with strongly supported phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analysis
Summary
The family Rutaceae contains flowering plants belonging to the order Sapindales. It comprises about 150–165 genera and approximately 2100 species widely distributed in the tropical and subtropical regions. Zanthoxylum is the second largest genus of Rutaceae, consisting of approximately 225 species, and it has a worldwide distribution [7,8]. Amyridoideae is the largest and diverse subfamily based on the current circumscription [10]. In this subfamily, four genera Phellodendron Rupr., Tetradium Lour., Toddalia Juss., and Zanthoxylum L. were found to produce alkaloids [8,11,12] and the relationship of these chemical constituents has been hypothesized for the past years. Toddalia is a monotypic genus with one species T. asiatica (L.) Lam., widely distributed in Africa and Asia
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