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. 2022 Jan 17;11(2):231.
doi: 10.3390/plants11020231.

Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia

Elizabeth Syowai Mutinda  1   2   3 , Elijah Mbandi Mkala  1   2   3   4 , Xiang Dong  1   2   3 , Jia-Xin Yang  1   2   3 , Emmanuel Nyongesa Waswa  1   2   3 , Consolata Nanjala  1   2   3 , Wyclif Ochieng Odago  1   2   3   4 , Guang-Wan Hu  1   2   3 , Qing-Feng Wang  1   2
Affiliations

Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia

Elizabeth Syowai Mutinda et al. Plants (Basel). .

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.

Keywords: Rutaceae; biogeography; comparative analysis; divergent hotspots; phylogeny.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Distribution map of Toddalia asiatica in Africa and Asia.
Figure 2
Figure 2
Gene map of Toddalia plastomes. Genes in the circle are transcribed clockwise, while the rest are transcribed counterclockwise. Dark gray shading in the inner circle indicates the GC content.
Figure 3
Figure 3
Comparison of the borders of large single copy (LSC), small single copy, (SSC), and inverted repeat (IR) regions among the Toddalia plastomes. Different color boxes indicate specific genes.
Figure 4
Figure 4
Total number of repeats found in Toddalia species.
Figure 5
Figure 5
The total number of simple sequence repeats present in Toddalia species.
Figure 6
Figure 6
Sequence alignment of plastomes of Toddalia species using the LAGAN method. A cut-off of 70% similarity was used for the plot and the y-scale represents the percent similarity ranging from 50–100%.
Figure 7
Figure 7
A sliding window analysis of nucleotide variability (Pi) values of different regions of Toddalia. X-axis: position of the midpoint of a window, Y-axis: nucleotide diversity of each window.
Figure 8
Figure 8
Phylogenetic tree construction of 35 taxa using maximum likelihood (ML) and Bayesian inference (BI) methods using 79 protein-coding genes.
Figure 9
Figure 9
Phylogenetic chronogram showing the evolutionary dating time taxa of the 15 genera in the family Rutaceae and two outgroups. The tree was estimated using Bayesian analysis of 79 protein-coding genes and 35 taxa in the Markov Chain Monte Carlo (MCMC) tree.
Figure 10
Figure 10
Lineage-through-time (LTT) plots and the rate shifts in the 15 genera used in the family Rutaceae. Black lines represent the LTT plots for 1000 trees randomly selected from the BEAST analysis. The red line shows the plot from the maximum clade credibility tree.
Figure 11
Figure 11
Ancestral area reconstructions of Toddalia species and closely related species based on the MBASR using R-software. The four biogeographical areas were defined based on the distribution of extant T. asiatica species. Area abbreviations: A, Asia; B, Africa; C, Madagascar. The base map was downloaded from Worldclim (https://www.worldclim.org, accessed on 26 September 2021).
Figure 12
Figure 12
Maps showing distribution modeling for Toddalia asiatica for the years 2050 and 2070.
See this image and copyright information in PMC

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