Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

Abstract

Chloroplast genomes are considered to be highly conserved. Nevertheless, differences in their sequences are an important source of phylogenetically informative data. Chloroplast genomes are increasingly applied in evolutionary studies of angiosperms, including Magnoliaceae. Recent studies have focused on resolving the previously debated classification of the family using a phylogenomic approach and chloroplast genome data. However, most Neotropical clades and recently described species have not yet been included in molecular studies. We performed sequencing, assembly, and annotation of 15 chloroplast genomes from Neotropical Magnoliaceae species. We compared the newly assembled chloroplast genomes with 22 chloroplast genomes from across the family, including representatives from each genus and section. Family-wide, the chloroplast genomes presented a length of about 160 kb. The gene content in all species was constant, with 145 genes. The intergenic regions showed a higher level of nucleotide diversity than the coding regions. Differences were higher among genera than within genera. The phylogenetic analysis in Magnolia showed two main clades and corroborated that the current infrageneric classification does not represent natural groups. Although chloroplast genomes are highly conserved in Magnoliaceae, the high level of diversity of the intergenic regions still resulted in an important source of phylogenetically informative data, even for closely related taxa.

Keywords: chloroplast assembly; comparative genomics; complete chloroplast genome; phylogenomics; whole genome sequencing.

Figure A1

Graphical maps of the 15 newly annotated plastomes generated by OGDRAW.

Figure A1

Graphical maps of the 15 newly annotated plastomes generated by OGDRAW.

Figure A1

Graphical maps of the 15 newly annotated plastomes generated by OGDRAW.

Figure A1

Graphical maps of the 15 newly annotated plastomes generated by OGDRAW.

Figure A2

Sequence identity plot produced by Shuffle-LAGAN alignment in mVista comparing 37 Magnolia species; Magnolia coco was used as reference. Grey arrows represent genes with their orientation. Pink areas are conserved non-coding sequences (CNS). Blue areas are exons. The Y-axis represents the percentage of conservation of each species against the reference.

Figure A2

Sequence identity plot produced by Shuffle-LAGAN alignment in mVista comparing 37 Magnolia species; Magnolia coco was used as reference. Grey arrows represent genes with their orientation. Pink areas are conserved non-coding sequences (CNS). Blue areas are exons. The Y-axis represents the percentage of conservation of each species against the reference.

Figure A2

Sequence identity plot produced by Shuffle-LAGAN alignment in mVista comparing 37 Magnolia species; Magnolia coco was used as reference. Grey arrows represent genes with their orientation. Pink areas are conserved non-coding sequences (CNS). Blue areas are exons. The Y-axis represents the percentage of conservation of each species against the reference.

Figure A2

Sequence identity plot produced by Shuffle-LAGAN alignment in mVista comparing 37 Magnolia species; Magnolia coco was used as reference. Grey arrows represent genes with their orientation. Pink areas are conserved non-coding sequences (CNS). Blue areas are exons. The Y-axis represents the percentage of conservation of each species against the reference.

Figure A2

Sequence identity plot produced by Shuffle-LAGAN alignment in mVista comparing 37 Magnolia species; Magnolia coco was used as reference. Grey arrows represent genes with their orientation. Pink areas are conserved non-coding sequences (CNS). Blue areas are exons. The Y-axis represents the percentage of conservation of each species against the reference.

Figure A2

Sequence identity plot produced by Shuffle-LAGAN alignment in mVista comparing 37 Magnolia species; Magnolia coco was used as reference. Grey arrows represent genes with their orientation. Pink areas are conserved non-coding sequences (CNS). Blue areas are exons. The Y-axis represents the percentage of conservation of each species against the reference.

Figure 1

Mauve progressive alignment, including all 37 Magnoliaceae plastomes. Blocks of the same color connected by a line represent colinear regions. Blocks below the graphs represent coding regions. Colinear regions appear in the same order in all species, which suggests that no significant rearrangement has been found.

Figure 1

Mauve progressive alignment, including all 37 Magnoliaceae plastomes. Blocks of the same color connected by a line represent colinear regions. Blocks below the graphs represent coding regions. Colinear regions appear in the same order in all species, which suggests that no significant rearrangement has been found.

Figure 2

Nucleotide diversity (Pi) values resulting from the sliding window analysis of the 37 included Magnoliaceae plastomes. The Pi values ranged from 0 to 0.0236. The most diverse sites corresponded to genes such as PetL, ccsA, and ndhD, while the IR regions presented the lowest diversity. LSC = large single copy region; IR = inverted repeat regions; SSC = small single copy region.

Figure 3

Expansion and contraction of 37 Magnoliaceae IR regions, analyzed with IRscope. All four junctions (LSC/IRb, IRb/SSC, SSC/IRa, and IRa/LSC) are shown, as well as their flanking genes.

Figure 4

Phylogenetic relationships obtained from the Bayesian inference analysis of the newly assembled plastomes from 15 Neotropical species plus 22 plastomes downloaded from the NCBI; Liriodendron was used as an outgroup. The classification was according to [51,60]; The Neotropical subsections are shown in dotted brackets. The numbers at the nodes represent the ML bootstrap and BI posterior probability support values, respectively; nodes without numbers correspond to 100/1 support values. * = Neotropical groups.