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.

Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species

“…Highly variable regions provide abundant phylogenetic information and can be used as potential molecular markers to delimit closely related taxa [ 55 ]. The Pi of highly variable regions within subgenus Gynopodium species was lower (< 0.008) compared with previously published values of other species [ 56 , 57 ] and some of Magnolia species [ 29 , 30 ]. The low genetic diversity of subgenus Gynopodium species and other Magnolia species, e.g., Magnolia ashei may relate to their limited habitat and small populations as threatened species [ 54 , 58 , 59 ].…”

“…Our results indicated that the CPGs of six subgenus Gynopodium species are similar in size (ca. 160 kb) and structure (quadripartite circular structure) to other Magnolia species [ 28 – 30 ] as well as other higher plants [ 31 ]. The total number, order, and composition of genes in the CPGs were highly conserved within subgenus Gynopodium , which is also consistent with most Magnolia species [ 32 , 33 ], suggesting a very conserved structure of CPGs of subgenus Gynopodium .…”

Comparative Chloroplast Genomes of Six Magnoliaceae Species Provide New Insights into Intergeneric Relationships and Phylogeny

“…However, such an expansion is small, and no important expansions or contractions were observed in these cp sequences. This result is similar to the expansion of the chloroplast genomes of other Magnoliaceae species in the IR region [ 30 ], but different from the contraction of Zingiberaceae and Arecaceae [ 31 , 32 ]. This indicates that different species have evolved under the influence of different factors, resulting in different degrees of expansion and contraction of IR/SC boundaries, thus showing the diversity in genome length and boundaries [ 33 ].…”

Comparative Analysis of Chloroplast Genomes for the Genus Manglietia Blume (Magnoliaceae): Molecular Structure and Phylogenetic Evolution

“…The plastome of five new sequences of Manglietia ranges from 157,093 bp (M. calcarea2) to 160,493 bp (M. kwangtungensis). It is similar in size to the plastomes of other previously published Magnoliaceae species [21,90]. The genome size of M. calcarea2 is approximately 3000 bp shorter than that of the other two samples, primarily due to a loss in the IR region encompassing the rrn16-trnI-GAU sequence.…”