Understanding angiosperm genome interactions and evolution: Insights from sacred lotus (Nelumbo nucifera) and the carrot family (Apiaceae)

Horizontal and intracellular gene transfers are driving forces in plant evolution. The transfer of DNA into a genome adds genetic diversity and successfully incorporated genes can retain their original function or develop new functions through mutation. While there are trends and hypotheses for the frequency of transfers, age of transfers, and potential mechanisms of transfer each system has its own evolutionary history. The major goal of this study was to investigate gene transfer events and organelle rare genomic changes in two plant systems—Nelumbo (Nelumbonaceae) and the apioid superclade of Apiaceae subfamily Apioideae. Genome sequences from the early diverging angiosperm Nelumbo nucifera ‘China Antique’ were used to describe both intra- and interspecific patterns of variation and investigate intracellular gene transfers (IGT). A percent similarity approach was used to compare DNA from each genome and determine a possible mechanism of DNA transfer, if it occurred. The mechanisms investigated included recombination and double-strand break repair, as evidenced by repeat DNA and the presence of transposable elements. The ‘China Antique’ plastome retains the ancestral gene synteny of Amborella and has no evidence of IGT. ‘China Antique’ has more smaller repeats in its mitochondrial genomes than reported for other angiosperms, but does not contain any large repeats, and its nuclear genome does not have as much organelle DNA as the other angiosperms investigated, including Arabidopsis . The lack of large repeats within the Nelumbo mitochondrial genome may explain the few instances of IGT detected. The few instances of organelle IGTs into its nucleus may be the result of its history of vegetative propagation, low nucleotide substitution rate, and lack of several paleo-duplications. Unlike N. nucifera, and the majority of other angiosperms, the plastomes of several members of the apioid superclade within the carrot family (Apiaceae or Umbelliferae) have instances of IGT into the plastome, in addition to other rare genomic changes (RGCs). To investigate the distribution and mechanism of IGT in species of the apioid superclade and the variable boundary between the two single copy regions and the IR, the complete plastomes of Anethum graveolens, Foeniculum vulgare, Carum carvi, and Coriandrum sativum were sequenced. To determine the distribution of and mechanisms causing these RGCs, the extent of IGT, and changes in gene synteny, the large single copy (LSC)-inverted repeat (IR) boundary in 34 additional species was also sequenced. Analyses of these sequence data suggest that there are several mechanisms at work creating these dynamic IR changes. There is evidence of double-strand break repair in Coriandrum, as well as repeat mediated changes near its IR boundaries. Short dispersed repeats are also implicated as a mechanism of IR change in the 34 additional species investigated. In Carum (tribe Careae) there is an IR boundary expansion, in addition to two small inversions. One of these inversions is near J LA and the other is between psbM and trnT . Anethum and Foeniculum plastomes contain double-strand break repair causing IGT of mtDNA into these plastomes. For the 34 additional species investigated, data support double-strand break repair as a mechanism of plastid evolution and is the likely cause of novel DNA insertions at LSC-IR boundaries. However, without a resolved phylogeny there is no context for how many gene transfer events there were or a timeline for when these events occurred. Molecular phylogenetic studies to date have been unable to produce a well-resolved apioid superclade phylogeny. To resolve relationships among the tribes and other higher-level clades within the group, determine the phylogenetic utility of RGCs, and determine the extent and timing of plastome RGCs in the group, the plastid regions psbM – psbD and psbA – trnH and the nuclear gene PHYA were sequenced. To these sequence data four RGCs were added, as were previously available data from the nrDNA internal transcribed spacer (ITS) region. These molecular data were analyzed separately and in various combinations using maximum likelihood and Bayesian inference methods. While these data were unable to fully resolve higher-level relationships in the apioid superclade, conclusions can be made regarding the distribution and number of RGC events that have occurred in the group. The IR boundary expansion into rps3 occurred only once in the lineage leading to tribes Careae and Pyramidoptereae. In addition, Careae is supported as monophyletic by the presence of the inversion of psbA and trnH . The contraction of the IR to rpl2 and the presence of putative mtDNA adjacent to J LA also likely occurred only once. Alternatively, while not as parsimonious, a maximum of six events is possible if each lineage gained these RGCs independently. Other major lineages within the group are not as strongly delimited and, for these clades RGCs cannot unambiguously support monophyly. Further study of the apioid superclade is necessary to resolve relationships and make further inferences into the evolution of plastomes within the clade.