Abstract
BackgroundOrganelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome (plastome). Thus far, less than 15 mitochondrial genome (mitogenome) sequences of Fabaceae have been published, all but four of which belong to the subfamily Papilionoideae, limiting the understanding of size variation and content across the family. To address this, four mitogenomes were sequenced and assembled from three different subfamilies (Cercidoideae, Detarioideae and Caesalpinioideae).ResultsPhylogenetic analysis based on shared mitochondrial protein coding regions produced a fully resolved and well-supported phylogeny that was completely congruent with the plastome tree. Comparative analyses suggest that two kinds of mitogenome expansions have occurred in Fabaceae. Size expansion of four genera (Tamarindus, Libidibia, Haematoxylum, and Leucaena) in two subfamilies (Detarioideae and Caesalpinioideae) occurred in relatively deep nodes, and was mainly caused by intercellular gene transfer and/or interspecific horizontal gene transfer (HGT). The second, more recent expansion occurred in the Papilionoideae as a result of duplication of native mitochondrial sequences. Family-wide gene content analysis revealed 11 gene losses, four (rps2, 7, 11 and 13) of which occurred in the ancestor of Fabaceae. Losses of the remaining seven genes (cox2, rpl2, rpl10, rps1, rps19, sdh3, sdh4) were restricted to specific lineages or occurred independently in different clades. Introns of three genes (cox2, ccmFc and rps10) showed extensive lineage-specific length variation due to large sequence insertions and deletions. Shared DNA analysis among Fabaceae mitogenomes demonstrated a substantial decay of intergenic spacers and provided further insight into HGT between the mimosoid clade of Caesalpinioideae and the holoparasitic Lophophytum (Balanophoraceae).ConclusionThis study represents the most exhaustive analysis of Fabaceae mitogenomes so far, and extends the understanding the dynamic variation in size and gene/intron content. The four newly sequenced mitogenomes reported here expands the phylogenetic coverage to four subfamilies. The family has experienced multiple mitogenome size fluctuations in both ancient and recent times. The causes of these size variations are distinct in different lineages. Fabaceae mitogenomes experienced extensive size fluctuation by recruitment of exogenous DNA and duplication of native mitochondrial DNA.
Highlights
Organelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome
Together with polymerase chain reaction (PCR) and Sanger sequencing of the mitochondrial DNA of plastid origin (MIPT) confirmed that the plastomefiltered assembly method successfully discriminated reads from the plastome and MIPTs in the mitogenomes
A BLAST search against the four mitogenomes completed in this study showed a strong match to an intergenic spacer (IGS) in Haematoxylum
Summary
Organelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome (plastome). More recent estimates using complete mitogenome sequences expanded this range from the exceptionally small genome of Viscum scurruloideum at 66 kb [4] to the large multipartite genome of 11.3 Mb in Silene conica [5]. This extensive size variation has been attributed to both internal and external factors. One primary internal cause is proliferation of repetitive sequences to include hundreds to thousands of repeat motifs [6, 7] This repetitive DNA is the main cause of rearrangements that generate the multipartite structure of mitogenomes [8, 9]. The predominant external factor in mitogenome expansion involves the gain of native DNA from other genomic compartments and foreign DNA from different organisms [10]
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