Abstract
Sophora japonica L. (Faboideae, Leguminosae) is an important traditional Chinese herb with a long history of cultivation. Its flower buds and fruits contain abundant flavonoids, and therefore, the plants are cultivated for the industrial extraction of rutin. Here, we determined the complete nucleotide sequence of the mitochondrial genome of S. japonica ‘JinhuaiJ2’, the most widely planted variety in Guangxi region of China. The total length of the mtDNA sequence is 484,916 bp, with a GC content of 45.4%. Sophora japonica mtDNA harbors 32 known protein-coding genes, 17 tRNA genes, and three rRNA genes with 17 cis-spliced and five trans-spliced introns disrupting eight protein-coding genes. The gene coding and intron regions, and intergenic spacers account for 7.5%, 5.8% and 86.7% of the genome, respectively. The gene profile of S. japonica mitogenome differs from that of the other Faboideae species by only one or two gene gains or losses. Four of the 17 cis-spliced introns showed distinct length variations in the Faboideae, which could be attributed to the homologous recombination of the short repeats measuring a few bases located precisely at the edges of the putative deletions. This reflects the importance of small repeats in the sequence evolution in Faboideae mitogenomes. Repeated sequences of S. japonica mitogenome are mainly composed of small repeats, with only 20 medium-sized repeats, and one large repeat, adding up to 4% of its mitogenome length. Among the 25 pseudogene fragments detected in the intergenic spacer regions, the two largest ones and their corresponding functional gene copies located in two different sets of medium-sized repeats, point to their origins from homologous recombinations. As we further observed the recombined reads associated with the longest repeats of 2,160 bp with the PacBio long read data set of just 15 × in depth, repeat mediated homologous recombinations may play important role in the mitogenomic evolution of S. japonica. Our study provides insightful knowledge to the genetic background of this important herb species and the mitogenomic evolution in the Faboideae species.
Highlights
Plant mitochondrial genomes differ from their animal counterparts mainly by the considerable expansion of the non-coding regions and dynamic genome structure induced by repeat-mediated homologous recombination [1]
The mt genome of S. japonica was assembled into a single circular molecule of 484,916 bp (Fig 1), and is larger than all the other seven mt genomes reported from the Faboideae, which range from 271,618 bp in M. truncatula to 425,718 bp in M. pinnata
The relatively large size of the mt genome of S. japonica is primarily due to the accumulation of species-specific noncoding sequences, especially the intergenic spacer expansions, which consist of 420,569 bp, or 86.7% of the mitogenome of S. japonica
Summary
Plant mitochondrial (mt) genomes differ from their animal counterparts mainly by the considerable expansion of the non-coding regions and dynamic genome structure induced by repeat-mediated homologous recombination [1]. Homologous recombination appears to be positively correlated with repeat length [2]: large repeats (!1,000 bp) are frequently reported to cause recombination equilibrium [12], whereas medium-sized (100–1000 bp) and small (
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