Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids

To date, publicly available plastid genomes of legumes have for the most part been limited to the subfamily Papilionoideae. Here we report 13 new plastid genomes of legumes spanning all three subfamilies. The genomes representing Caesalpinioideae and Mimosoideae are highly conserved in gene content and gene order, similar to the ancestral angiosperm genome organization. Genomes within the Papilionoideae, however, have reduced sizes due to deletions in nine intergenic spacers primarily in the large single copy region. Our study also indicates that rps16 has been independently lost at least five times in legumes, with additional gene and intron losses scattered among the papilionoids. Additionally, genera from two distinct lineages within the papilionoids, Lupinus and Robinia, have a parallel inversion of 36 kb and 39 kb, respectively. This parallel inversion is novel as it appears to be caused by a 29 bp repeat within two trnS genes. This repeat is present in all available legume plastid...

迄今为止，公开可用的豆科植物质体基因组（plastid genomes）绝大多数仅局限于蝶形花亚科（Papilionoideae）。本研究报道了13个全新的豆科植物质体基因组，其涵盖了豆科全部三个亚科。云实亚科（Caesalpinioideae）与含羞草亚科（Mimosoideae）的质体基因组在基因含量与基因排列顺序上高度保守，与被子植物祖先的基因组组织结构相一致。然而蝶形花亚科的质体基因组因9个主要位于大单拷贝区（large single copy region）的基因间隔区缺失，导致基因组尺寸缩减。本研究同时表明，rps16基因在豆科植物中至少独立丢失了5次，此外蝶形花亚科类群中还散布着额外的基因与内含子丢失事件。此外，蝶形花亚科内两个不同演化支的类群——羽扇豆属（Lupinus）与刺槐属（Robinia）——分别存在36 kb与39 kb的平行倒位。这种平行倒位的成因较为新颖，其似乎由两个trnS基因内的29 bp重复序列所介导。该重复序列存在于所有已公开的豆科质体……