Abstract
We generated a complete plastid genome (plastome) sequence for Lamprocapnos spectabilis, providing the first complete plastome from the subfamily Fumarioideae (Papaveraceae). The Lamprocapnos plastome shows large differences in size, structure, gene content, and substitution rates compared with two sequenced Papaveraceae plastomes. We propose a model that explains the major rearrangements observed, involving at least six inverted repeat (IR) boundary shifts and five inversions, generating a number of gene duplications and relocations, as well as a two-fold expansion of the IR and miniaturized small single-copy region. A reduction in the substitution rates for genes transferred from the single-copy regions to the IR was observed. Accelerated substitution rates of plastid accD and clpP were detected in the Lamprocapnos plastome. The accelerated substitution rate for the accD gene was correlated with a large insertion of amino acid repeat (AAR) motifs in the middle region, but the forces driving the higher substitution rate of the clpP gene are unclear. We found a variable number of AARs in Lamprocapnos accD and ycf1 genes within individuals, and the repeats were associated with coiled-coil regions. In addition, comparative analysis of three Papaveraceae plastomes revealed loss of rps15 in Papaver, and functional replacement to the nucleus was identified.
Highlights
Angiosperm plastid genomes generally exhibit two copies of an inverted repeat (IR) region, referred to as IRA and IRB1
The size of the large single copy (LSC) in the Lamprocapnos plastome is close to the median genome size (84,588 bp) for the selected angiosperm plastomes; the 1,645 bp small single copy (SSC) is the smallest SSC found in any plastome analyzed to date
The plastome contains 79 unique protein genes (18 of which are duplicated in the IR), 30 tRNA genes (11 are duplicated in the IR, including two trnI-CAU, for which a fifth copy is located in the LSC), and four rRNA genes, with 21 introns (20 cis-spliced and 1 trans-spliced) (Table S1)
Summary
Angiosperm plastid genomes (plastomes) generally exhibit two copies of an inverted repeat (IR) region, referred to as IRA and IRB1. Based on molecular (rbcL, matK, trnL-F, and 26 S nuclear ribosomal DNA) and morphological data[25], Papaveraceae s.l. has been classified into two subfamilies: Fumarioideae (DC) Endl. Complete plastome sequences have been reported for only two species of Papaveraceae[27,28], neither of which is a member of the subfamily Fumarioideae. As part of our ongoing research on the evolution of plastome and phylogenomic relationships among Papaveraceae, we uncovered the plastome sequence of Lamprocapnos spectabilis, representing the first sequenced member of the subfamily Fumarioideae. Comparison of three plastomes (from Lamprocapnos, Papaver and Coreanomecon) revealed extensive diversity in terms of size, structure, gene content, and substitution rates in Lamprocapnos. Our results provide new insights into the evolution of plastomes within the family Papaveraceae
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