Abstract
The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.
Highlights
Chloroplasts are important photosynthetic organelles that provide energy for the synthesis of glucose, fatty acids, and amino acids [1,2]
After screening these paired-end reads through alignment with S. vulgaris plastid genome, 585,206 (2.1%) reads of L. wilfordii and 661,807 (2.9%) reads of S. capitata were extracted with mean of coverage 980× and 1082×, respectively
The L. wilfordii and S. capitata genomes include a pair of inverted repeat (IR) of 27,709 bp and 25,371 bp separated by a small single copy (SSC) region of 12,914 bp and 17,313 bp and a large single copy (LSC) region of 83,988 bp and 82,169 bp, respectively (Fig 1, Table 2), similar to the published Caryophyllaceae chloroplast genomes [25,26,27,28]
Summary
Chloroplasts are important photosynthetic organelles that provide energy for the synthesis of glucose, fatty acids, and amino acids [1,2]. The chloroplast genome is the smallest of the plant genomes, ranging from 135 to 160 kb in most plants [3,4,5]. Most angiosperm chloroplast genomes have a quadripartite circular structure and contain two copies of inverted repeat (IR) regions, separating a large single copy (LSC) region and small single copy (SSC) region [5]. With the rapid development of next-generation sequencing platforms, many chloroplast genome sequences have been reported and used to help resolve plant phylogenies [6,7]. Chloroplast genomic data are widely used in various studies, such as those on molecular.
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