Abstract
The complete sequence of chloroplast genome (cpDNA) has been documented for single large columnar species of Cactaceae, lacking inverted repeats (IRs). We sequenced cpDNA for seven species of the short-globose cacti of Mammillaria and de novo assembly revealed three novel structures in land plants. These structures have a large single copy (LSC) that is 2.5 to 10 times larger than the small single copy (SSC), and two IRs that contain strong differences in length and gene composition. Structure 1 is distinguished by short IRs of <1 kb composed by rpl23-trnI-CAU-ycf2; with a total length of 110,189 bp and 113 genes. In structure 2, each IR is approximately 7.2 kb and is composed of 11 genes and one Intergenic Spacer-(psbK-trnQ)-trnQ-UUG-rps16-trnK-UUU-matK-trnK-UUU-psbA-trnH-GUG-rpl2-rpl23-trnI-CAU-ycf2; with a total size of 116,175 bp and 120 genes. Structure 3 has divergent IRs of approximately 14.1 kb, where IRA is composed of 20 genes: psbA-trnH-GUG-rpl23-trnI-CAU-ycf2-ndhB-rps7-rps12-trnV-GAC-rrn16-ycf68-trnI-GAU-trnA-AGC-rrn23-rrn4.5-rrn5-trnR-ACG-trnN-GUU-ndhF-rpl32; and IRB is identical to the IRA, but lacks rpl23. This structure has 131 genes and, by pseudogenization, it is shown to have the shortest cpDNA, of just 107,343 bp. Our findings show that Mammillaria bears an unusual structural diversity of cpDNA, which supports the elucidation of the evolutionary processes involved in cacti lineages.
Highlights
A new era in the study of evolutionary processes of chloroplasts and their genomes has arisen with the advent of massive sequencing [1]
Structure 1 was present in M. albiflora and M. pectinifera (Figure 1a), structure 2 in M. crucigera, M. huitzilopochtli, M
The three structures of cpDNA discovered in Mammillaria are novel and these have not been recorded in other eukaryote organisms
Summary
A new era in the study of evolutionary processes of chloroplasts and their genomes has arisen with the advent of massive sequencing [1]. Many studies have focused on determining the cyanobacterial origin of the DNA molecule contained in chloroplasts [1,3,4]. DNA sequences of complete genomes of contemporary cyanobacteria, algae, and plants have been analyzed, leading to the discovery that the chloroplast genome encompasses structural changes with significant evolutionary information. In comparison to cyanobacteria and algae, a significant reduction in the total length and in the number of genes has been documented in land plants [5]. Many genes lacking in the chloroplast genome have migrated to nuclear or mitochondrial genomes [6], which indicates a complex functional relationship among the three genomes contained in plants. Most encoding regions are regulated in operons which are transcribed into polycistronic units, as occurs in contemporary cyanobacteria [7]
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