Complete Sequence of the Duckweed (Lemna minor) Chloroplast Genome: Structural Organization and Phylogenetic Relationships to Other Angiosperms

Abstract

The complete nucleotide sequence of the duckweed (Lemna minor) chloroplast genome (cpDNA) was determined. The cpDNA is a circular molecule of 165,955 bp containing a pair of 31,223-bp inverted repeat regions (IRs), which are separated by small and large single-copy regions of 89,906 and 13,603 bp, respectively. The entire gene pool and relative positions of 112 genes (78 protein-encoding genes, 30 tRNA genes, and 4 rRNA genes) are almost identical to those of Amborella trichopoda cpDNA; the minor difference is the absence of infA and ycf15 genes in the duckweed cpDNA. The inverted repeat is expanded to include ycf1 and rps15 genes; this pattern is unique and does not occur in any other sequenced cpDNA of land plants. As in basal angiosperms and eudicots, but not in other monocots, the borders between IRs and a large single-copy region are located upstream of rps19 and downstream of trnH, so that trnH is not included in IRs. The model of rearrangements of the chloroplast genome during the evolution of monocots is proposed as the result of the comparison of cpDNA structures in duckweed and other monocots. The phylogenetic analyses of 61 protein-coding genes from 38 plastid genome sequences provided strong support for the monophyly of monocots and position of Lemna as the next diverging lineage of monocots after Acorales. Our analyses also provided support for Amborella as a sister to all other angiosperms, but in the bayesian phylogeny inference based on the first two codon positions Amborella united with Nymphaeales.

Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species

“…It is supposed that ribosomal genes (rrna4.5, rrna5, rrna16, rrna23) and coding regions (19, 8 ,10, 5) are responsible for high GC content in IR. GC content distribution of the each region is similar with other species (20,10,5). According to Gao (8) GC content was uneven across cp genome in Alsophila.…”

“…For instance ycf15, a non-functional gene in other plants (10,22,12) is also present in G. thurberi. The other example is infA, most mobile gene between chloroplast and nuclear genome, that codes for a translation initial factor 1 (29,30,31).…”

“…Therefore and In addition to phylogenetic analysis based on plastidic genomes, it is imperative to understand the chloroplast genome in order to logically design our next generation transplastomics. Accordingly, chloroplast genomes of many species have been sequenced (7)(8)(9)(10)(11)(12)(13)(14).…”

Molecular Analysis of Stemona Plants in China Based on Sequences of Four Chloroplast DNA Regions

“…(Accession no. NC 010109) 26) from Lemnaceae, of which complete sequence of cpDNA have been deposited in GenBank. Primers used in analysis of trnL-trnF sequence were the same as those of Taberlet et al 27) The reverse primer of petBpetD region was designed according to Loehne's report.…”

Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa

“…С помощью этого метода была получена полная последовательность пластидного генома только у одного представителя рода Allium -лука репчатого A. cepa (von Kohn et al, 2013). Третьим методом определены по-следовательности пластома многих видов растений, на-пример кувшинки Nymphaea alba (Goremykin et al, 2004), огурца Cucumis sativus (Chung et al, 2007), ряски Lemna minor (Mardanov et al, 2008) и др. Так как к настоящему времени секвенирована полная последовательность пла-стидного генома нескольких генотипов Allium cepa, то представлялось возможным разработать универсальную систему праймеров для амплификации перекрывающих-ся участков пластома у других видов Allium.…”