Complete chloroplast genome of Trachelium caeruleum: extensiverearrangements are associated with repeats and tRNAs Page: 2 of 32
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Abstract
Chloroplast genome structure, gene order and content are highly conserved in land plants.
We sequenced the complete chloroplast genome sequence of Trachelium caeruleum
(Campanulaceae) a member of an angiosperm family known for highly rearranged
chloroplast genomes. The total genome size is 162,321 bp with an IR of 27,273 bp, LSC
of 100,113 bp and SSC of 7,661 bp. The genome encodes 115 unique genes, with 19
duplicated in the IR, a tRNA (trnl-CAU) duplicated once in the LSC and a protein coding
gene (psbJ) duplicated twice, for a total of 137 genes. Four genes (ycf15, rp123, infA and
accD) are truncated and likely nonfunctional; three others (clpP, ycfl and ycf2) are so
highly diverged that they may now be pseudogenes. The most conspicuous feature of the
Trachelium genome is the presence of eighteen internally unrearranged blocks of genes
that have been inverted or relocated within the genome, relative to the typical gene order
of most angiosperm chloroplast genomes. Recombination between repeats or tRNAs has
been suggested as two means of chloroplast genome rearrangements. We compared the
relative number of repeats in Trachelium to eight other angiosperm chloroplast genomes,
and evaluated the location of repeats and tRNAs in relation to rearrangements.
Trachelium has the highest number and largest repeats, which are concentrated near
inversion endpoints or other rearrangements. tRNAs occur at many but not all inversion
endpoints. There is likely no single mechanism responsible for the remarkable number of
alterations in this genome, but both repeats and tRNAs are clearly associated with these
rearrangements.
Land plant chloroplast genomes are highly conserved in structure, gene order and
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Haberle, Rosemarie C.; Fourcade, Matthew L.; Boore, Jeffrey L. & Jansen, Robert K. Complete chloroplast genome of Trachelium caeruleum: extensiverearrangements are associated with repeats and tRNAs, article, January 9, 2006; Berkeley, California. (https://digital.library.unt.edu/ark:/67531/metadc897001/m1/2/: accessed April 20, 2024), University of North Texas Libraries, UNT Digital Library, https://digital.library.unt.edu; crediting UNT Libraries Government Documents Department.