A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower Page: 7 of 33
This report is part of the collection entitled: Office of Scientific & Technical Information Technical Reports and was provided to UNT Digital Library by the UNT Libraries Government Documents Department.
Extracted Text
The following text was automatically extracted from the image on this page using optical character recognition software:
Discussion
Genome organization
Although the sunflower and lettuce chloroplast genomes are identical in gene content and
arrangement, they differ in their length and in the extent of their IR regions. The lettuce IR is
401 bp longer than the sunflower IR, which adds twice that length to the whole genome.
Although the lettuce genome IR is longer, the sunflower IR actually has a greater expansion
along both edges by a total of 140 bp. The sunflower IR extends into ycfl with 576 bp (only 471
in sunflower) and into rps19 with 101 bp (only 60 bp in lettuce). This expansion of boundaries
in the sunflower IR is balanced by a deletion of 456 bp in ycf2 in the sunflower. Other smaller
indels across the IR add to this length difference. Since this 401 bp IR length difference is
doubled in the genome, it contributes half of the total genome difference, which is 1,668 bp
between the two genomes. The extent of the IR in both genomes is similar, although the exact
extent into the single-copy genes varies among other published genomes, like Glycine,
Nicotiana, Atropa, Eucalyptus, and Panax [11, 12, 19-21].
There is a 152 amino-acid (aa) deletion in the ycf2 gene in sunflower. ycf2 is one of five genes
absent in some species' chloroplast genomes; the other genes are accD, ycf1, rp123, infA [22].
Both ycfl and ycf2 are absent in monocot grains, namely maize, rice, and sugarcane [23-25].
However, knockout studies of ycf2 have confirmed it as an essential chloroplast gene for survival
in tobacco [26]. From this study, we can only hypothesize that the ycf2 gene in Helianthus is
functional because the rest of the gene is highly conserved compared to the lettuce copy, with
only 1.31% sequence divergence. If the large deletion in the Helianthus copy rendered it a
pseudogene, we would expect there to be higher sequence divergence with internal stop codons.
Upcoming Pages
Here’s what’s next.
Search Inside
This report can be searched. Note: Results may vary based on the legibility of text within the document.
Tools / Downloads
Get a copy of this page or view the extracted text.
Citing and Sharing
Basic information for referencing this web page. We also provide extended guidance on usage rights, references, copying or embedding.
Reference the current page of this Report.
Timme, Ruth E.; Kuehl, Jennifer V.; Boore, Jeffrey L. & Jansen, Robert K. A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower, report, January 20, 2006; Berkeley, California. (https://digital.library.unt.edu/ark:/67531/metadc935042/m1/7/: accessed April 19, 2024), University of North Texas Libraries, UNT Digital Library, https://digital.library.unt.edu; crediting UNT Libraries Government Documents Department.