The Complete Chloroplast Genome of <Emphasis Type="Italic">Coix lacryma-jobi</Emphasis> and a Comparative Molecular Evolutionary Analysis of Plastomes in Cereals |
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Authors: | Charles H Leseberg Melvin R Duvall |
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Institution: | (1) Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115-2861, USA |
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Abstract: | Graminoid molecular evolution was investigated by chloroplast genome (plastome) scale analyses. A complete plastome from Coix lacryma-jobi (Poaceae) and a draft plastome from Joinvillea plicata (Joinvilleaceae) were sequenced and analyzed. The draft plastome included conserved protein-coding loci routinely analyzed
in previous studies plus one additional locus of demonstrated phylogenetic utility. The methodological approach was to directly
sequence overlapping amplicons from known plastome regions. Over 100 pairs of amplification and sequencing primers were designed
and positioned to flank overlapping 1,200-base pair fragments around the entire plastome. Newly determined sequences were
analyzed with published plastomes from representatives of Panicoideae, Ehrhartoideae, and Pooideae. Considerable variation
was found for studies within the family and even within Andropogoneae. Readily interpreted mutation patterns were observed,
such as small inversions in hairpin-loop regions and indels, which were common in intergenic spacers. Maximum or near-maximum
bootstrap support was observed in all analyses resolving relationships between subfamilies. However, the addition of characters
from noncoding regions increased the number of parsimony-informative characters and lengthened short internal branches (Andropogoneae),
better defining intergeneric relationships. Thus, characters in complete plastomes can be used over a wide scope of phylogenetic
studies. |
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