Corrected sequence of the wheat plastid genome

Abstract

Wheat is the most important cereal in the world in terms of acreage and productivity. We sequenced and assembled the plastid genome of one Egyptian wheat cultivar using next-generation sequence data. The size of the plastid genome is 133,873 bp, which is 672 bp smaller than the published plastid genome of "Chinese Spring" cultivar, due mainly to the presence of three sequences from the rice plastid genome. The difference in size between the previously published wheat plastid genome and the sequence reported here is due to contamination of the published genome with rice plastid DNA, most of which is present in three sequences of 332, 131 and 131 bp. The corrected plastid genome of wheat has been submitted to GenBank (accession number KJ592713) and can be used in future comparisons.

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

“…Comparable to other studies (e.g. [32, 43]) we were not able to confirm all parts of GenBank-derived sequences obtained from whole-genome shotgun sequencing. It might be that they contain some non-identified assembly errors.…”

“…The alignment was manually curated. The sequences generated in the scope of this study were annotated by comparing them to the annotations of the GenBank accession number KJ592713 [43] in G eneious . All sequences were submitted to GenBank (accession numbers KX591961-KX592154 and KY635999-KY636181).…”

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes

“…The pattern of relationships among the three sampled Triticeae genera agree with plastid ( Petersen and Seberg 1997 ; Mason-Gamer et al 2002 ), nuclear ( Mason-Gamer 2005 ) and combined plastid/nuclear phylogenies ( Escobar et al 2011 ) of the subtribe. An earlier version of the T. aestivum plastome ( Ogihara et al 2000 ) was recently found to contain sequence from the rice plastid genome ( Bahieldin et al 2014 ). This contaminated genome was included in an early version of our plastome matrix, and in our preliminary MP and ML analyses the terminal branch of T. aestivum was considerably longer than those of the other Aegilops and Triticum taxa in the trees, indicative of this error (data not shown).…”

“…& Graebn. Middleton et al (2014) Secale cereale L. Middleton et al (2014) Triticum aestivum L. Bahieldin et al (2014) Triticum boeoticum Boiss. Middleton et al (2014) Triticum monococcum L. Middleton et al (2014) Triticum urartu Thumanjan ex Gandilyan Middleton et al (2014) Poeae Agrostidinae Agrostis stolonifera L. Saski et al (2007) Ammophila breviligulata Fernald USA New York: P.M. Peterson & J.M.…”

“…All newly assembled plastomes were then aligned, along with 20 previously published pooid plastomes and one bamboo outgroup plastome, Bambusa bambos (KJ870988) (Table 2 ), using the MAFFT alignment software ( Katoh et al 2005 ). We used the corrected sequence of Triticum aestivum ( Bahieldin et al 2014 ), as the earlier plastome ( Ogihara et al 2000 ) contained sequences from the rice plastome. The alignment was then inspected for structural mutations and adjusted manually to preserve tandem repeat boundaries and to identify inversions.…”