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Identification of immature stages was done by sequence comparison of the adult P. beata specimen as no sequences were available in BOLD and NCBI online databases for species identification.
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This may result from two different and not mutually exclusive factors: reduction of higher-order EULs due to deletion of unnecessary parts inherited from certain ancestors on the one hand, and on the other hand the persistence of lower-order EULs in several ancestors from which no sequences are available as yet.
Despite the low number of informative sites in the nLSU and nSSU loci, we favour the hypothesis based on the nuclear loci, as no close outgroup sequences were available for COX1 and the sequences used (Toxocara cati and Strongylida sp).
As sequences were available only in one direction for four genomic regions even after retrials, sequences for these regions were aligned using two individuals (Additional file 4).
As only mitochondrial sequences were available for this genus, additional data will be required to resolve the affinities of Notopteris.
This set was small in spite of the good sequence coverage for four of the tomato accessions, as not many sequences were available from other tomato materials.
As insufficient caprine sequences were available to create a dedicated goat array, a bovine Combimatrix 90K custom array was used [ 23].
Alternatively, the multiple sequences in different lineages may have independent parallel origins, as was suggested when fewer sequences were available [ 29].
Further L. salmonis transcript sequences were available as expressed sequence tags (EST) from GenBank.
Furthermore, as no genome sequences are available for cryptophytes, the same strategy was applied for an EST library of Guillardia theta (15,173 ESTs, 21 coding for CBPs; [ 53]), and we also took advantage of the availability of five CBP sequences obtained in a previous study by Broughton et al. on Rhodomonas sp. CS24 [ 35].
All DNA constructs as well as their nucleotide sequences are available upon request.
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