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On the basis of the phylogenetic tree (Fig. 1), clusters of the nsLTP genes in grass lineage have continuously expanded in type I, V, and VI, indicating rounds of duplications with different gene loss in each species.
Moreover, the syntenic non-Inparanoid pairs with an ICR < 0.5 (1.1% of all tested pairs) are also likely distant paralogs, by old tandem duplications with different gene structures resulting in lower ICR.
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Every gene tree was rooted using either midpoint rooting (if the gene family consisted of sequences from one organism) or most parsimonious gene tree/species tree reconciliation based upon a minimization of the number of inferred duplication events with different root placements (Berglund-Sonnhammer et al. 2006).
Patients with overlapping but different sized deletions or duplications might present with different phenotypes that correlate with the affected genes.
Clinical features of ADLD patients were similar in all patients in whom LMNB1 was the only gene completely duplicated, and we did not notice differences associated with different duplication extents.
Table 1 shows the distribution of inferred duplication events associated with different taxonomic units (sorted according to rank).
Gene duplication can occur with different functional consequences [ 4, 5] at the scale of a single gene or a medium-sized genomic segment, but also of a whole genome [ 3, 6- 8].
This view combines extensive gene duplications with rampant loss of different genes in different lineages.
In order to quantify the effect of gene duplication on the proportion of orthologs that are BBH, we simulated datasets of 30 genomes with different duplication rates using the software package ALF (Dalquen et al. 2012; see also Materials and Methods).
Different modes of gene duplication may be associated with different types, levels, and patterns of structural divergence.
We did not observe haplotypes shared among families with different duplication sizes suggesting that an "at risk" chromosomal haplotype is unlikely (Table 2).
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