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Phylogenetic analysis showed that the tandem pair was most likely to be a segmental duplication of Tb32.3 and Tb32.4.
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Paralogs located in tandem would be considered a segmental duplication, which are hotspots for CNVs [ 9].
This means that the closest a SNP is to a segmental duplication, the strongest the degree of allele specific gene expression, probably because of regulatory effects attributable to SDs.
In a second example, LOC_Os11g03210 and LOC_Os12g02960 are from a segmental duplication event involving chromosomes 11 and 12 which includes 160 collinear gene pairs.
The Populus genome contains three paralogous Hsp90 gene pairs, but only PtHsp90-5a/PtHsp90-5b in loconservedconserved positions in duplicated blocks, suggesting that it may be derived from a segmental duplication event during evolution.
Recent gene duplicates are expected to be found in tandem, unless they are the result of a segmental duplication, or retrotransposition is involved.
CNVs have also been identified as a cause of non-syndromic hearing loss (NSHL), the most well-known example being deletion of a segmental duplication region of chromosome 15 that includes the gene STRC and causes autosomal recessive NSHL (ARNSHL) at the DFNB16 locus [ 5, 6] or deafness-infertility syndrome (DIS) if the adjacent CATSPER2 gene also is involved [ 7].
A partial segment of the region between these two genes was involved in a segmental duplication, which possibly gave rise to LOC_Os03g24960 and LOC_Os03g24970 after the divergence of O. sativa and O. punctata (∼2 5 Ma).
Thus, the artiodactyl-specific genes for Ast1 and BTC1_14RD appear to have been created by a segmental duplication.
A 30-kb telomeric region containing three functional new genes was generated through a segmental duplication of an unmapped annotated region in O. sativa genome (supplementary figs. S1 and S2 A C, Supplementary Material online).
Paralogs with more than five genes between them were considered to be a result of a segmental duplication event (Hanada et al. 2008).
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