Although high RIP process in the P. fici genome may result in the lack of highly duplicated sequences, gene duplication has occurred before the emergence of RIPs.
The highly duplicated F3'5'Hs that reside in segmental duplications on chr6 are preferentially expressed in berry skin.
A track for duplications can be inserted into GBrowse [ 10], however, for highly duplicated genomes, new classifications and ontology for representing large-scale genome duplications had to be developed [ 4].
This error rate may indicate the presence of segmental duplication as many immune genes are known to be highly duplicated [ 33].
The second cluster, composed of most Illumina metagenomes, has an intermediate level of duplication (27.1 to 37.3%), but also an excess of highly duplicated reads (10.4 to 15.6%).
Evolutionary studies have suggested that the paleopolyploid soybean genome experienced two whole-genome duplication events at ∼59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies.
Panax ginseng, the most famous medicinal herb, has a highly duplicated genome structure.
Furthermore, the occurrence of (highly) duplicated genome sequences in crops such as maize [3], wheat [4], soybean [5] and pepper [6] impedes conversion of identified polymorphisms into genotyping assays for application in breeding.
In contrast, in Clostridium, Listeria, and Fusobacterium COG03920 is not highly duplicated and is adjacent on the chromosome to the ethanolamine utilization operon, which encodes a cobalamine-dependent enzyme, ethanolamine-ammonia lyase.
The highly duplicated SOCS2 may lead to higher bone mineral density.
Interestingly, Group 2 Rup sequences are highly duplicated with as many as six copies per genome.
