Recombination between homeologous chromosomes, also known as homeologous exchange (HE), plays a significant role in shaping genome structure and gene expression in interspecific hybrids and allopolyploids of several plant species. However, the molecular mechanisms that govern HEs are not well understood. Here, we studied HE events in the progeny of a nascent allotetraploid (genome AADD) derived from two diploid progenitors of hexaploid bread wheat using cytological and whole-genome sequence analyses. In total, 37 HEs were identified and HE junctions were mapped precisely. HEs exhibit typical patterns of homologous recombination hotspots, being biased toward low-copy, subtelomeric regions of chromosome arms and showing association with known recombination hotspot motifs. But, strikingly, while homologous recombination preferentially takes place upstream and downstream of coding regions, HEs are highly enriched within gene bodies, giving rise to novel recombinant transcripts, which in turn are predicted to generate new protein fusion variants. To test whether this is a widespread phenomenon, a dataset of high-resolution HE junctions was analyzed for allopolyploid Brassica, rice, Arabidopsis suecica, banana, and peanut. Intragenic recombination and formation of chimeric genes was detected in HEs of all species and was prominent in most of them. HE thus provides a mechanism for evolutionary novelty in transcript and protein sequences in nascent allopolyploids.
Here we compare the exonic sequences of four Group 1 mouse major urinary protein (MUP) genes and four Group 1 cDNA sequences. These define seven different nucleotide sequences which differ from each other by 0.35% of bases on average, and which would code for seven different MUP proteins that could probably be resolved physically into at least five classes. The sequences differ at 13 nucleotide positions and at six codons, and although they are closely related their descent cannot be described by a simple series of duplications. We also describe the sequence of another liver cDNA (pMUP15) which has diverged from the Group 1 consensus sequence in 14.6% of bases. The divergence is much greater over exons 1‐3 than over exons 4‐6, suggesting that an ancestral gene conversion event has occurred. pMUP15 also differs from the Group 1 genes in having a longer signal peptide sequence and a different splice configuration between exons 6 and 7. Unlike the Group 1 sequences, pMUP15 contains a potential N‐linked glycosylation site. Other published work has shown that a shorter cDNA clone which is identical over their common sequence to pMUP15 codes for MUP proteins that are unusually large in size and acidic in pI. We show here that mouse urine does indeed contain a glycosylated MUP protein with those properties, presumably the product of the gene that corresponds to pMUP15.
Pleurotus tuoliensis (Bailinggu, designated Pt) and P. eryngii var. eryngii (Xingbaogu, designated Pe) are highly valued edible mushrooms. We report de novo assemblies of high-quality genomes for both mushrooms based on PacBio RS II sequencing and annotation of all identified genes. A comparative genomics analysis between Pt and Pe with P. ostreatus as an outgroup taxon revealed extensive genomic divergence between the two mushroom genomes primarily due to the rapid gain of taxon-specific genes and disruption of synteny in either taxon. The re-appraised phylogenetic relationship between Pt and Pe at the genome-wide level validates earlier proposals to designate Pt as an independent species. Variation of the identified wood-decay-related gene content can largely explain the variable adaptation and host specificity of the two mushrooms. On the basis of the two assembled genome sequences, methylomes and the regulatory roles of DNA methylation in gene expression were characterized and compared. The genome, methylome and transcriptome data of these two important mushrooms will provide valuable information for advancing our understanding of the evolution of Pleurotus and related genera and for facilitating genome- and epigenome-based strategies for mushroom breeding.
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