Abstract
Chloroplast (cp) genomics will play an important role in the characterization of crop wild relative germplasm conserved in worldwide gene banks, thanks to the advances in genome sequencing. We applied a multiplexed shotgun sequencing procedure to sequence the cp genomes of 25 Avena species with variable ploidy levels. Bioinformatics analysis of the acquired sequences generated 25 de novo genome assemblies ranging from 135,557 to 136,006 bp. The gene annotations revealed 130 genes and their duplications, along with four to six pseudogenes, for each genome. Little differences in genome structure and gene arrangement were observed across the 25 species. Polymorphism analyses identified 1313 polymorphic sites and revealed an average of 277 microsatellites per genome. Greater nucleotide diversity was observed in the short single-copy region. Genome-wide scanning of selection signals suggested that six cp genes were under positive selection on some amino acids. These research outputs allow for a better understanding of oat cp genomes and evolution, and they form an essential set of cp genomic resources for the studies of oat evolutionary biology and for oat wild relative germplasm characterization.
Highlights
These research outputs allow for a better understanding of oat cp genomes and evolution, and they form an essential set of cp genomic resources for the studies of oat evolutionary biology and for oat wild relative germplasm characterization
Chloroplast genomics will play an important role in the characterization of crop wild relative (CWR) germplasm conserved in worldwide gene banks
Four MiSeq runs generated a total of 95 million sequence reads for 25 Avena samples, each having
Summary
Chloroplast (cp) genomics will play an important role in the characterization of crop wild relative (CWR) germplasm conserved in worldwide gene banks. There are more than 31,000 accessions of oat wild relative germplasm conserved in more than 20 gene banks worldwide [13]. These genetic resources are known to harbor an important source of genetic variability [14] for oat genetic improvement through interspecific crossing and introgression [7,15,16]. Conserving and managing these wild relative accessions are challenging tasks [17]. It was our hope that these analyses would provide baseline information that could give us a better understanding of the oat cp genome and evolution and for oat wild relative germplasm characterization
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