Horticultural Plants Genomics

Chinese plum (Prunus salicina L.), also known as Japanese plum, is gaining importance because of its extensive genetic diversity and nutritional attributes that are beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. In this study,... [Read More]

Valcano The pipeline to characterize the LTR-RTs family, classify and predict the burst families** How it works: 1） Get the 5-LTR sequence perl list_to_5ltr.pl reference.fa.pass.list reference.fa > ltr.fa 2）cluster the 5-LTR sequence and obtain the LTR lib and list cd-hit-est -i ltr.fa -o clust.out -c 0.8 -aL 0.8 -T 0... [Read More]

Previous genetic mapping helped detect a ~7.52 Mb putative genomic region for the pollen fertility trait on peach Chromosome 06 (Chr.06), which was too long for candidate gene characterization. In this study, using the whole-genome re-sequencing data of 201 peach accessions, we performed a genome-wide association study to identify key... [Read More]

Phylogeny-based classification of plant retrotransposons LTR retrotransposons are class I transposable element characterized by the presence of long terminal repeats (LTRs) directly flanking an internal coding region. As retrotransposons, they mobilize through reverse transcription of their mRNA and integration of the newly created cDNA into another location. Their mechanism of... [Read More]

Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive... [Read More]