Chloroplast genome of the invasive Pyrus calleryana

The complete chloroplast genome of Pyrus calleryana (BioSample SAMC013142) was developed by de novo assembly from whole-genome sequencing data. Reference-guided (P. phaeocarpa) read mapping and assembly were followed by annotation and phylogenetic comparisons. The Pyrus calleryana chloroplast genome of 159,965 bp in length (36,56% of GC content) represents a classical quadripartite architecture, with two inverted repeats regions (IRs; each 26,392 bp in length) separating the large single-copy region (LSC; 87,942 bp) and the small single-copy region (SSC; 19.239 bp). In total, 115 unique genes were predicted and annotated in that genome, including 81 protein coding genes, 30 tRNA coding genes, and 4 rRNA coding genes. Phylogenetic analyses based on the whole chloroplast genome sequences places the P. calleryana among other Rosaceae plants, specifically among the Asian species of Pyrus.

Methods
Ubuntu 20.4 code used for processing of P. calleryana SRA paired-end files:

bwa-mem2 index ../cp*.txt #Reference indexing

bwa-mem2 mem -t 12 ../cp*.txt ../*F.fastq.gz ../*R.fastq.gz > draft1.sam  #Reference mapping

samtools view --threads 12 -b -o draft1.bam -S draft1.sam #Samtools modification of mapped reads into .bam file

samtools sort --threads 12 draft1.bam > draft1.sorted.bam #Samtool sorting of the mapped reads

samtools index -@ 12 draft1.sorted.bam #Samtools indexing of the sorted mapped reads

pilon --genome ../cp*.txt --frags draft1.sorted.bam --tracks --threads 12 #Reference-guided assembly of the indexed, sorted mapped reads into a circular genome