mtDNA Customer Publications

ndonesian local rabbit (Oryctolagus cuniculus) is a local breed in Indonesia. We reveal the mitochondrial genome sequence of the Indonesian local Rabbit for the first time. A better understanding of the mechanisms underlying these beneficial aspects of local breeds over imported ones requires detailed genetic investigations, of which mtDNA genome sequencing is of particular importance. Such an investigation will solve the major issues of misidentification with Javanese hares (Lepus nigricollis) and maternal lineage. In addition, this information will guide better statistics on the Indonesian local rabbit breed population and strategies for its conservation and breeding plans. This study aimed to identify and explore the characteristics of the mtDNA genomes of Indonesian local rabbits.This study observed that the length of the mtDNA genome is 17,469 bp, consisting of two ribosomal RNA (12S rRNA, 16S rRNA), 22 transfer RNA genes (trnR, trnG, trnK, trnD, trnS, trnY, trnC, trnN, trnA, trnW, trnM, trnQ, trnl, trnL, trnV, trnF, trnP, trnT, trnE, trnL, trnS, trnH), 13 protein-coding genes (PCGs) (ND4l, ND3, COX3, ATP6, ATP8, COX2, COX1, ND2, ND1, CYTB, ND6, ND5, ND4), a replication origin, and a noncoding control region (D-loop).mtDNA genome of Indonesian local rabbit was the longest and had the most extended D-loop sequence among the other references of Oryctolagus cuniculus. Other specific differences were also found in the percentage of nucleotides and variation in most of the PCGs when they were aligned with Oryctolagus cuniculus references from GenBank. Indonesian local Rabbits strongly suspected brought from Europe during the colonial period in Indonesia.

Myristica teysmannii Miq. is an endemic and endangered plant, with narrow distribution to the southern part of East Java, Indonesia. This study was aimed to determine the complete chloroplast genome sequence of M. teysmannii using the Illumina NextSeq 500 platform and reconstruct the phylogenetic relationship with selected Magnoliids taxa. Results showed that the chloroplast genome of M. teysmannii is 155,975 bp in size, with a large single copy region (87,187 bp), a small single copy region (20,656 bp), and two inverted repeat regions (24,066 bp each). The chloroplast genome consists of 126 genes, including 85 protein-coding genes and eight ribosomal RNA and 35 transfer RNA genes. Phylogenetic analysis showed that M. teysmannii is placed in the Myristica clade along with M. yunnanensis, M. fatua, M. fragrans, and M. argentea. This phylogeny may be used as a foundation for further studies of this endemic and endangered plant species. Additionally, the position of Eusyderoxylon zwageri in the Endocomia clade instead of Lauraceae is surprising; further studies need to be conducted to confirm this finding.