Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.)

Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae

“…The former is one of the best-known plant families with significant rearrangements while the latter is relatively conserved without known dramatic variations. The repeats found in the palm family, representing by coconut, oil palm and date palm range between seven to 13 and the longest one is 39 bp in length [50, 51, 52]. In contrast, repeats in Poaceae are more abundant (>30 in some taxa) and longer in size (>100 bp) [53, 54].…”

Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos nucifera)

“…The frequency of codon usage in the coconut cp genome is summarized in Table 2. Similar to many cp genomes of angiosperms [2], [3], [19]–[22], a strong bias toward an A or T in the third position of synonymous codons is also observed in the coconut cp genome. The most and least prevalent amino acids are leucine (2624) and cysteine (323), respectively.…”

“…GUG codons have been shown to be more efficient than ACG in initiating translation and have a relative strength varying from 15 to 30% of AUG activity [24]. In angiosperms, a GUG start codon has been found in the cemA gene [5], [25]–[27] and rps19 gene [2], [3], [5], [8], [26], [28]–[32]. A transcript starting with an ACG start codon has been observed in the ndhD gene in some species of Nicotiana [33], [34].…”

“…The average read length and insert size were 151 bp and 340 bp respectively. The assembled contigs shorter than 200 bp were removed from the scaffold while those with coverage larger than 10X were selected for BLAST search against plastid genomes of date palm [2], oil palm [3], and other chloroplast sequences with an e-value cutoff of 10 −5 (199 sequences in total). Gaps between contigs were filled by PCR amplification with specific primers that were designed based on contig sequences or homologous sequence alignments (Table S1).…”

“…The predicted editing sites were verified by reverse transcription polymerase chain reaction (RT-PCR) experiments. In addition to those genes predicted by the program, we also investigated rpl22 , rpl23 , rps3 , rps7 , ycf1 , ycf2 , and ycf4 genes, within which RNA editing sites were reported in the cp genome of oil palm [3]. The Plant Total RNA Miniprep Purification Kit (GMbiolab Co., Ltd.) was applied to extract total RNA from leaf of the same seedling used for DNA extraction.…”