The complete plastid genome sequence of Abies koreana (Pinaceae: Abietoideae)

Abstract

The nucleotide sequence of the chloroplast genome from Abies koreana is the first to have complete genome sequence from genus Abies of family Pinaceae. The circular double-stranded DNA, which consists of 121,373 base pairs (bp), contains a pair of very short inverted repeat regions (IRa and IRb) of 264 bp each, which are separated by a small and large single-copy regions (SSC and LSC) of 54,197 and 66,648 bp, respectively. The genome contents of 114 genes (68 peptide-encoding genes, 35 tRNA genes, four rRNA genes, six open reading frames and one pseudogene) are similar to the chloroplast DNA of other species of Abietoideae. Loss of ndh genes was also identified in the genome of A. koreana like other genomes in the family Pinaceae. Thirteen genes contain one (11 genes) or two (rps12 and ycf3 genes) introns. In phylogenetic analysis, the tree confirms that Abies, Keteleeria and Cedrus are strongly supported as monophyletic. Other inverted repeat sequences located in 42-kb inversion points (1186 bp) include trnS-psaM-ycf12- ψtrnG genes.

The complete chloroplast genome of the Taiwan red pine Pinus taiwanensis (Pinaceae)

“…The cpDNA of the Taiwan red pine comprised 115 genes, including 74 protein-coding genes (73 PCG species), 4 ribosomal RNA genes (four rRNA species) and 37 transfer RNA genes (22 tRNA species). The overall AT content of the Taiwan red pine cpDNA is 61.5%, which is similar to that of the other species of family Pinaceae (Cronn et al, 2008;Yi et al, 2015). The most of gene species occurred in a single copy, while one tRNA gene species (trnS) occurred in four copies, four tRNA gene species (trnI, trnL, trnR & trnT) occurred in three copies, and seven tRNA gene species (trnG, trnH, trnP & trnV) occurred in double copies.…”

Resolving phylogenetic relationships and species delimitations in closely related gymnosperms using high-throughput NGS, Sanger sequencing and morphology

“…As a consequence, NGS has allowed for the description of a rapidly increasing number of nuclear, mitochondrial and plastid genomes (Rounsley et al 2009;Deschamps and Campbell 2010) and is set to contribute to a deeper understanding of both phylogeny and evolution in many lineages. Among the three types of genomes, data of entire plastid genomes have been widely used to seek for markers for the purpose of DNA barcoding (Hollingsworth et al 2011;Nock et al 2011), to investigate population genetics, and in phylogeographic studies (Powell et al 1995;Provan et al 2001;Mariac et al 2014), as well as to efficiently address phylogenetic questions in both angiosperms (Jansen et al 2007;Moore et al 2011;Huang et al 2014) and gymnosperms (Parks et al 2009;Lin et al 2010;Yi et al 2015). Here, we use data from NGS, combined with data from traditional Sanger sequencing and morphology, with the primary aim of resolving the phylogeny and species delimitation among Chinese lianoid species of Gnetum L. (Gnetales).…”

The complete chloroplast genome sequence of Abies nephrolepis (Pinaceae: Abietoideae)

“…It contains 114 individual genes including 68 protein encoding genes, 35 tRNA and four rRNA genes, six open reading frames, and one pseudogene. A. nephrolepis is identical to A. koreana in cp genome content and structure (Yi et al 2015). Fifty-three protein coding and 16 tRNA genes, three open reading frames, and one pseudogene are located in the LSC region, while 15 protein coding and 17 tRNA genes, four rRNA, and three open reading frames are sited in the SSC region.…”

“…A. nephrolepis shows close relationships with Abies koreana, Abies sachalinensis, Abies sibirica, and Abies veitchii. Complete cp genome sequence of Abies koreana has already been published (Yi et al 2015). Thus, analysis of cp genome structure of A. nephrolepis and close related species, as well as sequence comparison, will contribute to a better understanding of the evolutionary mode of the cp genome and marker development for using in Abies genus classification.…”