The complete chloroplast genome sequence of Korean Lonicera japonica and intra-species diversity

Lonicera oblata , a critically endangered species endemic to North China with about 30 wild individuals, has long been ignored for conservation since its publication because of little attention on its living situation. In this study, we characterized the complete chloroplast (cp) genome of L. oblata . The cp genome was 155,481 bp in length, included a large single-copy (LSC) region of 89,139 bp, a small single-copy (SSC) region of 18,676 bp, and two inverted repeat (IR) regions of 23,833 bp each. The genome contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic position of L. oblata was also investigated based on cp genome phylogeny of Lonicera representatives. This study is valuable for molecular phylogenetic study and conservation of Lonicera and related taxa.

“… 2012 ) with Lonicera japonica (Kang et al. 2018 ) as a reference sequence. The assembled chloroplast genome was then annotated using the Plann (Huang and Cronk 2015 ).…”

mentioning

confidence: 99%

The complete chloroplast genome of Lonicera oblata, a critically endangered species endemic to North China

Zhu

Shen

et al. 2019

“…In summary, almost all of the mutations (66/68) in coding regions were substitution mutations, while 76/128 (59%) substitutions and 52/128 (41%) indels in IGS, 13/26 (50%) substitutions and indels respectively in intron. The comparison results indicated higher intra-species diversity such as Panax ginseng and Lonicera japonica (Kim et al 2015;Kang et al 2018).…”

Section: Lindera; Complete Chloroplast Genome Lauraceae Phylogenymentioning

confidence: 96%

The complete chloroplast genome sequence of China Lindera praecox (Lauraceae) and intra-species diversity

Dong

2021

Lindera praecox is a signature composition in the broadleaved deciduous forest of East China and Japan. Presently, the complete chloroplast (cp) genome of this species was sequenced, assembled, and annotated. It is 152,818 bp in length and encodes 85 protein-coding genes, 36 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated intraspecific varieties within L. praecox species collected in China and Japan. This chloroplast genome sequencing offers genetic background for resources conservation and phylogenetic studies.

“…Co., Ltd. ( http://oebiotech.bioon.com.cn/ , Shanghai, China). We used Map function of Geneious R11 (Kearse et al 2012 ) to select chloroplast reads using published chloroplast genome of L. japonica as reference (Kang et al 2018 ). Then, these filtered reads were de novo assembled with Geneious R11.…”

mentioning

confidence: 99%

Characterization of the complete chloroplast genome of a subalpine deciduous shrub Lonicera angustifolia var. myrtillus (Caprifoliaceae)

Zhu

et al. 2021

The genus Lonicera (Caprifoliaceae) is of great economical significance. It has been taxonomically studied frequently in history, while phylogenetic relationships intra the genus are still obscure. Here, we reported the first species complete chloroplast genome sequence in the section Isoxylosteum, Lonicera angustifolia var. myrtillus. It is 156,222 bp in length, comprising a large single-copy (LSC) region of 89,838 bp, a small single-copy (SSC) region of 19,211 bp, and a pair of inverted repeats (IRs) of 23,509 bp. In L. angustifolia var. myrtillus chloroplast genome, a total of 114 functional genes were identified, with an overall GC content of 38.4%. The phylogenetic relationships of Lonicera based on maximum-likelihood (ML) showed that L. angustifolia var. myrtillus is most closely related to L. nervosa in section Isika. Our study contributes to the molecular phylogenetic studies of Lonicera and Caprifoliaceae.