The complete chloroplast genome of Amomum tsao-ko

Abstract

Amomum tsao-ko (Zingiberaceae) is an important edible and medicinal crop. The complete chloroplast (cp) genome of A. tsao-ko was determined using Illumina sequencing platform. The size of whole cp genome was 163,648 bp, containing a small single copy (SSC) region of 15,355 bp and a large single copy (LSC) region of 88,741 bp, which were separated by a pair of inverted repeat (IRs) regions (29,776 bp). The A. tsao-ko cp genome contained 133 genes, including eight ribosomal RNA genes (4 rRNA species), 38 transfer RNA genes (30 tRNA species) and 87 protein-coding genes (79 PCG species). The overall GC content of A. tsao-ko cp genome is 36.02%. To investigate the evolution status of A. tsao-ko, as well as Zingiberales, a phylogenetic tree with A. tsao-ko and other 16 species was constructed based on their complete chloroplast genomes. Phylogenetic analysis revealed that A. tsao-ko was closely related to Alpinia zerumbet.

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)

“…Based on NR alignment results, most of the unigenes were annotated to Musa acuminata (80.4% similarity), similar to the report in Curcuma alismatifolia (Zingiberaceae family) (80.4% similarity) [ 42 ]. Zingiberaceae ( A. tsaoko ) and Musaceae ( Musa acuminata ) belong to Zingiberacea, and both are tropical plants, which may explain the large number of homologous genes between them [ 48 ]. In addition, 8.3% of the homologous sequences have not been matched, which may because some unigene fragments are too small to match a single data sequence.…”

“…To date, there are only a few reports about molecular markers in A. tsaoko [1,17,35]. Recently, 123 SSRs were identified in the A. tsaoko chloroplast genome; the mean density of SSR loci is up to 1/1.33 kb; however, they have not been validated for A. tsaoko [48]. In recent years, the use of transcriptome data to obtain sequences containing microsatellites, and the study of their genetic diversity has been successfully reported [52][53][54].…”

Amomum tsao-ko Crevost & Lemarié: a comprehensive review on traditional uses, botany, phytochemistry, and pharmacology

“…DNA barcoding sequence analysis revealed that ITS , matK , psbA-trnH and ycf1 could accurately distinguish A. tsao-ko from 18 other Amomum genus (Hu et al 2019b ). Chloroplast genome was also workable, as revealed by phylogenetic analysis using complete chloroplast genome of A. tsao-ko and 16 other related species (Ma and Lu 2020 ).…”

“…Genetic diversity assay based on phenotypic traits revealed that A. tsao-ko cultivars clustered into a number of large groups and sub-groups, indicating A. tsao-ko germplasm has high genetic diversity (Yan 2012 ; Yang et al 2014 ; Ma et al 2017b , a , 2020 ; Hu et al 2018a , 2019a , b ; Xie et al 2018 ; Lu et al 2019 ; Ma and Lu 2020 ). As mentioned above, the concentration of EO varied in different shape fruits (Ma et al 2008 ), which indicated that the chemical profiles may be related to morphological characteristics such as fruit forms.…”

“…In these years, DNA molecule labeling technology has been explored to study the genetic property of A. tsao-ko and the related plant species. The Internal Transcribed Spacer (ITS), Random Amplified Polymorphic DNA Markers (RAPD), Simple Sequence Repeat (SSR) or Microsatellite sequence (MS), and complete chloroplast genome of A. Tsaoko have been explored (Yan 2012 ; Yang et al 2014 ; Ma et al 2017b , a , 2020 ; Hu et al 2018a , 2019a , b ; Xie et al 2018 ; Lu et al 2019 , 2021 ; Ma and Lu 2020 ). DNA barcoding sequence analysis revealed that ITS , matK , psbA-trnH and ycf1 could accurately distinguish A. tsao-ko from 18 other Amomum genus (Hu et al 2019b ).…”