Abstract
Kenaf (Hibiscus cannabinus) is one of the most fast-growing bast in the world and belongs to the family Malvaceae. However, the systematic classification and chloroplast (cp) genome of kenaf has not been reported to date. In this study, we sequenced the cp genome of kenaf and conducted phylogenetic and comparative analyses in the family of Malvaceae. The sizes of H. cannabinus cp genomes were 162,903 bp in length, containing 113 unique genes (79 protein-coding genes, four rRNA genes, and 30 tRNA genes). Phylogenetic analysis indicated that the cp genome sequence of H. cannabinus has closer relationships with Talipariti hamabo and Abelmoschus esculentus than with Hibiscus syriacus, which disagrees with the taxonomical relationship. Further analysis obtained a new version of the cp genome annotation of H. syriacus and found that the orientation variation of small single copy (SSC) region exists widely in the family of Malvaceae. The highly variable ycf1 and the highly conserved gene rrn32 were identified among the family of Malvaceae. In particular, the explanation for two different SSC orientations in the cp genomes associated with phylogenetic analysis is discussed. These results provide insights into the systematic classification of the Hibiscus genus in the Malvaceae family.
Highlights
Chloroplast, a type of plastid characterized by its double-layer membrane and thylakoid structures, contains a high concentration of chlorophyll and is the site for the cell to conduct photosynthesis (Mustardy et al, 2008; Schattat et al, 2011), through which light energy in photons is received and converted into chemical energy via redox reactions (Jagendorf and Uribe, 1966; Neuhaus and Emes, 2003) to sustain life on earth by providing food, clothing, fuel, and oxygen (Jin and Daniell, 2015)
The contigs were assembled with PE150 reads using SPAdes 3.6.1 (Bankevich et al, 2012) and SOAP denovo2 (Luo et al, 2015), respectively, and the contigs derived from the cp genome were identified by the local Blast program using Arabidopsis and Rice cp genomes as the reference (Altschul et al, 1997)
The complete cp genome of H. cannabinus is 162903 bp in size, including a pair of inverted repeats (IRs) (26533 bp each) that separate the rest of genome sequences into two single-copy regions: a large-single-copy region (LSC) region (90351 bp in length) and a small-singlecopy region (SSC) region (19486 bp in length)
Summary
Chloroplast (cp), a type of plastid characterized by its double-layer membrane and thylakoid structures, contains a high concentration of chlorophyll and is the site for the cell to conduct photosynthesis (Mustardy et al, 2008; Schattat et al, 2011), through which light energy in photons is received and converted into chemical energy via redox reactions (Jagendorf and Uribe, 1966; Neuhaus and Emes, 2003) to sustain life on earth by providing food, clothing, fuel, and oxygen (Jin and Daniell, 2015). Cp genomes of land plants contain 110–113 distinct genes, the majority of which encode proteins involved in photosynthesis (approximately 79), and the remainder of which encode transfer RNAs (approximately 30) and ribosome RNAs (4) (Jansen et al, 2005; Dong et al, 2013b; Daniell et al, 2016). Cp genomes are the most conserved in DNA sequences, organization, and structure compared with nuclear and mitochondrial genomes. For these reasons, the cp genomes were widely used for the phylogenetic analysis among the plant species. Wu et al (2017) elucidate the evolutionary relationships in Commelinids based on the sequences of 58 shared cp protein-coding genes (Wu et al, 2017), and Shen et al (2017) revealed a sister relationship between A. annua and A. fukudo based on sequence divergence analysis of five Asteraceae species (Shen et al, 2017)
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