Abstract
In this study, we reported and characterized the complete chloroplast genome sequence of Catalpa fargesii Bur. f. duclouxii (Dode) Gilmour. The chloroplast genome was determined to be 158,250 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 84,929 bp and 12,663 bp, respectively, which were separated by a pair of 30,329 bp inverted repeat (IR) regions. The genome is predicted to contain 121 genes, including 78 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. The overall GC content of the genome is 38.1%. A phylogenetic tree reconstructed by 12 chloroplast genomes reveals that C. fargesii is mostly related to Catalpa. ovata and Catalpa. speciosa. This study identified the unique characteristics of the C. fargesii cp genome, which will provide a theoretical basis for species identification and biological research.
Keywords: Catalpa fargesii, chloroplast genome, phylogenetic analysis
Catalpa fargesii Bur. f. duclouxii (Dode) Gilmour belongs to the Catalpa genus of the Bignoniaceae family and is native to China. C. fargesii is distributed within the Yunnan-Guizhou plateau. It is recognized for its straight stems and high-quality timber, which is of high density and has high bending strength and hardness. These characteristics make it a valuable material for furniture production (Xiao et al. 2019). Here, we characterized the complete chloroplast (cp) genome sequence of C. fargesii, a complete chloroplast genome sequence from the genus Catalpa genus, based on the genome skimming sequencing data. Our data will contribute to our understanding of the genetic resources and evolution of C. fargesii based on the diversity in its chloroplast genome and also facilitate the exploration, utilization, and application of conservation genetics of this species.
Chloroplasts are essential organelles in plant cells that play important roles in photosynthesis, carbon fixation, and synthesis of pigments, starch, fatty acids, and amino acids (Daniell et al. 2016). Genome sequencing is frequently used to analyze phylogenetic relationships, genetic diversity, and evolutionary studies (Jose et al. 2015). Three independent genomes offering genetic information are those of the chloroplast, mitochondrion, and nucleus. Compared with the nuclear genome, the chloroplast genome has a small size, single parental inheritance, low nucleotide substitution rate, haploid nature, and highly conserved genomic structure (Wei et al. 2005). Therefore, the chloroplast genome has been considered the perfect model for diversity and evolution studies.
The fresh leaves of C. fargesii were collected from Southwest Forestry University Kunming, China. (Yunnan, China; geospatial coordinates: 102°45′41″E, 25°04′00″N). The voucher specimens of C. fargesii were deposited at the herbarium of Southwest Forestry University (Voucher number: SWFU-2020-DQ01), and DNA samples were stored at the Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China. The total genomic DNA was extracted by using the Magnetic beads plant genomic DNA preps Kit (TSINGKE Biological Technology, Beijing, China). The genome skimming sequencing was conducted on the Illumina HiSeq 2000 Sequencing platform. Genome annotation was assembled with the program Geneious R8 (Biomatters Ltd, Auckland, New Zealand). Finally, the chloroplast DNA sequence with complete annotation information was submitted to GenBank with accession number MW043481.
The complete cp genome of C. fargesii is 158,250 bp in length, was 105 bp smaller than that of Catalpa. ovata (158,355 bp, MT186670). It was also 11 bp larger than Catalpa. Speciosa (158,239 bp, MT319918). The chloroplast genome has the usual quadripartite structure, featuring a LSC region (large single-copy region 84,929 bp), a SSC region (small single-copy region 12,663 bp), and a pair of IR (inverted repeats 30,329 bp). The overall GC content is 38.10% (LSC, 36.43%; SSC, 33.60%; IR, 41.30%). respectively. A total of 121 functional genes were contained in the cp genome, including 78 protein-coding genes, 35 tRNA genes, and 8 rRNA genes.
To determine the phylogenetic location of C. fargesii with respect to the other Bignoniaceae with fully sequenced chloroplast genomes, the complete C. fargesii chloroplast was used to reconstruct the phylogenetic relationships. With the chloroplast of Sesamum indicum (Sesamum Pedaliaceae KC569603) and S. indicum (Sesamum Pedaliaceae JN637766) as an out-group, 12 chloroplast genome sequences of Bignoniaceae, including Crescentia cujete (KT182634), Spathodea campanulata (MN106255), Oroxylum indicum (MN933930), C. ovata (MT186670), C. speciosa (MT319818), Podranea ricasoliana (MG831877), Tecomaria capensis (MG831880), Incarvillea arguta (MG763885), and Sesamum indicum (KC569603), aligned by the MAFFT version 7 programme (Katoh and Standley 2013). A maximum-likelihood analysis based on the GTR + F+R2 model was performed with iqtree version 1.6.7 using 1000 bootstrap replicates (Nguyen et al. 2015). The phylogenetic tree reveals that C. ovata and C. speciosa is most closely related to C. fargessi (Figure 1), the chloroplast genome of C. fargesii has enough genetic information to distinguish it from other plants (Wang et al. 2020). This information is crucial for the correct identification of C. fargesii and provides valuable genetic resources for the future development of chloroplast derived molecular markers. Our results provide fundamental information for further evolutionary and phylogenetic researches of C. fargesii. The chloroplast genome will contribute to the research and conservation of C. fargesii.
Figure 1.
Phylogenetic relationships among 12 complete chloroplast genomes (C. fargesii in this study and 11 previously reported species). Bootstrap values based on 1000 replicates were provided near branches. The ML phylogenetic tree for C. fargesii based on other 11 species (three in Catalpa, one in Crescentia, one in Spathodea, one in Oroxylum, one in Pyrostegia, one in Podranea, one in Tecomaria, one in Incarvillea, one in Sesamum L., and one in Sesamum) chloroplast genomes.
Funding Statement
The study was supported by the National Natural Science Foundation of China [Grant Number: 31760204 & 31860203] and the Youth Top Talent Program of the Ten Thousand Talents Program of Yunnan Province.
Disclosure statement
No potential conflict of interest was reported by the author(s).
Data availability statement
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. MW043481. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA685030, SUB8727632, and SAMN17075338 respectively.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. MW043481. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA685030, SUB8727632, and SAMN17075338 respectively.