Dataset Information

The complete chloroplast genome of Catalpa fargesii Bur. f. duclouxii (Dode) Gilmour.

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.

SUBMITTER: Sun J

PROVIDER: S-EPMC7954416 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundAssociation study is a powerful means for identifying molecular markers, such as single-nucleotide polymorphisms (SNPs) associated with important traits in forest trees. Catalpa fargesii Bur is a valuable commercial tree in China and identifying SNPs that associate with wood property would make a foundation of the marker-assisted breeding in the future. However, related work has not been reported yet.ResultsWe cloned a 2887 bp long sucrose synthase (SUS) gene from the genome of C. fargesii, which is a key enzyme in sucrose metabolism and also associated to wood formation in trees, coding 806 amino acids that expressed mainly in young branches, xylem, and leaves according to real-time quantitative PCR. Then we identified allelic variations of CfSUS associated with nine wood quality associated traits in Catalpa fargesii Bur. Totally, 135 SNPs were identified through cloning and sequencing the CfSUS locus from a mapping population (including 93 unrelated individuals) and 47 of which were genotyped as common SNPs (minor allele frequency > 5%) in the association population that comprised of 125 unrelated individuals collected from main distribution area. Nucleotide diversity and linkage disequilibrium (LD) analysis showed CfSUS has a relative low SNP diversity (πT = 0.0034) and low LD (r2 dropped below 0.1 within 1600 bp). Using the association analysis, we found 11 common SNPs and 14 haplotypes were significantly associated with the traits (false discovery rate, Q<0.1), explaining 3.21-12.41% of the phenotypic variance. These results provide molecular markers above associated with wood basic density, pore rate, and six other traits of wood, which have potential applications in breeding of Catalpa fargesii Bur.ConclusionWe first cloned a SUS gene in C. fargesii, then identified several SNPs and haplotypes that associated with wood properties within this gene, suggesting CfSUS participates in the wood formation of C. fargesii. Moreover, molecular markers we identified in this study may be applied into marker-assisted breeding of C. fargesii in the future.

Dataset Information

The complete chloroplast genome of Catalpa fargesii Bur. f. duclouxii (Dode) Gilmour.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets