Comparative Chloroplast Genomics of The Genus Taxodium 

Abstract Background: Chloroplast(cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood.Results: We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the three cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat(TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Ycf1 was the only one gene that has an indel in CDS, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes. Conclusions: This study would advance our understanding of the complexity, dynamics, and evolution of cp genome in Cupressophytes.