Abstract
BackgroundChloroplast (cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood.ResultsWe determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613 bp 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 3 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. Hypothetical cp open reading frame 1(Ycf1) was the only one gene that has an indel in coding DNA sequence, 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.ConclusionsThis study added new evidence for the role of repeats in the dynamics mechanism of cp genome mutation and rearrangement. Moreover, the information of TRs and hypervariable regions would provide reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure and biodiversity for the genus Taxodium and Cupressophytes.
Highlights
Chloroplast genome information would facilitate the development and utilization of Taxodium resources
Sequencing of Taxodium plastid genomes Illumina 150-bp paired-end sequencing of long-range PCR-amplified plastid DNA generated 5045–6946 Mb clean reads for the three sampled Taxodium species (Table 1)
Using the combination of de novo and reference-guided assembly, we obtained complete plastid nucleotide sequences for all three species
Summary
Chloroplast (cp) genome information would facilitate the development and utilization of Taxodium resources. Cp genome characteristics of Taxodium were poorly understood. Taxodium belongs to the family Cupressaceae, is native to North America and Mexico, and contains three tax: bald cypress, pond cypress and montezuma cypress. There have been continuous debates concerning the taxonomy of these three taxa as one, two, or three species from the nineteenth century to the present [1,2,3]. We temporarily consider treating them as three species. Taxodium have strong resistance to biotic and abiotic stresses, and their life span can be as long as thousands of years [4]. As an semi-autonomous replication organelles, the chloroplast genome has some unique advantages compared with nuclear and mitochondrion genome [5].
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