The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae

Abstract

Glyptostrobus pensilis, belonging to the monotypic genus Glyptostrobus (Family: Cupressaceae), is an ancient conifer that is naturally distributed in low-lying wet areas. Here, we report the complete chloroplast (cp) genome sequence (132,239 bp) of G. pensilis. The G. pensilis cp genome is similar in gene content, organization and genome structure to the sequenced cp genomes from other cupressophytes, especially with respect to the loss of the inverted repeat region A (IRA). Through phylogenetic analysis, we demonstrated that the genus Glyptostrobus is closely related to the genus Cryptomeria, supporting previous findings based on physiological characteristics. Since IRs play an important role in stabilize cp genome and conifer cp genomes lost different IR regions after splitting in two clades (cupressophytes and Pinaceae), we performed cp genome rearrangement analysis and found more extensive cp genome rearrangements among the species of cupressophytes relative to Pinaceae. Additional repeat analysis indicated that cupressophytes cp genomes contained less potential functional repeats, especially in Cupressaceae, compared with Pinaceae. These results suggested that dynamics of cp genome rearrangement in conifers differed since the two clades, Pinaceae and cupressophytes, lost IR copies independently and developed different repeats to complement the residual IRs. In addition, we identified 170 perfect simple sequence repeats that will be useful in future research focusing on the evolution of genetic diversity and conservation of genetic variation for this endangered species in the wild.

Development of chloroplast microsatellite markers for Glyptostrobus pensilis (Cupressaceae)

“…We searched the complete chloroplast genome of G. pensilis (Hao et al., ; GenBank accession number ) for microsatellite loci exhibiting a minimum of eight repeats as these loci are likely to exhibit a higher level of polymorphism (Ueno et al., ). For loci with a minimum of eight repeats, primers were designed using the online software Primer3Plus (Untergasser et al., ) using default parameters.…”

“…Glyptostrobus pensilis (Staunton ex D. Don) K. Koch, the only extant species in the genus Glyptostrobus Endl., is a relict conifer in the family Cupressaceae (Hao et al., ). In China, it is mainly distributed in the Pearl River delta region of Guangdong Province, the central region of Fujian Province, the lower reaches of the Minjiang River, and northeastern Jiangxi Province (Li and Xia, ).…”

“…and designed for use in Pinaceae species (Vendramin et al., ). In this study, we developed new species‐specific chloroplast microsatellite loci using the complete chloroplast genome of G. pensilis (Hao et al., ). Additionally, we tested the transferability of these loci in four related species: Cryptomeria japonica (Thunb.…”

Characterization of the complete chloroplast genome of Malus baccata var. xiaojinensis

“…Therefore, the antiiron deficiency characteristics will make it the most valued rootstock resource in the future. Besides, the chloroplast genome has shown great potential for solving phylogenetic problems (Hao et al 2016) and is applicable for elucidating the taxonomic characteristics of the species and origin of the hybrid progeny (Jansen et al 2007;Givnish et al 2010). The comparative analysis of the cp genomes toward related species helps to understand the relationship between the important traits under the control of plastid genome (Liu et al 2013;Yan et al 2019).…”

Development of microsatellite markers for a monotypic and globally endangered species, Glyptostrobus pensilis (Cupressaceae)

“…These markers are also cross‐amplified in Taxodium distichum (L.) Rich. (Appendix ), the phylogenetically most closely related species in Cupressaceae (Hao et al., ).…”