Chloroplast Genomes of Genus Tilia: Comparative Genomics and Molecular Evolution

Abstract

Tilia is a complex genus in the family Malvaceae that has high ecological and economical values. Owing to the lack of sufficient distinguishable morphological and molecular characteristics, interspecific relationships in this genus are not clear. Chloroplast (cp) genomes are small, meanwhile most angiosperms usually undergo matrilineal inheritance. Consequently, they can be used in molecular systematics and phylogenetic analyses. Here, we sequenced and assembled cp genomes from T. endochrysea, T. tomentosa, T. miqueliana, T. americana and T. cordata, and compared them with those of seven previously reported Tilia species. Similar gene contents, gene orders and GC contents existed among the 12 cp genomes, which ranged from 162,564 to 162,855 bp and encoded 113 unique genes. Abundant simple sequence repeats (119–127) and dispersed repeats (97–135) were detected in Tilia cp genomes. In total, 11 hypervariable regions were identified that could be suitable for species identification and phylogenetic studies. A phylogenetic analysis of Malvaceae based on 5 hypervariable genes (matK + ndhF + rpoB + rpoC2+ycf1) revealed that all eight subfamilies were monophyletic groups. Additionally, the genus Tilia was divided into three groups on the basis of all 521 molecular variation loci. The current study provides valuable insights into the genomic evolution of the genus Tilia.

The Impact of Magnetic Field and Gibberellin Treatment on the Release of Dormancy and Internal Nutrient Transformation in Tilia miqueliana Maxim. Seeds

“…Its flowers have medicinal uses and serve as an important source of honey. Additionally, Tilia is also considered to be timber [3]. Currently, the natural habitat of Tilia is facing threats, resulting in a sharp decline in population and individual numbers, indicating its endangered status [4].…”

Comparative analyses of complete chloroplast genomes reveal interspecific difference and intraspecific variation of Tripterygium genus

“…The structure of chloroplast genomes was divided into four parts, two copies of inverted repeat (IR) regions, a large single-copy (LSC) region, and a small single-copy (SSC) region ( Palmer, 1985 ; Xu et al., 2023 ). The chloroplast genome was highly conserved (typically between 120 and 220 kb) and had relatively moderate evolutionary rate, which could provide vital information for the classification and phylogenetic relationship construction among species ( Yan et al., 2022 ).…”