Comparative Analysis of the Complete Chloroplast Genome of Four Endangered Herbals of Notopterygium

Abstract

Notopterygium H. de Boissieu (Apiaceae) is an endangered perennial herb endemic to China. A good knowledge of phylogenetic evolution and population genomics is conducive to the establishment of effective management and conservation strategies of the genus Notopterygium. In this study, the complete chloroplast (cp) genomes of four Notopterygium species (N. incisum C. C. Ting ex H. T. Chang, N. oviforme R. H. Shan, N. franchetii H. de Boissieu and N. forrestii H. Wolff) were assembled and characterized using next-generation sequencing. We investigated the gene organization, order, size and repeat sequences of the cp genome and constructed the phylogenetic relationships of Notopterygium species based on the chloroplast DNA and nuclear internal transcribed spacer (ITS) sequences. Comparative analysis of plastid genome showed that the cp DNA are the standard double-stranded molecule, ranging from 157,462 bp (N. oviforme) to 159,607 bp (N. forrestii) in length. The circular DNA each contained a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs). The cp DNA of four species contained 85 protein-coding genes, 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes, respectively. We determined the marked conservation of gene content and sequence evolutionary rate in the cp genome of four Notopterygium species. Three genes (psaI, psbI and rpoA) were possibly under positive selection among the four sampled species. Phylogenetic analysis showed that four Notopterygium species formed a monophyletic clade with high bootstrap support. However, the inconsistent interspecific relationships with the genus Notopterygium were identified between the cp DNA and ITS markers. The incomplete lineage sorting, convergence evolution or hybridization, gene infiltration and different sampling strategies among species may have caused the incongruence between the nuclear and cp DNA relationships. The present results suggested that Notopterygium species may have experienced a complex evolutionary history and speciation process.

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

“…Higher nucleotide diversity has been found in SCs compared with IRs and in noncoding regions compared with coding regions, which is in accordance with the results found for other taxa [43][44][45]63,68], although exceptions have been identified [32,69]. A cp genome has a copy-dependent repair mechanism that ensures the uniformity and stability of two IR regions in sequence and enhances the stability and conservation of the genome [70,71], which might explain the lower sequence divergence in the IRs compared with the LSC or SSC regions, because natural selection coding regions are more conserved than non-coding regions [72].…”

“…In subsequent studies, the main challenge in oak classification will be infrasectional classification. With the rapid development of sequencing technology, genomic databases are becoming increasingly vital for in-depth studies of plant phylogenetics [31,32]. However, due to the use of plastid and nuclear data, incongruent phylogenies have been observed in not only Quercus but also other genera [33][34][35].…”

Comparative Chloroplast Genomics of Endangered Euphorbia Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny

“…Previously, it was identified that the alignment of many genomes contributes and identifies mutational hotspots, which are widely used for interspecies discrimination and species-level phylogenetic studies [52]. The coding region in many previous studies has been proven to play an important role in species-level phylogenetic analyses like some of the genes, such as ycf1 in Anemopaegma [53] and rps16, psaI, psbT, psbH, petB, rpoA, and rps11 in Notopterygium [54], which were more divergent than non-coding regions.…”

Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship

“…The inconsistent results indicated that the nrITS may be affected by hybridization and incomplete lineage sorting. Plastid DNA, which is maternally inherited, is longer and has less mutation than the nuclear ITS region, so it will provide more phylogenetic information and not be interfered with by paralogous genes in the phylogenetic studies [23,78]. Therefore, plastid DNA can better reflect the evolutionary relationship.…”