Comparitive Analysis of the Chloroplast Genomes of Three Houpoea Plants

Abstract

The genus Houpoea belongs to the family Magnoliaceae, and the species in this genus have important medicinal values. However, the investigation of the correlation between the evolution of the genus and its phylogeny has been severely hampered by the unknown range of species within the genus and the paucity of research on its chloroplast genome. Thus, we selected three species of Houpoea: Houpoea officinalis var officinalis (OO), Houpoea officinalis var. biloba (OB), and Houpoea rostrata (R). With lengths of 160,153 bp (OO), 160,011 bp (OB), and 160,070 bp (R), respectively, the whole chloroplast genomes (CPGs) of these three Houpoea plants were acquired via Illumina sequencing technology, and the findings were annotated and evaluated. These three chloroplast genomes were revealed by the annotation findings to be typical tetrads. A total of 131, 132, and 120 different genes were annotated. The CPGs of the three species had 52, 47, and 56 repeat sequences, which were primarily found in the ycf2 gene. A useful tool for identifying species is the approximately 170 simple sequence repeats (SSRs) that have been found. The border area of the reverse repetition region (IR) was studied, and it was shown that across the three Houpoea plants, it is highly conservative, with only changes between H. rostrata and the other two plants observed. Numerous highly variable areas (rps3-rps19, rpl32-trnL, ycf1, ccsA, etc.) have the potential to serve as the barcode label for Houpoea, according to an examination of mVISTA and nucleotide diversity (Pi). Phylogenetic relation indicates that Houpoea is a monophyletic taxon, and its genus range and systematic position are consistent with the Magnoliaceae system of Sima Yongkang-Lu Shugang, including five species and varieties of H. officinalis var. officinalis, H. rostrata, H. officinalis var. biloba, Houpoea obovate, and Houpoea tripetala, which evolved and differentiated from the ancestors of Houpoea to the present Houpoea in the above order. This study provides valuable information on the genus Houpoea, enriches the CPG information on Houpoea genus, and provides genetic resources for the further classification of and phylogenetic research on Houpoea.

Comparative Analysis of the Chloroplast Genomes of Eight Species of the Genus Lirianthe Spach with Its Generic Delimitation Implications

“…Early differentiated lineages, like those found in the Magnoliaceae, have a greater GC content [31]. Compared to the median GC content of 35% in most angiosperms, plants of the genus Houpoea N. H. Xia & C. Y. Wu have a higher GC content of around 39.2% [32], which is almost identical to the GC content of 39.3% in the Lirianthe species in this study. The GC content in the IR region of all Lirianthe species is notably high (43.2%), and alignment is increasingly conducted using chloroplast genome-scale data, with similar findings in other plants like Carthamus (43.2%) [33] and Cypripedium (42.7%) [34], potentially due to the inclusion of four highly conserved rRNA genes with high GC content (Figure 1).…”

“…SSR markers have been widely used in population genetics research due to their reliability and high variability. In this study, a small amount of SSR markers were detected, with about 170 in Houpoea species [32] and 246 in Bougainvillea spectabilis [35], while our findings indicated only 42~49 SSRs. The primary explanation is the use of different search parameters, as Carthamus species can only recognize 36-40 SSRs [33] when the same parameters (1-10 2-6 3-5 4-5 5-5 6-5) are applied.…”

“…The analysis of CPG DNA polymorphism is a proven approach to detecting mutation hotspots, which can function as distinct DNA barcodes. Two of the ten genes or DNA segments with the highest assessment of nucleotide diversity detected in this study, rpl32-trnL and petA-psbJ , are also present in the genus Houpoea [ 32 ], which also belongs to the Magnoliaceae family. trnH-psbA is one of the early recommended plant DNA barcodes [ 37 ] and was also the second most polymorphic fragment in this study.…”

Complete Chloroplast Genomes and the Phylogenetic Analysis of Three Native Species of Paeoniaceae from the Sino-Himalayan Flora Subkingdom

“…Vascular plant chloroplast genomes usually exhibit the contraction or expansion of boundaries within different genera or even within the same genus, which is the main factor leading to variations in the length and number of genes in various species [ 35 , 36 , 37 ]. The LSC/IRb boundary was generally located on the rps19 gene in nine Paeoniaceae species, except for P. rockii , where the expansion of the IR region resulted in the rpl2 gene being inside the IRb.…”

“…The trnH genes were shifted to varying degrees to the IRa region, and expansion of the IR also resulted in partially replicated ycf1 genes being in the IRb region, thus generating the pseudogene ycf1 at the IRb/SSC boundary. Most land plants always have pseudogenes in their chloroplast genomes at the SSC/IRa boundary [ 36 , 37 ].…”