Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae

Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae

The Annonaceae stands as the most species rich family in the Magnoliales, a basal group of angiosperms. Widely distributed in tropical and subtropical regions, it holds significant ecological and economic value. The plastid genome (plastome) is often employed in studies related to plant phylogenetics, comparative genomics, evolutionary biology, and genetic engineering. Nonetheless, research progress on plastid genomics in the Annonaceae has been relatively slow. In this study, we analyzed the structure and repetitive sequence features of plastomes from 28 Annonaceae species. Among them, Mitrephora tomentosa and Desmos chinensis were newly sequenced, with sizes of 160,157 bp and 192,167 bp, and GC contents of 38.3% and 38.4%, respectively. The plastome size in the Annonaceae ranged from 158,837 bp to 202,703 bp, with inverted repeat (IR) region sizes ranging from 64,621 bp to 25,861 bp. Species exhibiting expansion in the IR region showed an increase in plastome size and gene number, frequent boundary changes, different expansion modes (bidirectional or unidirectional), and an increase in repetitive sequences. Specifically, a large number of dispersed repetitive sequences lead to an increase in the size of the LSC region in Goniothalamus tamirensis. Phylogenetic analysis revealed Annonoideae and Malmeoideae as monophyletic groups and sister clades, with Cananga odorata outside of them, followed by Anaxagorea javanica. This research uncovers the structural variation characteristics of plastomes in the Annonaceae, providing valuable information for understanding the phylogeny and plastome evolution of Annonaceae.

Characterization of the complete chloroplast genome of Gastrochilus sinensis (Orchidaceae, Epidendroideae), a beautiful epiphytic orchid from China

Gastrochilus sinensis is a beautiful epiphytic orchid with high ornamental value. In this study, the first complete chloroplast genome sequence of G. sinensis was determined using next-generation sequencing (NGS). The de novo assembled chloroplast genome was 148,020 bp in length, including a pair of inverted repeat regions (IRs; 25,987 bp), a small single-copy region (SSC; 11,045 bp), and a large single-copy region (LSC; 85,001 bp). The chloroplast genome encodes 109 unique genes, including 75 protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes. The total GC content of the chloroplast genome was 36.8%. The phylogenetic analysis showed a close relationship between G. sinensis and G. formosanus species. The complete chloroplast genome provides fundamental information for genetic diversity and phylogenetic relationships in Gastrochilus.

Complete Chloroplast Genomes of Saussurea katochaete, Saussurea superba, and Saussurea stella: Genome Structures and Comparative and Phylogenetic Analyses

Saussurea plants are widely distributed in Asia and Europe; however, their complex phylogenetic relationships have led to many difficulties in phylogenetic studies and interspecific identification. In this study, we assembled, annotated, and analyzed the chloroplast genomes of three Saussurea plants: Saussurea katochaete, Saussurea superba, and Saussurea stella. The results showed that the full-length sequences of the three Saussurea plants were 152,561 bp, 151,452 bp, and 152,293 bp, respectively, which represent the typical quadripartite structure, and the genomes were relatively conserved. The gene annotation results showed that the chloroplast genomes of S. katochaete, S. superba, and S. stella were annotated with 128, 124, and 127 unique genes, respectively, which included 83, 80, and 83 protein-coding genes (PCGs), respectively, 37, 36, and 36 tRNA genes, respectively, and 8 rRNA genes. Moreover, 46, 45, and 43 SSR loci, respectively, and nine highly variable regions (rpl32-trnL-UAG, rpl32, ndhF-rpl32, ycf1, trnC-GCA-petN, trnC-GCA, rpcL, psbE-petL, and rpl16-trnG-UUG) were identified and could be used as potential molecular markers for population identification and phylogenetic study of Saussurea plants. Phylogenetic analyses strongly support the sisterhood of S. katochaete with S. superba and S. stella, and are all clustered with S. depsagensis, S. inversa, S. medusa, and S. gossipihora, of which S. gossipiphora is most closely related. Additionally, the phylogenetic results indicate a high frequency of differentiation among different species of Saussurea plants, and many different species or genera are morphologically very different from each other, which may be related to certain genetic material in the chloroplasts. This study provides an important reference for the identification of Saussurea plants and studies their evolution and phylogenetics.

Comparative Analyses of Complete Chloroplast Genomes and Karyotypes of Allotetraploid Iris koreana and Its Putative Diploid Parental Species (Iris Series Chinenses, Iridaceae)

The Iris series Chinenses in Korea comprises four species (I. minutoaurea, I. odaesanensis, I. koreana, and I. rossii), and the group includes some endangered species, owing to their high ornamental, economic, and conservation values. Among them, the putative allotetraploid, Iris koreana (2n = 4x = 50), is hypothesized to have originated from the hybridization of the diploids I. minutoaurea (2n = 2x = 22) and I. odaesanensis (2n = 2x = 28) based on morphological characters, chromosome numbers, and genome size additivity. Despite extensive morphological and molecular phylogenetical studies on the genus Iris, little is known about Korean irises in terms of their complete chloroplast (cp) genomes and molecular cytogenetics that involve rDNA loci evolution based on fluorescence in situ hybridization (FISH). This study reports comparative analyses of the karyotypes of the three Iris species (I. koreana, I. odaesanensis, and I. minutoaurea), with an emphasis on the 5S and 35S rDNA loci number and localization using FISH together with the genome size and chromosome number. Moreover, the cp genomes of the same individuals were sequenced and assembled for comparative analysis. The rDNA loci numbers, which were localized consistently at the same position in all species, and the chromosome numbers and genome size values of tetraploid Iris koreana (four 5S and 35S loci; 2n = 50; 1C = 7.35 pg) were additively compared to its putative diploid progenitors, I. minutoaurea (two 5S and 35S loci; 2n = 22; 1C = 3.71 pg) and I. odaesanensis (two 5S and 35S loci; 2n = 28; 1C = 3.68 pg). The chloroplast genomes were 152,259–155,145 bp in length, and exhibited a conserved quadripartite structure. The Iris cp genomes were highly conserved and similar to other Iridaceae cp genomes. Nucleotide diversity analysis indicated that all three species had similar levels of genetic variation, but the cp genomes of I. koreana and I. minutoaurea were more similar to each other than to I. odaesanensis. Positive selection was inferred for psbK and ycf2 genes of the three Iris species. Phylogenetic analyses consistently recovered I. odaesanensis as a sister to a clade containing I. koreana and I. minutoaurea. Although the phylogenetic relationship, rDNA loci number, and localization, together with the genome size and chromosome number of the three species, allowed for the inference of I. minutoaurea as a putative maternal taxon and I. odaesanensis as a paternal taxon, further analyses involving species-specific molecular cytogenetic markers and genomic in situ hybridization are required to interpret the mechanisms involved in the origin of the chromosomal variation in Iris series Chinenses. This study contributes towards the genomic and chromosomal evolution of the genus Iris.