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.

Full-length transcriptome analysis of Ophioglossum vulgatum: effects of experimentally identified chloroplast gene clusters on expression and evolutionary patterns.

Genes with similar or related functions in chloroplasts are often arranged in close proximity, forming clusters on chromosomes. These clusters are transcribed coordinated to facilitate the expression of genes with specific function. Our previous study revealed a significant negative correlation between the chloroplast gene expression level of the rare medicinal fern Ophioglossum vulgatum and its evolutionary rates as well as selection pressure. Therefore, in this study, we employed a combination of SMRT and Illumina sequencing technology to analyze the full-length transcriptome sequencing of O. vulgatum for the first time. In particular, we experimentally identified gene clusters based on transcriptome data and investigated the effects of chloroplast gene clustering on expression and evolutionary patterns. The results revealed that the total sequenced data volume of the full-length transcriptome of O. vulgatum amounted to 71,950,652,163 bp, and 110 chloroplast genes received transcript coverage. Nine different types of gene clusters were experimentally identified in their transcripts. The chloroplast cluster genes may cause a decrease in non-synonymous substitution rate and selection pressure, as well as a reduction in transversion rate, transition rate, and their ratio. While expression levels of chloroplast cluster genes in leaf, sporangium, and stem would be relatively elevated. The Mann-Whitney U test indicated statistically significant in the selection pressure, sporangia and leaves groups (P < 0.05). We have contributed novel full-length transcriptome data resources for ferns, presenting new evidence on the effects of chloroplast gene clustering on expression land evolutionary patterns, and offering new theoretical support for transgenic research through gene clustering.

Copy number variation of the restorer Rf4 underlies human selection of three-line hybrid rice breeding.

Cytoplasmic male sterility (CMS) lines are important for breeding hybrid crops, and utilization of CMS lines requires strong fertility restorer (Rf) genes. Rf4, a major Rf for Wild-Abortive CMS (CMS-WA), has been cloned in rice. However, the Rf4 evolution and formation of CMS-WA/Rf system remain elusive. Here, we show that the Rf4 locus emerges earlier than the CMS-WA gene WA352 in wild rice, and 69 haplotypes of the Rf4 locus are generated in the Oryza genus through the copy number and sequence variations. Eight of these haplotypes of the Rf4 locus are enriched in modern rice cultivars during natural and human selections, whereas non-functional rf4i is preferentially selected for breeding current CMS-WA lines. We further verify that varieties carrying two-copy Rf4 haplotype have stronger fertility restoration ability and are widely used in three-line hybrid rice breeding. Our findings increase our understanding of CMS/Rf systems and will likely benefit crop breeding.

Chloroplast gene expression level is negatively correlated with evolutionary rates and selective pressure while positively with codon usage bias in Ophioglossum vulgatum L.

BACKGROUND: Characterization of the key factors determining gene expression level has been of significant interest. Previous studies on the relationship among evolutionary rates, codon usage bias, and expression level mostly focused on either nuclear genes or unicellular/multicellular organisms but few in chloroplast (cp) genes. Ophioglossum vulgatum is a unique fern and has important scientific and medicinal values. In this study, we sequenced its cp genome and transcriptome to estimate the evolutionary rates (dN and dS), selective pressure (dN/dS), gene expression level, codon usage bias, and their correlations. RESULTS: The correlation coefficients between dN, dS, and dN/dS, and Transcripts Per Million (TPM) average values were -0.278 (P = 0.027 < 0.05), -0.331 (P = 0.008 < 0.05), and -0.311 (P = 0.013 < 0.05), respectively. The codon adaptation index (CAI) and tRNA adaptation index (tAI) were significantly positively correlated with TPM average values (P < 0.05). CONCLUSIONS: Our results indicated that when the gene expression level was higher, the evolutionary rates and selective pressure were lower, but the codon usage bias was stronger. We provided evidence from cp gene data which supported the E-R (E stands for gene expression level and R stands for evolutionary rate) anti-correlation.

The complete chloroplast genome of Miliusa glochidioides (Annonaceae) and phylogenetic analysis.

The chloroplast (cp) genome of Miliusa glochidioides has been fully sequenced. The cp genome of this species has a typical quadripartite structure comprised of four parts: a large single copy (LSC; 88,782 bp) region, a small single copy (SSC; 18,949 bp) region, and two inverted repeat (IR; 26,029 bp each) regions. The full length of the cp genome is 159,789 bp; its GC content is 36.7%, and it encodes a total of 129 genes including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Among the protein-coding genes, nine (rps16, rpl2, rpl16, atpF, rpoC1, petB, petD, ndhA, and ndhB) contain one intron, and three (rps12, clpP, and ycf3) have two introns. A maximum-likelihood (ML) phylogenetic tree shows that M. glochidioides is a sister to Chieniodendron hainanense.

Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein-coding genes.

Plastid genomes (plastomes) have a quadripartite structure, but some species have drastically reduced or lost inverted repeat (IR) regions. IR regions are important for genome stability and the evolution rate. In the evolutionary process of gymnosperms, the typical IRs of conifers were lost, possibly affecting the evolutionary rate and selection pressure of genomic protein-coding genes. In this study, we selected 78 gymnosperm species (51 genera, 13 families) for evolutionary analysis. The selection pressure analysis results showed that negative selection effects were detected in all 50 common genes. Among them, six genes in conifers had higher ω values than non-conifers, and 12 genes had lower ω values. The evolutionary rate analysis results showed that 9 of 50 common genes differed between conifers and non-conifers. It is more obvious that in non-conifers, the rates of psbA (trst, trsv, ratio, dN, dS, and ω) were 2.6- to 3.1-fold of conifers. In conifers, trsv, ratio, dN, dS, and ω of ycf2 were 1.2- to 3.6-fold of non-conifers. In addition, the evolution rate of ycf2 in the IR was significantly reduced. psbA is undergoing dynamic change, with an abnormally high evolution rate as a small portion of it enters the IR region. Although conifers have lost the typical IR regions, we detected no change in the substitution rate or selection pressure of most protein-coding genes due to gene function, plant habitat, or newly acquired IRs.

Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae.

The simple sequence repeats (SSRs) of plant chloroplasts show considerable genetic variation and have been widely used in species identification and phylogenetic relationship determination. Whether chloroplast genome SSRs can be used to classify Cyatheaceae species has not yet been studied. Therefore, the chloroplast genomes of eight Cyatheaceae species were sequenced, and their SSR characteristics were compared and statistically analyzed. The results showed that the chloroplast genome structure was highly conserved (genome size: 154,046-166,151 bp), and the gene content (117 genes) and gene order were highly consistent. The distribution characteristics of SSRs (number, relative abundance, relative density, GC content) showed taxon specificity. The primary results were the total numbers of SSRs and mononucleotides: Gymnosphaera (61-67 and 40-47, respectively), Alsophila (121-122 and 95-96), and Sphaeropteris (102-103 and 77-80). Statistical and clustering analyses of SSR characteristics showed that their distribution was consistent with the recent classification of Cyatheaceae, which divided the eight Cyatheaceae species into three genera. This study indicates that the distribution characteristics of Cyatheaceae chloroplast SSRs can provide useful phylogenic information at the genus level.

The complete chloroplast genome of Ophioglossum vulgatum L. (Ophioglossaceae) and phylogenetic analysis.

Ophioglossum vulgatum is a rare and ancient fern. In this study, the chloroplast (cp) genome of O. vulgatum was completely sequenced. The genome size is 138,562 bp, which contains a large single-copy (LSC) region with 99,351 bp, a small single-copy (SSC) region with 19,661 bp, and two inverted repeats (IR) regions of 9,775 bp each. Additionally, the overall GC content is 42.14%. It encodes a total 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The Bayesian phylogenetic tree shows that O. vulgatum and O. californicum formed a monophyletic branch. This study can provide a molecular basis for studying the phylogenetic genomics and population variation of Ophioglossaceae.

Molecular evolution and SSRs analysis based on the chloroplast genome of Callitropsis funebris.

Chloroplast genome sequences have been used to understand evolutionary events and to infer efficiently phylogenetic relationships. Callitropsis funebris (Cupressaceae) is an endemic species in China. Its phylogenetic position is controversial due to morphological characters similar to those of Cupressus, Callitropsis, and Chamaecyparis. This study used next-generation sequencing technology to sequence the complete chloroplast genome of Ca. funebris and then constructed the phylogenetic relationship between Ca. funebris and its related species based on a variety of data sets and methods. Simple sequence repeats (SSRs) and adaptive evolution analysis were also conducted. Our results showed that the monophyletic branch consisting of Ca. funebris and Cupressus tonkinensis is a sister to Cupressus, while Callitropsis is not monophyletic; Ca. nootkatensis and Ca. vietnamensis are nested in turn at the base of the monophyletic group Hesperocyparis. The statistical results of SSRs supported the closest relationship between Ca. funebris and Cupressus. By performing adaptive evolution analysis under the phylogenetic background of Cupressales, the Branch model detected three genes and the Site model detected 10 genes under positive selection; and the Branch-Site model uncovered that rpoA has experienced positive selection in the Ca. funebries branch. Molecular analysis from the chloroplast genome highly supported that Ca. funebris is at the base of Cupressus. Of note, SSR features were found to be able to shed some light on phylogenetic relationships. In short, this chloroplast genomic study has provided new insights into the phylogeny of Ca. funebris and revealed multiple chloroplast genes possibly undergoing adaptive evolution.

The complete chloroplast genome of Araucaria cunninghamii (Araucariaceae).

The chloroplast genome of the Araucaria cunninghamii has been completely sequenced. The genome size is 146,337 bp, and the overall GC content is 36.7%. This cp genome does not contain cannonical IRs, it encodes a total 122 genes including 82 protein-coding genes, 36 tRNA genes and four rRNA genes. Among them, eight protein-coding genes (rpl2, rpl16, petB, petD, rpoC1, atpF, ndhA and ndhB) have two exon, and two genes (rps12 and ycf3) have three exons. Also, trnI-CAU and rrn5 has two copies. The Maximum-likelihood tree shows that A. cunninghamii is sister to A. heterophylla.

Complete chloroplast genome of Sphaeropteris brunoniana (Cyatheaceae).

Illumina sequencing was employed to determine the complete chloroplast (cp) genome sequence of Sphaeropteris brunoniana (S. brunoniana), which is a relict fern. The cp genome of S. brunoniana is indeed a circular DNA molecule with 156,659 bp. It includes an inverted repeats (IRs) pair with 24,011 bp each and two single-copy regions with 86,196 bp and 22,441 bp, respectively. Additionally, the genome contains 117 unique genes encoding 85 proteins, 28 tRNAs, four rRNAs. Pseudogenes of ycf66 and trnT-UGU are also detected in this genome.Bayesian phylogenetic tree strongly supports the deduction that S. brunoniana belongs to Cyatheaceae. To date, this is the first cp genome for the genus S. brunoniana.

Complete chloroplast genome of the tree fern Alsophila podophylla (Cyatheaceae).

The chloroplast genome of the tree fern Alsophila podophylla has been completely sequenced. The genome is 166,151 bp in size and features a typical quadripartite structure with the large (LSC, 86,762 bp) and small single copy (SSC, 21,641 bp) regions separated by a pair of inverted repeats (IRs, 28,874 bp each). It encodes 133 genes including 91 protein-coding genes, 33 tRNA genes, eight rRNA genes, and one pseudogene. Maximum-likelihood tree indicates that A. podophylla is sister to A. spinulosa. This work provides a solid molecular resource for surveying phylogeny and chloroplast genomics of ferns.