Extensive Genomic Rearrangements Research Articles

Evolutionary patterns and functional effects of 3D chromatin structures in butterflies with extensive genome rearrangements

Chromosome rearrangements may distort 3D chromatin architectures and thus change gene regulation, yet how 3D chromatin structures evolve in insects is largely unknown. Here, we obtain chromosome-level genomes for four butterfly species, Graphium cloanthus, Graphium sarpedon, Graphium eurypylus with 2n = 30, 40, and 60, respectively, and Papilio bianor with 2n = 60. Together with large-scale Hi-C data, we find that inter-chromosome rearrangements very rarely disrupted the pre-existing 3D chromatin structure of ancestral chromosomes. However, some intra-chromosome rearrangements changed 3D chromatin structures compared to the ancestral configuration. We find that new TADs and subTADs have emerged across the rearrangement sites where their adjacent compartments exhibit uniform types. Two intra-chromosome rearrangements altered Rel and lft regulation, potentially contributing to wing patterning differentiation and host plant choice. Notably, butterflies exhibited chromatin loops between Hox gene cluster ANT-C and BX-C, unlike Drosophila. Our CRISPR-Cas9 experiments in butterflies confirm that knocking out the CTCF binding site of the loops in BX-C affected the phenotypes regulated by Antp in ANT-C, resulting in legless larva. Our results reveal evolutionary patterns of insect 3D chromatin structures and provide evidence that 3D chromatin structure changes can play important roles in the evolution of traits.

De novo assembly and comprehensive analysis of the mitochondrial genome of Taxus wallichiana reveals different repeats mediate recombination to generate multiple conformations

Taxus plants are the exclusive source of paclitaxel, an anticancer drug with significant medicinal and economic value. Interspecies hybridization and gene introgression during evolution have obscured distinctions among Taxus species, complicating their phylogenetic classification. While the chloroplast genome of Taxus wallichiana, a widely distributed species in China, has been sequenced, its mitochondrial genome (mitogenome) remains uncharacterized.We sequenced and assembled the T. wallichiana mitogenome using BGI short reads and Nanopore long reads, facilitating comparisons with other gymnosperm mitogenomes. The T. wallichiana mitogenome spanning 469,949 bp, predominantly forms a circular configuration with a GC content of 50.51%, supplemented by 3 minor configurations mediated by one pair of LRs and two pairs of IntRs. It includes 32 protein-coding genes, 7 tRNA genes, and 3 rRNA genes, several of which exist in multiple copies.We detailed the mitogenome's structure, codon usage, RNA editing, and sequence migration between organelles, constructing a phylogenetic tree to elucidate evolutionary relationships. Unlike typical gymnosperm mitochondria, T. wallichiana shows no evidence of mitochondrial-plastid DNA transfer (MTPT), highlighting its unique genomic architecture. Synteny analysis indicated extensive genomic rearrangements in T. wallichiana, likely driven by recombination among abundant repetitive sequences. This study offers a high-quality T. wallichiana mitogenome, enhancing our understanding of gymnosperm mitochondrial evolution and supporting further cultivation and utilization of Taxus species.

Abstract 4349: Characterization of a centrosome loss-induced tumorigenic signature in prostate epithelial cells

Abstract Prostate cancer (PCa) stands as the second leading cause of cancer death in American men, with overtreatment being common given the difficulty in distinguishing between indolent and aggressive cases. Unlike many cancers, PCa lacks hallmark mutations in key oncogenes and tumor-suppressor genes. Instead, PCa exhibit extensive genomic rearrangements and chromosomal instability (CIN). CIN occurs during PCa progression, producing ETS gene family fusions, PTEN loss and androgen receptor amplification. Importantly, the mechanism underlying CIN in PCa remains unclear. Previously, we found that cell within early-grade human primary prostate adenocarcinomas (PRAD) frequently lack centrosomes, and this frequency correlates with tumor grade. We demonstrated that transient removal of centrosomes within non-tumorigenic human prostate epithelial cells (hPrEC) induces CIN and was, strikingly, sufficient to transform subpopulations of cells capable of producing xenograft tumors in mice. To unravel the molecular mechanisms underlying this path to tumorigenesis, we isolated DNA and RNA from parental hPrECs, clonal lines subjected to transient centrosome loss, and xenograft tumor cells and performed whole genome sequencing (WGS) and bulk RNA-seq. This allowed us to characterize the genomic profiles induced by centrosome loss and to identify an associated mutational signature. We used MUTECT2 to identify single nucleotide variants. Kataegis loci were observed on multiple chromosomes in all transient centrosome removal samples. Copy number variations were also detected in these samples using FACETS and SEQUENZA. Next, we extracted the copy number (CN) signature with SigProfiler and Sigminer, comparing it to COSMIC CN signatures and WGS data from PRAD patients. Our results revealed that the transient centrosome loss signature bears similarity to CN signatures associated with chromothripsis, loss of heterozygosity, and homologous recombination repair deficiency. Patients with PRAD displaying the centrosome loss CN signature had a poorer prognosis. Additionally, our CN analysis discovered that centrosome loss induced mosaic loss of chromosome Y in our samples. To detect structural variations, we employed DELLY, MANTA, SVABA, revealing a high occurrence of both non-clustered and clustered translocations in transient centrosome loss samples. These translocations were validated in our RNA-seq data using STAR-Fusion. Ongoing analyses include inferring CNV from PCa scRNA-seq data, and determining cell populations with the centrosome loss CN-signature and their associated transcriptome features. This work unveils a comprehensive genomic profile stemming from centrosome loss and demonstrates its role in driving oncogenesis in PCa. These findings have the potential to establish centrosome loss as a hallmark in PCa stratification, and lead to a significant advancement in prostate tumor treatment. Citation Format: Jiawen Yang, Diogo de Oliveira Pessoa, John M. Ryniawec, Emily Loertscher, Anne E. Cress, Megha Padi, Gregory C. Rogers. Characterization of a centrosome loss-induced tumorigenic signature in prostate epithelial cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4349.

The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites.

Aglaia odorata, native to Guangdong, Guangxi, and Hainan provinces in China, has long been utilized as an herbal remedy in ancient China. In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. odorata, which spans a total length of 537,321 bp. Conformation of the A. odorata recombination was verified through PCR experiments and Sanger sequencing. We identified and annotated 35 protein-coding genes (PCGs), 22 tRNA genes, and 3 rRNA genes within the mitogenome. Analysis of repeated elements revealed the presence of 192 SSRs, 29 pairs of tandem repeats, and 333 pairs of dispersed repeats in the A. odorata mitogenome. Additionally, we analyzed codon usage and mitochondrial plastid DNAs (MTPTs). Twelve MTPTs between the plastome and mitogenome of A. odorata were identified, with a combined length of 2,501 bp, accounting for 0.47% of the mitogenome. Furthermore, 359 high-confidence C to U RNA editing sites were predicted on PCGs, and four selected RNA editing sites were specially examined to verify the creation of start and/or stop codons. Extensive genomic rearrangement was observed between A. odorata and related mitogenomes. Phylogenetic analysis based on mitochondrial PCGs were conducted to elucidate the evolutionary relationships between A. odorata and other angiosperms.

Genomic analysis of Ralstonia pickettii reveals the genetic features for potential pathogenicity and adaptive evolution in drinking water.

Ralstonia pickettii, the most critical clinical pathogen of the genus Ralstonia, has been identified as a causative agent of numerous harmful infections. Additionally, Ralstonia pickettii demonstrates adaptability to extreme environmental conditions, such as those found in drinking water. In this study, we conducted a comprehensive genomic analysis to investigate the genomic characteristics related to potential pathogenicity and adaptive evolution in drinking water environments of Ralstonia pickettii. Through phylogenetic analysis and population genetic analysis, we divided Ralstonia pickettii into five Groups, two of which were associated with drinking water environments. The open pan-genome with a large and flexible gene repertoire indicated a high genetic plasticity. Significant differences in functional enrichment were observed between the core- and pan-genome of different groups. Diverse mobile genetic elements (MGEs), extensive genomic rearrangements, and horizontal gene transfer (HGT) events played a crucial role in generating genetic diversity. In drinking water environments, Ralstonia pickettii exhibited strong adaptability, and the acquisition of specific adaptive genes was potentially facilitated by genomic islands (GIs) and HGT. Furthermore, environmental pressures drove the adaptive evolution of Ralstonia pickettii, leading to the accumulation of unique mutations in key genes. These mutations may have a significant impact on various physiological functions, particularly carbon metabolism and energy metabolism. The presence of virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance indicated the potential pathogenicity of Ralstonia pickettii, making it capable of causing multiple nosocomial infections. This study provides comprehensive insights into the potential pathogenicity and adaptive evolution of Ralstonia pickettii in drinking water environments from a genomic perspective.

The Presence of Ring Chromosomes in Patients with Myeloid Neoplasms Is Predictive of a Poor Outcome

Cytogenomic analysis is an important tool in the risk stratification of patients with hematologic malignancies. Complex chromosomal alterations are associated with a poor prognosis (Döhner et al., Blood 2022). Ring chromosomes (RC) are circular chromosomal structures associated with loss or gain/amplification of genetic material and are associated with poor prognosis in acute myeloid leukemias (AML) and myelodysplastic syndromes (MDS) (Rosenbaum et al., Human Path 2017). Due to their rarity, the impact of RC on response to therapy has not yet been well characterized. We further examined the significance of RC in AML, MDS and myeloproliferative neoplasms (MPN) by retrospectively analyzing records of patients identified to have RC and myeloid neoplasms at our institution between 2017 and 2023 and collected demographic, diagnostic, treatment, molecular, cytogenomic, and outcomes data. We identified 27 cases with RC with clinical data available for 25. Demographic and treatment details are described in Table 1. The most common chromosomes involved were r(11) and r(7), 6 and 4 cases respectively, followed by r(6) and r(19) with 2 cases each. The most frequently observed diagnosis was AML in 12 patients (48%) followed by MDS with 9 cases (36%) and MPN in 4 cases (16%). In 17 cases (68%) the RC was cytogenetically detected at diagnosis and was not observed in the context of prior therapy. Remarkably, mutations in TP53 were present in 14 cases (56%) and accompanied by loss of 17p (bi-allelic) in 7 cases (28%). The next most commonly observed gene mutations were in DNMT3A (7 cases), TET2 (4 cases) and ASXL1 (3 cases). In 11 cases (44%) the alterations in TP53 were not associated with prior therapy for other malignancies. The median time from prior chemotherapy to detection of the RC was 5.1 years (range 0.6 to 13.5 years). Chromothripsis (a single DNA catastrophic event resulting in extensive genomic rearrangements of one or a few chromosomes) as detected by CGH+SNP array and homogenous staining regions (autonomously replicating extra-chromosomal elements that are frequently associated with gene amplification) were observed in 3 patients each. RC were the sole genetic abnormality in 5 patients. A Kaplan-Meier analysis of median overall survival (mOS) in patients with AML and MDS with RC at diagnosis revealed that patients who received supportive care had significantly shorter mOS than patients who received hypomethylating agents (HMA), HMA/Venetoclax(VEN), or anthracycline-based chemotherapy (log rank test, p = 0.001). A significant difference in mOS between patients who received HMA alone versus HMA/VEN versus chemotherapy was not observed (11.4 vs 3.1 vs 7.3 months, p = 0.8) (Figure 1). Patients who received any of the therapies outlined above likewise demonstrated a significantly longer progression free survival (log rank test, p = 0.001). There was no effect on mOS for any of the other tested prognostic parameters, including the presence of a complex karyotype, TP53 allele status, or therapy-related neoplasm, nor for pair-wise interactions between those categories and first-line therapies (p > 0.05 for all tested associations). These data represent a large single-institution cohort of patients with RC and is the first to investigate the impact of therapy and molecular profiles in this population. We observed a high prevalence of TP53 mutations and loss of 17p, however we lacked longitudinal data to make causal inferences regarding the relationship between these abnormalities and ring formation. Of note, 68% of patients did not have prior exposure to therapy, and 36% of all patients lacked TP53 mutations or chromosomal p53 loss, indicating a high rate of de novo ring formation. This is a novel finding perhaps suggesting that inherent chromosomal instability characterizes these patients. Comparing response to type of therapy and outcomes of patients, we conclude that the mOS in patients with RC without therapy is significantly shortened compared with any of the therapeutic options described above, and that the addition of VEN to HMA did not positively influence mOS or PFS compared to HMA alone or chemotherapy in our cohort. Furthermore, the presence of a complex karyotype or a mutation and/or deletion of TP53 with a RC was not independently associated with inferior mOS, suggesting that the presence of a ring chromosome alone may be an important adverse risk factor in myeloid malignancies.

Assembly and comparative analysis of the complete mitochondrial genome of Viburnum chinshanense

BackgroundViburnum chinshanense is an endemic species found exclusively in the North-Central and South-Central regions of China. This species is a lush garden ornamental tree and is extensively utilized for vegetation restoration in rocky desertification areas.ResultsIn this study, we obtained 13.96 Gb of Oxford Nanopore data for the whole genome, and subsequently, by combining Illumina short-reads, we successfully assembled the complete mitochondrial genome (mitogenome) of the V. chinshanense using a hybrid assembly strategy. The assembled genome can be described as a circular genome. The total length of the V. chinshanense mitogenome measures 643,971 bp, with a GC content of 46.18%. Our annotation efforts have revealed a total of 39 protein-coding genes (PCGs), 28 tRNA genes, and 3 rRNA genes within the V. chinshanense mitogenome. The analysis of repeated elements has identified 212 SSRs, 19 long tandem repeat elements, and 325 pairs of dispersed repeats in the V. chinshanense mitogenome. Additionally, we have investigated mitochondrial plastid DNAs (MTPTs) and identified 21 MTPTs within the mitogenome and plastidial genome. These MTPTs collectively span a length of 9,902 bp, accounting for 1.54% of the mitogenome. Moreover, employing Deepred-mt, we have confidently predicted 623 C to U RNA editing sites across the 39 protein-coding genes. Furthermore, extensive genomic rearrangements have been observed between V. chinshanense and the mitogenomes of related species. Interestingly, we have also identified a bacterial-derived tRNA gene (trnC-GCA) in the V. chinshanense mitogenome. Lastly, we have inferred the phylogenetic relationships of V. chinshanense with other angiosperms based on mitochondrial PCGs.ConclusionsThis study marks the first report of a mitogenome from the Viburnum genus, offering a valuable genomic resource for exploring the evolution of mitogenomes within the Dipsacales order.

The complete mitochondrial genome of Amorphophallus albus and development of molecular markers for five Amorphophallus species based on mitochondrial DNA.

Amorphophallus albus is an herbaceous, cormous, perennial plant used as a food source and traditional medicine in Asia. In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. albus. Then we analyzed the repeated elements and mitochondrial plastid sequences (MTPTs), predicted RNA editing sites in mitochondrial protein-coding genes (PCGs). Lastly, we inferred the phylogenetic relationships of A. albus and other angiosperms based on mitochondrial PCGs, and designed two molecular markers based on mitochondrial DNA. The complete mitogenome of A. albus consists of 19 circular chromosomes. And the total length of A. albus mitogenome is 537,044 bp, with the longest chromosome measuring 56,458 bp and the shortest measuring 12,040 bp. We identified and annotated a total of 36 protein-coding genes (PCGs), 21 tRNA genes, and 3 rRNA genes in the mitogenome. Additionally, we analyzed mitochondrial plastid DNAs (MTPTs) and identified 20 MTPTs between the two organelle genomes, with a combined length of 22,421 bp, accounting for 12.76% of the plastome. Besides, we predicted a total of 676 C to U RNA editing sites on 36 protein-coding genes of high confidence using Deepred-mt. Furthermore, extensive genomic rearrangement was observed between A. albus and the related mitogenomes. We conducted phylogenetic analyses based on mitochondrial PCGs to determine the evolutionary relationships between A. albus and other angiosperms. Finally, we developed and validated two molecular markers, Ai156 and Ai976, based on two intron regions (nad2i156 and nad4i976) respectively. The discrimination success rate was 100 % in validation experiments for five widely grown konjac species. Our results reveal the multi-chromosome mitogenome of A. albus, and the developed markers will facilitate molecular identification of this genus.

From oral structure to molecular evidence: new insights into the evolutionary phylogeny of the ciliate order Sessilida (Protista, Ciliophora), with the establishment of two new families and new contributions to the poorly studied family Vaginicolidae.

Ciliated protists represent one of the most primitive and diverse lineages of eukaryotes, with nuclear dimorphism, a distinctive sexual process (conjugation), and extensive genome rearrangements. Among divergent ciliate lineages, the peritrich order Sessilida includes members with a colonial lifestyle, which may hint to an independent evolutionary attempt for multicellularity, although they are still single-celled organisms. To date, the evolution and phylogeny of this group are still far from clear, in part due to the paucity of molecular and/or morphological data for many taxa. In this study, we extend taxon sampling of a loricate group of sessilids by obtaining 69 new rDNA (SSU rDNA, ITS1-5.8S rDNA-ITS2, and LSU rDNA) sequences from 20 well-characterized representative species and analyze the phylogenetic relationships within Sessilida. The main findings are: (i) the genera Rhabdostyla and Campanella each represents a unique taxon at family level, supporting the establishment of two new families, i.e., Rhabdostylidae n. fam. and Campanellidae n. fam., respectively, the former being sister to a morphologically heterogeneous clade comprising Astylozoidae and several incertae sedis species and the latter occupying the basal position within the Sessilida clade; (ii) the structure of infundibular polykinety 3 is likely to be a phylogenetically informative character for resolving evolutionary relationships among sessilids; (iii) differences between sparsely and the densely arranged silverline systems could be a suprageneric taxonomic character; (iv) the monophyly of Vaginicolidae is confirmed, which is consistent with its specialized morphology, i.e., the possession of a typical peritrich lorica which might be an apomorphy for this group; (v) within Vaginicolidae, the monotypic Cothurniopsis sensu Stokes, 1893 is a synonym of Cothurnia Ehrenberg, 1831, and a new combination is created, i.e., Cothurnia valvata nov. comb.; (vi) Vaginicola sensu lato comprises at least two distinctly divergent clades, one affiliated with Thuricola and the other with a systematically puzzling clade represented by Vaginicola tincta.

De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Chaenomeles speciosa (Sweet) Nakai Revealed the Existence of Two Structural Isomers.

As a valuable Chinese traditional medicinal species, Chaenomeles speciosa (Sweet) Nakai (C. speciosa) is a natural resource with significant economic and ornamental value. However, its genetic information is not well understood. In this study, the complete mitochondrial genome of C. speciosa was assembled and characterized to explore the repeat sequences, recombination events, rearrangements, and IGT, to predict RNA editing sites, and to clarify the phylogenetic and evolutionary relationship. The C. speciosa mitochondrial genome was found to have two circular chromosomes as its major conformation, with a total length of 436,464 bp and 45.2% GC content. The mitochondrial genome contained 54 genes, including 33 unique protein-coding genes, 18 tRNAs, and 3 rRNA genes. Seven pairs of repeat sequences involving recombination events were analyzed. Both the repeat pairs, R1 and R2, played significant roles in mediating the major and minor conformations. In total, 18 MTPTs were identified, 6 of which were complete tRNA genes. There were 454 RNA editing sites in the 33 protein-coding sequences predicted by the PREPACT3 program. A phylogenetic analysis based on 22 species of mitochondrial genomes was constructed and indicated highly conserved PCG sequences. Synteny analyses showed extensive genomic rearrangements in the mitochondrial genome of C. speciosa and closely related species. This work is the first to report the C. speciosa mitochondrial genome, which is of great significance for conducting additional genetic studies on this organism.

Extensive reorganization of the chloroplast genome of Corydalis platycarpa: A comparative analysis of their organization and evolution with other Corydalis plastomes.

The chloroplast (cp) is an autonomous plant organelle with an individual genome that encodes essential cellular functions. The genome architecture and gene content of the cp is highly conserved in angiosperms. The plastome of Corydalis belongs to the Papaveraceae family, and the genome is comprised of unusual rearrangements and gene content. Thus far, no extensive comparative studies have been carried out to understand the evolution of Corydalis chloroplast genomes. Therefore, the Corydalis platycarpa cp genome was sequenced, and wide-scale comparative studies were conducted using publicly available twenty Corydalis plastomes. Comparative analyses showed that an extensive genome rearrangement and IR expansion occurred, and these events evolved independently in the Corydalis species. By contrast, the plastomes of its closely related subfamily Papaveroideae and other Ranunculales taxa are highly conserved. On the other hand, the synapomorphy characteristics of both accD and the ndh gene loss events happened in the common ancestor of the Corydalis and sub-clade of the Corydalis lineage, respectively. The Corydalis-sub clade species (ndh lost) are distributed predominantly in the Qinghai-Tibetan plateau (QTP) region. The phylogenetic analysis and divergence time estimation were also employed for the Corydalis species. The divergence time of the ndh gene in the Corydalis sub-clade species (44.31 - 15.71 mya) coincides very well with the uplift of the Qinghai-Tibet Plateau in Oligocene and Miocene periods, and maybe during this period, it has probably triggered the radiation of the Corydalis species. To the best of the authors' knowledge, this is the first large-scale comparative study of Corydalis plastomes and their evolution. The present study may provide insights into the plastome architecture and the molecular evolution of Corydalis species.

Comparative analysis of Vibrio cholerae isolates from Ghana reveals variations in genome architecture and adaptation of outbreak and environmental strains.

Recurrent epidemics of cholera denote robust adaptive mechanisms of Vibrio cholerae for ecological shifting and persistence despite variable stress conditions. Tracking the evolution of pathobiological traits requires comparative genomic studies of isolates from endemic areas. Here, we investigated the genetic differentiation among V. cholerae clinical and environmental isolates by highlighting the genomic divergence associated with gene decay, genome plasticity, and the acquisition of virulence and adaptive traits. The clinical isolates showed high phylogenetic relatedness due to a higher frequency of shared orthologs and fewer gene variants in contrast to the evolutionarily divergent environmental strains. Divergence of the environmental isolates is linked to extensive genomic rearrangements in regions containing mobile genetic elements resulting in numerous breakpoints, relocations, and insertions coupled with the loss of virulence determinants acf, zot, tcp, and ctx in the genomic islands. Also, four isolates possessed the CRISPR-Cas systems with spacers specific for Vibrio phages and plasmids. Genome synteny and homology analysis of the CRISPR-Cas systems suggest horizontal acquisition. The marked differences in the distribution of other phage and plasmid defense systems such as Zorya, DdmABC, DdmDE, and type-I Restriction Modification systems among the isolates indicated a higher propensity for plasmid or phage disseminated traits in the environmental isolates. Our results reveal that V. cholerae strains undergo extensive genomic rearrangements coupled with gene acquisition, reflecting their adaptation during ecological shifts and pathogenicity.

Phylogenetic analysis based on single-copy orthologous proteins in highly variable chloroplast genomes of Corydalis

Corydalis is one of the few lineages that have been reported to have extensive large-scale chloroplast genome (cp-genome) rearrangements. In this study, novel cp-genome rearrangements of Corydalis pinnata, C. mucronate, and C. sheareri are described. C. pinnata is a narrow endemic species only distributed at Qingcheng Mountain in southwest China. Two independent relocations of the same four genes (trnM-CAU-rbcL) were found relocated from the typically posterior part of the large single-copy region to the front of it. A uniform inversion of an 11–14-kb segment (ndhB-trnR-ACG) was found in the inverted repeat region; and extensive losses of accD, clpP, and trnV-UAC genes were detected in all cp-genomes of all three species of Corydalis. In addition, a phylogenetic tree was reconstructed based on 31 single-copy orthologous proteins in 27 cp-genomes. This study provides insights into the evolution of cp-genomes throughout the genus Corydalis and also provides a reference for further studies on the taxonomy, identification, phylogeny, and genetic transformation of other lineages with extensive rearrangements in cp-genomes.

Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation.

The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including Nitzschia ovalis, Nitzschia traheaformis, Cylindrotheca spp., Psammodictyon constrictum, Bacillaria paxillifer, two strains of Haslea tsukamotoi, Haslea avium, Navicula arenaria, and Pleurosigma sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera Nitzschia, Cylindrotheca, Navicula and Haslea. Additionally, comparative analysis suggested that the positioning of species in the genus Haslea should be transferred to the genus Navicula. Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.

Diatom Biodiversity and Speciation Revealed by Comparative Analysis of Mitochondrial Genomes

Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically significant groups of phytoplankton, comprising 100,000–200,000 species in three classes Bacillariophyceae, Mediophyceae, and Coscinodiscophyceae. However, due to the limited resolution of common molecular markers including 18S rDNA, 28S rDNA, ITS, rbcL, and cox1, diatom biodiversity has not been adequately ascertained. Organelle genomes including mitochondrial genomes (mtDNAs) have been proposed to be “super barcodes” for distinguishing diatom species because of their rich genomic content, and the rapid progress of DNA sequencing technologies that has made it possible to construct mtDNAs with increasing throughout and decreasing cost. Here, we constructed complete mtDNAs of 15 diatom species including five Coscinodiscophyceae species (Guinardia delicatula, Guinardia striata, Stephanopyxis turris, Paralia sulcata, and Actinocyclus sp.), four Mediophyceae species (Hemiaulus sinensis, Odontella aurita var. minima, Lithodesmioides sp., and Helicotheca tamesis), and six Bacillariophyceae species (Nitzschia ovalis, Nitzschia sp., Nitzschia traheaformis, Cylindrotheca closterium, Haslea tsukamotoi, and Pleurosigma sp.) to test the practicality of using mtDNAs as super barcodes. We found that mtDNAs have much higher resolution compared to common molecular markers as expected. Comparative analysis of mtDNAs also suggested that mtDNAs are valuable in evolutionary studies by revealing extensive genome rearrangement events with gene duplications, gene losses, and gains and losses of introns. Synteny analyses of mtDNAs uncovered high conservation among species within an order, but extensive rearrangements including translocations and/or inversions between species of different orders within a class. Duplication of cox1 was discovered for the first time in diatoms in Nitzschia traheaformis and Haslea tsukamotoi. Molecular dating analysis revealed that the three diatom classes split 100 Mya and many diatom species appeared since 50 Mya. In conclusion, more diatom mtDNAs representing different orders will play great dividends to explore biodiversity and speciation of diatoms in different ecological regions.

Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives

BackgroundAlthough plastomes are highly conserved with respect to gene content and order in most photosynthetic angiosperms, extensive genomic rearrangements have been reported in Fabaceae, particularly within the inverted repeat lacking clade (IRLC) of Papilionoideae. Two hypotheses, i.e., the absence of the IR and the increased repeat content, have been proposed to affect the stability of plastomes. However, this is still unclear for the IRLC species. Here, we aimed to investigate the relationships between repeat content and the degree of genomic rearrangements in plastomes of Medicago and its relatives Trigonella and Melilotus, which are nested firmly within the IRLC.ResultsWe detected abundant repetitive elements and extensive genomic rearrangements in the 75 newly assembled plastomes of 20 species, including gene loss, intron loss and gain, pseudogenization, tRNA duplication, inversion, and a second independent IR gain (IR ~ 15 kb in Melilotus dentata) in addition to the previous first reported cases in Medicago minima. We also conducted comparative genomic analysis to evaluate plastome evolution. Our results indicated that the overall repeat content is positively correlated with the degree of genomic rearrangements. Some of the genomic rearrangements were found to be directly linked with repetitive sequences. Tandem repeated sequences have been detected in the three genes with accelerated substitution rates (i.e., accD, clpP, and ycf1) and their length variation could be explained by the insertions of tandem repeats. The repeat contents of the three localized hypermutation regions around these three genes with accelerated substitution rates are also significantly higher than that of the remaining plastome sequences.ConclusionsOur results suggest that IR reemergence in the IRLC species does not ensure their plastome stability. Instead, repeat-mediated illegitimate recombination is the major mechanism leading to genome instability, a pattern in agreement with recent findings in other angiosperm lineages. The plastome data generated herein provide valuable genomic resources for further investigating the plastome evolution in legumes.

Genome of the world\u2019s smallest flowering plant, Wolffia australiana, helps explain its specialized physiology and unique morphology

Watermeal, Wolffia australiana, is the smallest known flowering monocot and is rich in protein. Despite its great potential as a biotech crop, basic research on Wolffia is in its infancy. Here, we generated the reference genome of a species of watermeal, W. australiana, and identified the genome-wide features that may contribute to its atypical anatomy and physiology, including the absence of roots, adaxial stomata development, and anaerobic life as a turion. In addition, we found evidence of extensive genome rearrangements that may underpin the specialized aquatic lifestyle of watermeal. Analysis of the gene inventory of this intriguing species helps explain the distinct characteristics of W. australiana and its unique evolutionary trajectory.

Complete mitochondrial genome of Rhizosolenia setigera (Coscinodiscophyceae, Bacillariophyta)

Rhizosolenia is a species-rich genus with 144 described species, many of which are harmful algal species (HABs) with significant negative ecological impact. Despite their significance in primary production and their potential to induce HABs, genome data of these species remain extremely limited. In this study, the complete mitochondrial genome (mtDNA) of Rhizosolenia setigera Brightwell 1858 was determined for the first time, which also represented the first mtDNA of the order Rhizosoleniales. The circular mtDNA was 34,792 bp in length with GC content of 23.28%. It encoded 63 genes including 35 protein-coding genes (PCGs), 24 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 conserved open reading frames (orfs). Phylogenetic analysis using concatenated PCGs revealed that R. setigera and Melosira undulate, which also belongs to the class Coscinodiscophyceae, clustered together as expected. However, comparison of these two mtDNAs revealed extensive genome rearrangement events, suggesting large evolutionary distance. The complete mtDNA of R. setigera will facilitate research on the phylogenetic relationship among Rhizosolenia species, which will in turn facilitate exploration of the evolutionary relationships in the class of Coscinodiscophyceae.

Mitochondrial genomes within bark lice (Insecta: Psocodea: Psocomorpha) reveal novel gene rearrangements containing phylogenetic signal

ABSTRACTPsocodea (booklice and parasitic lice) is an order of insects containing species with extensive mitochondrial genome rearrangements, particularly within the suborder Troctomorpha, in which some species possess an extremely fragmented mitochondrial genome with several small minichromosomes. In the remaining suborders of Psocodea, there are groups with the ancestral pancrustacean arrangement, quite extensive rearrangements (e.g. Trogiomorpha), or in which the small number of species analysed to date have rearrangements of only a few protein‐coding genes and/or tRNAs (e.g. Psocomorpha). Despite the apparent high rate of rearrangements in the order as a whole, a small number of complete mitochondrial genomes are available, especially for suborder Psocomorpha, the largest free‐living suborder. To understand the evolution of the gene arrangement of the mitochondrial genome within Psocomorpha and its phylogenetic implications, we assembled and analysed the mitochondrial genomes of 33 species of bark lice belonging to nine families in two infraorders. Within the infraorder Homilopsocidea, four families were analysed, mainly from Lachesillidae (which included 22 species of this family). Within the infraorder Caeciliusetae, seven species representing five families were analysed. Mitochondrial gene rearrangements were identified in seven of the nine families. Some of these rearrangements were unique to a single species, while some contained phylogenetic signal, being shared by related species. These rearrangements typically corresponded to transpositions and inversions of tRNAs, possibly caused by tandem duplication–random loss (TDRL) and/or recombination events. Phylogenetic analyses of mitochondrial gene sequences provided phylogenetic resolution for several branches of the tree, including monophyly of Lachesillinae. The genus Hemicaecilius Enderlein was found to be embedded within the genus Lachesilla Westwood, rending the latter paraphyletic. Monophyly was also never recovered for Lachesillidae and Elipsocidae as currently defined. However, instability was observed for some higher level relationships within Psocomorpha, including the relationships among the major clades of Lachesillidae.

The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes

Dragon fruits are tropical fruits economically important for agricultural industries. As members of the family of Cactaceae, they have evolved to adapt to the arid environment. Here we report the draft genome of Hylocereus undatus, commercially known as the white-fleshed dragon fruit. The chromosomal level genome assembly contains 11 longest scaffolds corresponding to the 11 chromosomes of H. undatus. Genome annotation of H. undatus found ~29,000 protein-coding genes, similar to Carnegiea gigantea (saguaro). Whole-genome duplication (WGD) analysis revealed a WGD event in the last common ancestor of Cactaceae followed by extensive genome rearrangements. The divergence time between H. undatus and C. gigantea was estimated to be 9.18 MYA. Functional enrichment analysis of orthologous gene clusters (OGCs) in six Cactaceae plants found significantly enriched OGCs in drought resistance. Fruit flavor-related functions were overrepresented in OGCs that are significantly expanded in H. undatus. The H. undatus draft genome also enabled the discovery of carbohydrate and plant cell wall-related functional enrichment in dragon fruits treated with trypsin for a longer storage time. Lastly, genes of the betacyanin (a red-violet pigment and antioxidant with a very high concentration in dragon fruits) biosynthetic pathway were found to be co-localized on a 12 Mb region of one chromosome. The consequence may be a higher efficiency of betacyanin biosynthesis, which will need experimental validation in the future. The H. undatus draft genome will be a great resource to study various cactus plants.