Short Inverted Repeats Research Articles

Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales

BackgroundThe plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants.ResultsWe acquired 93 plastomes, representing all the 16 families and 5 major clades of Poales to reveal the extent of their variation and evolutionary pattern. Extensive variation including the largest one in monocots with 225,293 bp in size, heterogeneous GC content, and a wide variety of gene duplication and loss were revealed. Moreover, rare occurrences of three inverted repeat (IR) copies in angiosperms and one IR loss were observed, accompanied by short IR (sIR) and small direct repeat (DR). Widespread structural heteroplasmy, diversified inversions, and unusual genomic rearrangements all appeared in Poales, occasionally within a single species. Extensive repeats in the plastomes were found to be positively correlated with the observed inversions and rearrangements. The variation all showed a “small-large-moderate” trend along the evolution of Poales, as well as for the sequence substitution rate. Finally, we found some positively selected genes, mainly in C4 lineages, while the closely related lineages of those experiencing gene loss tended to have undergone more relaxed purifying selection.ConclusionsThe variation of plastomes in Poales may be related to its successful diversification into diverse habitats and multiple photosynthetic pathway transitions. Our order-scale analyses revealed unusual evolutionary scenarios for plastomes in the photoautotrophic order of Poales and provided new insights into the plastome evolution in angiosperms as a whole.

Exploring the Roles of Different DNA Repair Proteins in Short Inverted Repeat Mediated Genomic Instability: A Pilot Study

Repetitive DNA sequences are abundant in the human genome and can adopt alternative (i.e., non-B) DNA structures. These sequences contribute to diverse biological functions, including genomic instability. Previously, we found that Z-DNA-, H-DNA- and cruciform DNA-forming sequences are mutagenic, implicating them in cancer etiology. These sequences can stimulate the formation of DNA double-strand breaks (DSBs), causing deletions via cleavage by the endonuclease ERCC1-XPF. Interestingly, the activity of ERCC1-XPF in H-DNA-induced mutagenesis is nucleotide excision repair (NER)-dependent, but its role in Z-DNA-induced mutagenesis is NER-independent. Instead, Z-DNA is processed by ERCC1-XPF in a mechanism dependent on the mismatch repair (MMR) complex, MSH2-MSH3. These observations indicate distinct mechanisms of non-B-induced genomic instability. However, the roles of NER and MMR proteins, as well as additional nucleases (CtIP and MRE11), in the processing of cruciform DNA remain unknown. Here, we present data on the processing of cruciform-forming short inverted repeats (IRs) by DNA repair proteins using mammalian cell-based systems. From this pilot study, we show that, in contrast to H-DNA and Z-DNA, short IRs are processed in a NER- and MMR-independent manner, and the nucleases CtIP and MRE11 suppress short IR-induced genomic instability in mammalian cells.

CircUBE3A(2,3,4,5) promotes adenylate-uridylate-rich binding factor 1 nuclear translocation to suppress prostate cancer metastasis

Metastatic progression is the primary cause of mortality in prostate cancer (PCa) patients. Although circular RNAs (circRNAs) have been implicated in cancer progression and metastasis, our current understanding of their role in PCa metastasis remains limited. In this study, we identified that circUBE3A(2,3,4,5), which originated from exons 2, 3, 4 and 5 of the human ubiquitin-protein ligase E3A (UBE3A) gene, was specifically downregulated in PCa tissues and correlated with the Gleason score, bone metastasis, and D'Amico risk classification. Through the in vitro and in vivo experiments, we demonstrated that overexpression of circUBE3A(2,3,4,5) inhibited PCa cell migration, invasion, metastasis, and proliferation. Mechanistically, circUBE3A(2,3,4,5) was found to bind to adenylate-uridylate-rich binding factor 1 (AUF1), promoting the translocation of AUF1 into the nucleus. This led to decreased AUF1 in the cytoplasm, resulting in methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) mRNA instability and a subsequent reduction at the protein level. The downregulation of MTHFD2 further inhibited vimentin expression, thereby suppressing PCa cell epithelial-mesenchymal transition. Additionally, two pairs of the short-inverted repeats (TSIRs) in flanking introns were identified to synergistically facilitate the generation of circUBE3A(2,3,4,5) and other circRNAs. In summary, TSIRs-induced circUBE3A(2,3,4,5) acts as a suppressor of PCa metastasis by enhancing AUF1 nuclear translocation, reducing MTHFD2, and subsequently inhibiting vimentin expression. This study characterizes circUBE3A(2,3,4,5) as a functional circRNA and proposes it as a highly promising target for preventing PCa metastasis.

Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA.

Inherited and germ-line de novo copy number variants (CNVs) are increasingly found to be correlated with human developmental and cancerous phenotypes. Several models for template switching during replication have been proposed to explain the generation of these gross chromosomal rearrangements. We proposed a model of template switching (ODIRA-origin dependent inverted repeat amplification) in which simultaneous ligation of the leading and lagging strands at diverging replication forks could generate segmental inverted triplications through an extrachromosomal inverted circular intermediate. Here, we created a genetic assay using split-ura3 cassettes to trap the proposed inverted intermediate. However, instead of recovering circular inverted intermediates, we found inverted linear chromosomal fragments ending in native telomeres-suggesting that a template switch had occurred at the centromere-proximal fork of a replication bubble. As telomeric inverted hairpin fragments can also be created through double strand breaks we tested whether replication errors or repair of double stranded DNA breaks were the most likely initiating event. The results from CRISPR/Cas9 cleavage experiments and growth in the replication inhibitor hydroxyurea indicate that it is a replication error, not a double stranded break that creates the inverted junctions. Since inverted amplicons of the SUL1 gene occur during long-term growth in sulfate-limited chemostats, we sequenced evolved populations to look for evidence of linear intermediates formed by an error in replication. All of the data are compatible with a two-step version of the ODIRA model in which sequential template switching at short inverted repeats between the leading and lagging strands at a replication fork, followed by integration via homologous recombination, generates inverted interstitial triplications.

The complete chloroplast genome sequence of Rosa ‘Limoncello’ (Rosales: Rosaceae)

Rosa ‘Limoncello’ finds applications in gardening and landscaping. In this study, we assembled and annotated the complete chloroplast genome of this variety for the first time. The length of its chloroplast genome was 156,493 bp, containing two short inverted repeat regions of 26,052 bp, each separated by a large single-copy region of 85,649 bp and a small single-copy region of 18,740 bp. The chloroplast DNA of R. ‘Limoncello’ consisted of 135 genes, including 90 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. On comparing the complete chloroplast sequence of R. ‘Limoncello’ with that of other Rosa species, R. ‘Limoncello’ was found to be closely related to Rosa cymosa. Thus, information on the chloroplast genome sequence of this rose variety can facilitate phylogenetic studies of the genus Rosa.

Hiker, a new family of DNA transposons encoding transposases with DD35E motifs, displays a distinct phylogenetic relationship with most known DNA transposon families of IS630-Tc1-mariner (ITm)

DNA transposons play a crucial role in determining the size and structure of eukaryotic genomes. In this study, a new family of IS630-Tc1-mariner (ITm) DNA transposons, named Hiker (HK), was identified. HK is characterized by a DD35E catalytic domain and is distinct from all previously known families of the ITm group. Phylogenetic analyses showed that DD35E/Hiker forms a monophyletic clade with DD34E/Gambol, indicating that they may represent a separate superfamily of ITm. A total of 178 Hiker species were identified, with 170 found mainly in Actinopterygii, one in Chondrichthyes, six in Anura and one in Mollusca. Gambol (GM), on the other hand, are found in invertebrates, with 18 in Arthropoda and one in Platyhelminthes. Hiker transposons have a total length ranging from 2.14 to 3.67 kb and contain a single open reading frame that encodes a protein of approximately 370 amino acids (range 311–413 aa). They are flanked by short terminal inverted repeats (TIRs) of 16–30 base pairs and two base pair (TA) target-site duplications. In contrast, most transposons of the Gambol family have a total length of 1.35–5.96 kb, encode a transposase protein of approximately 350 amino acids (range 306–374 aa), and are flanked by TIRs that range from 32 to 1097 bp in length. Both Hiker and Gambol transposases have several conserved motifs, including helix-turn-helix (HTH) motifs and a DDE domain. Our study observed multiple amplification waves and repeated horizontal transfer (HT) events of HK transposons in vertebrate genomes, indicating their role in diversifying and shaping the genomes of Actinopterygii, Chondrichthyes, and Anura. Conversely, GM transposons showed few Horizontal transfer events. According to cell-based transposition assays, most HK transposons are likely inactive due to the truncated DNA binding domains of their transposases. We present an updated classification of the ITm group based on these findings, which will enhance the understanding of both the evolution of ITm transposons and that of their hosts.

Complete genome sequence analysis, morphology and structural protein identification of two Bacillus subtilis phages, BSTP4 and BSTP6, which may form a new species in the genus Salasvirus.

In the present study, two new Bacillus subtilis phages, BSTP4 and BSTP6, were isolated and studied further. Morphologically, BSTP4 and BSTP6 are podoviruses with complete genome of 19,145 (39.9% G + C content) and 19,367bp (39.8% G + C content), respectively, which became among the smallest Bacillus phages. Three most prominent structural proteins were separated and identified as pre-neck appendage, major head, and head fiber proteins using LC-MS/MS. Both phages encode putative terminal proteins (TP) and contain short inverted terminal repeats (ITRs) which may be important for their replication. In addition, non-coding RNA (pRNA) and parS sites were identified which may be required for DNA packaging and their maintenance inside the host, respectively. Furthermore, the phage genome sequences show significant similarity to B. subtilis group species genome sequences. Finally, phylogenomic and phylogenetic analyses suggest that BSTP4 and BSTP6 may form a new species in the genus Salasvirus, subfamily Picovirinae of family Salasmaviridae. Considering the small numbers of ICTV-accepted B. subtilis phages and the importance of the host in the food industry and biotechnology, the current study helps to improve our understanding of the diversity of B. subtilis phages and shed light on the phage-host relationships.

Sequence Motif Analysis of PRDM9 and Short Inverted Repeats Suggests Their Contribution to Human Microdeletion and Microduplication Syndromes

Holliday junctions are the first recognized templates of legitimate recombination. Their prime physiological role is meiotic homologous recombination, resulting in rearrangements of the genetic material. In humans, recombination hotspots follow a distinct epigenetic pattern designated by the presence of PR domain-containing protein 9 (PRDM9). Repetitive DNA elements can replicate in the genome and can pair with short inverted repeats (SIRs) that form Holliday junctions in a significantly high frequency in vitro. Remarkably, PRDM9 and SIR sequence motifs, which may have the potential to act as recombination primers associated with transposable elements (TEs) and their presence, may lead to gradual spreading of recombination events in human genomes. Microdeletion and microduplication syndromes (MMSs) constitute a significant entity of genetic abnormalities, almost equal in frequency to aneuploidies. Based on our custom database, which includes all MMSs shorter than 5 Mbs in length which is the cut-off point for the standard cytogenetic resolution, we found that the majority of MMSs were present in sequences shorter than 0.5 Mbs. A high probability of TE-associated and non-TE-associated PRDM9/SIR sequence motifs was found in short and long MMSs. Significantly, following the Reactome pathway analysis, a number of affected genes have been associated with the pathophysiological pathways linked to MMSs. In conclusion, PRDM9 or SIR sequence motifs in regions spanning MMSs hotspots underlie a potential functional mechanism for MMS occurrences during recombination.

A unique eukaryotic lineage of composite-like DNA transposons encoding a DDD/E transposase and a His-Me finger homing endonuclease

BackgroundDNA transposons are ubiquitous components of eukaryotic genomes. A major group of them encode a DDD/E transposase and contain terminal inverted repeats (TIRs) of varying lengths. The Kolobok superfamily of DNA transposons has been found in a wide spectrum of organisms.ResultsHere we report a new Kolobok lineage, designated KolobokP. They were identified in 7 animal phyla (Mollusca, Phoronida, Annelida, Nemertea, Bryozoa, Chordata, and Echinodermata), and are especially rich in bivalves. Unlike other Kolobok families, KolobokP adopts a composite-like architecture: an internal region (INT) flanked by two long terminal direct repeats (LTDRs), which exhibit their own short terminal inverted repeats ranging up to 18 bps. The excision of LTDRs was strongly suggested. The LTDR lengths seem to be constrained to be either around 450-bp or around 660-bp. The internal region encodes a DDD/E transposase and a small His-Me finger nuclease, which likely originated from the homing endonuclease encoded by a group I intron from a eukaryotic species. The architecture of KolobokP resembles composite DNA transposons, usually observed in bacterial genomes, and long terminal repeat (LTR) retrotransposons. In addition to this monomeric LTDR-INT-LTDR structure, plenty of solo LTDRs and multimers represented as (LTDR-INT)n-LTDR are also observed. Our structural and phylogenetic analysis supported the birth of KolobokP in the late stage of the Kolobok evolution. We propose KolobokP families propagate themselves in two ways: the canonical transposition catalyzed by their transposase and the sequence-specific cleavage by their endonuclease followed by the multimerization through the unequal crossover.ConclusionsThe presence of homing endonuclease and long terminal direct repeats of KolobokP families suggest their unique dual replication mechanisms: transposition and induced unequal crossover.

The complete chloroplast genome of Zanthoxylum stenophyllum Hemsl. (Rutaceae), a traditional Chinese medicinal plant

Zanthoxylum stenophyllum Hemsl., a type species for the genus Zanthoxylum (Rutaceae), is a traditional medicinal plant. We studied the complete chloroplast genome of this species using BGISEQ-500 platform. The chloroplast genome was 158,314 bp in size with a GC content of 38.45%. The genome contained two short inverted repeat (IRa and IRb) regions of 27,052 bp, a large single-copy region (LSC, 86,029 bp) and a small single-copy region (SSC, 18,181 bp). The annotated complete chloroplast genome contains 133 distinct genes, including 88 protein-coding genes, 37 transfer RNAs (tRNAs), and 8 ribosomal RNAs (rRNAs). Phylogenetic analysis indicated that Z. stenophyllum is clustered with Z. schiniflium and Z. pinnatum in the same branch with 100% bootstrap support. This complete chloroplast genome provides valuable genomic information for the molecular phylogeny and sustainable utilization of Zanthoxylum.

The short inverted repeats-induced circEXOC6B inhibits prostate cancer metastasis by enhancing the binding of RBMS1 and HuR

Circular RNAs (circRNAs) are a novel class of endogenous RNAs with a covalently closed loop structure. Many circRNAs have been found to participate in cancer progression. However, the detailed generation process, functions, and related mechanisms of circRNAs in prostate cancer (PCa) remain largely unknown. In the present study, we identified circEXOC6B, a novel suppressor in the metastasis of PCa. Functionally, circEXOC6B, originating from the exocyst complex component 6B (EXOC6B) gene, inhibited migration and invasion of PCa invitro and invivo. Mechanistically, by acting as a protein scaffold, circEXOC6B enhanced the binding of human RNA binding motif single strand interacting protein 1 (RBMS1) and human antigen R (HuR) and further increased A-kinase anchoring protein 12 (AKAP12) expression to inhibit PCa metastasis. Unlike previous studies, we found that one pair of short inverted repeats in flanking introns at least partly promoted the circularization of circEXOC6B. Our study presents a novel mechanism for the inhibitory role of circEXOC6B in PCa metastasis and provides new insight into the molecular process of circRNA generation.

The complete chloroplast genome of Bletilla ochracea Schltr., a medicinal plant with yellow flowers

Bletilla ochracea Schltr. (Orchidaceae) is a traditional medicinal plant widely distributed in the south-central part of China. The complete chloroplast genome of B. ochracea was sequenced using the Illumina HiSeq X Ten platform. The chloroplast genome was 160,018 bp in length, which contained two short inverted repeat (IRa and IRb) regions of 26,295 bp and was separated by a large single copy (LSC) region of 88,270 bp and a small single copy (SSC) region of 19,158 bp. The GC content of the whole chloroplast genome was 37.2%. The chloroplast DNA of B. ochracea consisted of 114 distinct genes, including 80 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The phylogenetic tree showed that B. ochracea was sister to B. formosana. Meanwhile, the monophyletic clade formed by all species of genus Bletilla was closely related to genus Thunia.

Horizontal transfer of Buster transposons across multiple phyla and classes of animals

Transposable elements (TEs) are mobile genetic elements in the genome and broadly distributed across both prokaryotes and eukaryotes, and play an important role in shaping the genome evolution of their hosts. hAT elements are thought to be the most widespread cut-and-paste DNA transposon found throughout the tree of life. Buster is a recently recognized family of hAT. However, the evolutionary profile of the Buster family, such as its taxonomic distribution, evolutionary pattern, and activities, remains largely unknown. We conducted a systematic analysis of the evolutionary landscape of the Buster family and found that most Buster transposons are 1.72–4.66 kilobases (kb) in length, encode 500–736-amino acid (aa) transposases and are flanked by short (10–18 bp) terminal inverted repeats (TIRs) and 8 bp target site duplications (TSDs). Buster family is widely distributed in 609 species, involving eight classes of invertebrates and most lineage of vertebrates (including mammals). Horizontal transfer events were detected across multiple phyla and classes of animals, which may have contributed to their wide distribution, and both parasites and invasive species may facilitate HT events of Buster in vertebrates. Our data also suggest that Buster transposons are young, highly active, and appear as intact copies in multiple lineages of animals. High percentages of intact copies (>30%) were identified in some Arthropoda, Actinopterygii, Agnatha, and reptile species, and some of these may be active. These data will help increase understanding of the evolution of the hAT superfamily and its impact on eukaryotic genome evolution.

Satellitome comparison of two oedipodine grasshoppers highlights the contingent nature of satellite DNA evolution

BackgroundThe full catalog of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evolutionary mechanisms and pathways of satDNA evolution have never been analyzed for full satellitomes. We compare here the satellitomes of two Oedipodine grasshoppers (Locusta migratoria and Oedaleus decorus) which shared their most recent common ancestor about 22.8 Ma ago.ResultsWe found that about one third of their satDNA families (near 60 in every species) showed sequence homology and were grouped into 12 orthologous superfamilies. The turnover rate of consensus sequences was extremely variable among the 20 orthologous family pairs analyzed in both species. The satDNAs shared by both species showed poor association with sequence signatures and motives frequently argued as functional, except for short inverted repeats allowing short dyad symmetries and non-B DNA conformations. Orthologous satDNAs frequently showed different FISH patterns at both intra- and interspecific levels. We defined indices of homogenization and degeneration and quantified the level of incomplete library sorting between species.ConclusionsOur analyses revealed that satDNA degenerates through point mutation and homogenizes through partial turnovers caused by massive tandem duplications (the so-called satDNA amplification). Remarkably, satDNA amplification increases homogenization, at intragenomic level, and diversification between species, thus constituting the basis for concerted evolution. We suggest a model of satDNA evolution by means of recursive cycles of amplification and degeneration, leading to mostly contingent evolutionary pathways where concerted evolution emerges promptly after lineages split.

Study of the genus Torreya (Taxaceae) based on chloroplast genomes.

Species of the genus Torreya are similar in morphology, and their morphological taxonomic characteristics are not stable because of environmentally induced changes. Therefore, morphology is insufficient for understanding their relationships. Chloroplast genome sequencing technology provides a powerful tool for molecular analysis to get more infomation for classification and identification of Torreya genus. A total of 4 chloroplast genome of Torreya, including T. Parvifolia, T. nucifera, T. fargesii var. Yunnanensis and T. grandis var. jiulongshanensis, were sequenced and annotated. Campartive genome and phylogenetic tree were provided for variation analysis. The chloroplast genome size of the four samples is about 137 kb, the inverted repeat (IR) regions are identified in the genus Torreya. Genome comparison using mVISTA showed high sequence similarity among different species. Regions with divergence in exon regions include accD, ndhB, ndhF, psbA, psbJ, rpl2, rps3, rps16, rps18, ycf1, and ycf2. The phylogenetic tree based on 73 single-copy genes showed a clearer relationships among different species of Torreya. All genomes of the four Torreya species consist of two short IR regions, and results of the phylogenetic analysis concluded that T. parvifolia should be considered as T. fargesii var. yunnanensis or treated as a sister species. T. grandis var. jiulongshanensis should be treated as a variety of T. grandis according to molecular evidence, supporting the originally published proposal.

Characterization of the complete chloroplast genome sequence of Gynostemma microspermum (Cucurbitaceae)

Gynostemma microspermum C. Y. Wu et S. K. Chen is an endemic creeping herbaceous species mainly distributed in dense forests on limestone in northwestern China. Here, the complete chloroplast genome sequence of G. microspermum was obtained by Illumina pair-end sequencing. The circular complete chloroplast genome of G. microspermum is 158,692 bp in length and contains a large single copy region (87,452 bp), a small single copy region (19,068 bp) and two short inverted repeat regions (26,086 bp). The genome sequence encodes 133 genes including 87 protein-coding genes, 37 transfer RNA genes, 8 ribosomal RNA genes and 1 pseudogene. The maximum likelihood (ML) phylogeny estimation shows that G. microspermum is sister to all other analyzed species of the genus Gynostemma with high bootstrap support.

Plastome Structural Evolution and Homoplastic Inversions in Neo-Astragalus (Fabaceae).

The plastid genomes of photosynthetic green plants have largely maintained conserved gene content and order as well as structure over hundreds of millions of years of evolution. Several plant lineages, however, have departed from this conservation and contain many plastome structural rearrangements, which have been associated with an abundance of repeated sequences both overall and near rearrangement endpoints. We sequenced the plastomes of 25 taxa of Astragalus L. (Fabaceae), a large genus in the inverted repeat-lacking clade of legumes, to gain a greater understanding of the connection between repeats and plastome inversions. We found plastome repeat structure has a strong phylogenetic signal among these closely related taxa mostly in the New World clade of Astragalus called Neo-Astragalus. Taxa without inversions also do not differ substantially in their overall repeat structure from four taxa each with one large-scale inversion. For two taxa with inversion endpoints between the same pairs of genes, differences in their exact endpoints indicate the inversions occurred independently. Our proposed mechanism for inversion formation suggests the short inverted repeats now found near the endpoints of the four inversions may be there as a result of these inversions rather than their cause. The longer inverted repeats now near endpoints may have allowed the inversions first mediated by shorter microhomologous sequences to propagate, something that should be considered in explaining how any plastome rearrangement becomes fixed regardless of the mechanism of initial formation.

The complete chloroplast genome of Keteleeria evelyniana

Here, we report the complete chloroplast genome of Keteleeria evelyniana. The genome is 116,940 bp in size, which is comprised of a large single-copy (LSC) region of 74,075 bp, a small single-copy (SSC) region of 40,425 bp, and two short inverted repeat (IR) regions of 1,220 bp. The overall GC content of the plastome was 38.5%. The new sequence comprised 103 unique genes, including 74 protein-coding genes, 4 rRNA genes, and 25 tRNA genes. Phylogenetic analysis showed that K.evelyniana was close to Keteleeria hainanensis and Keteleeria davidiana.

Divergent evolution profiles of DD37D and DD39D families of Tc1/mariner transposons in eukaryotes

DNA transposons play a significant role in shaping the size and structure of eukaryotic genomes. The Tc1/mariner transposons are the most diverse and widely distributed superfamily of DNA transposons and the structure and distribution of several Tc1/mariner families, such as DD35E/TR, DD36E/IC, DD37E/TRT, and DD41D/VS, have been well studied. Nonetheless, a greater understanding of the structure and diversity of Tc1/mariner transposons will provide insight into the evolutionary history of eukaryotic genomes. Here, we conducted further analysis of DD37D/maT and DD39D (named Guest, GT), which were identified by the specific catalytic domains DD37D and DD39D. Most transposons of the maT family have a total length of approximately 1.3 kb and harbor a single open reading frame encoding a ~ 346 amino acid (range 302–398 aa) transposase protein, flanked by short terminal inverted repeats (TIRs) (13–48 base pairs, bp). In contrast, GTs transposons were longer (2.0–5.8 kb), encoded a transposase protein of ~400 aa (range 140–592 aa), and were flanked by short TIRs (19–41 bp). Several conserved motifs, including two helix–turn–helix (HTH) motifs, a GRPR (GRKR) motif, a nuclear localization sequence, and a DDD domain, were also identified in maT and GT transposases. Phylogenetic analyses of the DDD domain showed that the maT and GT families each belong to a monophyletic clade and appear to be closely related to DD41D/VS and DD34D/mariner. In addition, maTs are mainly distributed in invertebrates (144 species), whereas GTs are mainly distributed in land plants through a small number of GTs are present in Chromista and animals. Sequence identity and phylogenetic analysis revealed that horizontal transfer (HT) events of maT and GT might occur between kingdoms and phyla of eukaryotes; however, pairwise distance comparisons between host genes and transposons indicated that HT events involving maTs might be less frequent between invertebrate species and HT events involving GTs may be less frequent between land plant species. Overall, the DD37D/maT and DD39D/GT families display significantly different distribution and tend to be identified in more ancient evolutionary families. The discovery of intact transposases, perfect TIRs, and target site duplications (TSD) of maTs and GTs illustrates that the DD37D/maT and DD39D/GT families may be active. Together, these findings improve our understanding of the diversity of Tc1/mariner transposons and their impact on eukaryotic genome evolution.

The complete chloroplast genome of Madhuca hainanensis (Sapotaceae), an endemic and endangered timber species in Hainan Island, China

Madhuca hainanensis Chun & F.C.How is an endangered and endemic species in Hainan Island, and it was ranked as a VU (Vulnerable) species in China. In this study, we reported its complete chloroplast (cp) genome sequence based on high throughput sequencing data. The complete cp genome was 159,630 bp in length, containing two short inverted repeat (IRs) of 26,093 bp, a large single copy (LSC) region of 88,846 bp and a small single copy (SSC) region of 18,598 bp. Totally, the cp genome contained 131 genes, including 86 protein coding genes (PCG), eight rRNA genes and 37 tRNAs. The GC contents of this genome was 36.8%. A maximum likelihood (ML) phylogenetic analysis indicates that M. hainanensis is closely related to Sinosideroxylon wightianum.