The Complete Chloroplast Genome of Ginkgo biloba Reveals the Mechanism of Inverted Repeat Contraction

We determined the complete chloroplast genome (cpDNA) of Ginkgo biloba (common name: ginkgo), the only relict of ginkgophytes from the Triassic Period. The cpDNA molecule of ginkgo is quadripartite and circular, with a length of 156,945 bp, which is 6,458 bp shorter than that of Cycas taitungensis. In ginkgo cpDNA, rpl23 becomes pseudo, only one copy of ycf2 is retained, and there are at least five editing sites. We propose that the retained ycf2 is a duplicate of the ancestral ycf2, and the ancestral one has been lost from the inverted repeat A (IRA). This loss event should have occurred and led to the contraction of IRs after ginkgos diverged from other gymnosperms. A novel cluster of three transfer RNA (tRNA) genes, trnY-AUA, trnC-ACA, and trnSeC-UCA, was predicted to be located between trnC-GCA and rpoB of the large single-copy region. Our phylogenetic analysis strongly suggests that the three predicted tRNA genes are duplicates of trnC-GCA. Interestingly, in ginkgo cpDNA, the loss of one ycf2 copy does not significantly elevate the synonymous rate (Ks) of the retained copy, which disagrees with the view of Perry and Wolfe (2002) that one of the two-copy genes is subjected to elevated Ks when its counterpart has been lost. We hypothesize that the loss of one ycf2 is likely recent, and therefore, the acquired Ks of the retained copy is low. Our data reveal that ginkgo possesses several unique features that contribute to our understanding of the cpDNA evolution in seed plants

Regulatory T Cells: Potential Target in Anticancer Immunotherapy

SummaryThe concept of regulatory T cells was first described in the early 1970s, and regulatory T cells were called suppressive T cells at that time. Studies that followed have demonstrated that these suppressive T cells negatively regulated tumor immunity and contributed to tumor growth in mice. Despite the importance of these studies, there was extensive skepticism about the existence of these cells, and the concept of suppressive T cells left the center stage of immunologic research for decades. Interleukin-2 receptor α-chain, CD25, was first demonstrated in 1995 to serve as a phenotypic marker for CD4+ regulatory cells. Henceforth, research of regulatory T cells boomed. Regulatory T cells are involved in the pathogenesis of cancer, autoimmune disease, transplantation immunology, and immune tolerance in pregnancy. Recent evidence has demonstrated that regulatory T cellmediated immunosuppression is one of the crucial tumor immune evasion mechanisms and the main obstacle of successful cancer immunotherapy. The mechanism and the potential clinical application of regulatory T cells in cancer immunotherapy are discussed

Role of Apamin-Sensitive Calcium-Activated Small-Conductance Potassium Currents on the Mechanisms of Ventricular Fibrillation in Pacing-Induced Failing Rabbit Hearts

BACKGROUND: Ventricular fibrillation (VF) during heart failure is characterized by stable reentrant spiral waves (rotors). Apamin-sensitive small-conductance calcium-activated potassium currents (IKAS) are heterogeneously upregulated in failing hearts. We hypothesized that IKAS influences the location and stability of rotors during VF. METHODS AND RESULTS: Optical mapping was performed on 9 rabbit hearts with pacing-induced heart failure. The epicardial right ventricular and left ventricular surfaces were simultaneously mapped in a Langendorff preparation. At baseline and after apamin (100 nmol/L) infusion, the action potential duration (APD80) was determined, and VF was induced. Areas with a >50% increase in the maximum action potential duration (ΔAPD) after apamin infusion were considered to have a high IKAS distribution. At baseline, the distribution density of phase singularities during VF in high IKAS distribution areas was higher than in other areas (0.0035±0.0011 versus 0.0014±0.0010 phase singularities/pixel; P=0.004). In addition, high dominant frequencies also colocalized to high IKAS distribution areas (26.0 versus 17.9 Hz; P=0.003). These correlations were eliminated during VF after apamin infusion, as the number of phase singularities (17.2 versus 11.0; P=0.009) and dominant frequencies (22.1 versus 16.2 Hz; P=0.022) were all significantly decreased. In addition, reentrant spiral waves became unstable after apamin infusion, and the duration of VF decreased. CONCLUSIONS: The IKAS current influences the mechanism of VF in failing hearts as phase singularities, high dominant frequencies, and reentrant spiral waves all correlated to areas of high IKAS. Apamin eliminated this relationship and reduced VF vulnerability

Role of apamin sensitive small conductance calcium-activated potassium currents in long term cardiac memory in rabbits

Background Apamin-sensitive small conductance calcium-activated K current (IKAS) is upregulated during ventricular pacing and masks short-term cardiac memory (CM). Objective – To determine the role of IKAS in long-term CM. Methods – CM was created with 3-5 weeks of ventricular pacing and defined by a flat or inverted T-wave off pacing. Epicardial optical mapping was performed in both paced and normal ventricles. Action potential duration (APD80) was determined during RA pacing. Ventricular stability was tested before and after IKAS blockade. Four paced hearts and 4 normal hearts were used for western blotting and histology. Results – There were no significant differences in either the echocardiographic parameters or in fibrosis levels between groups. Apamin induced more APD80 prolongation in CM than in normal ventricles (9.6% [8.8%-10.5%] vs 3.1% [1.9%-4.3%], p<0.001). Apamin significantly lengthend the APD80 in the CM model at late activation sites, indicating significant IKAS upregulation at those sites. The CM model also had altered Ca2+ handling as the 50% Ca2+ transient duration and amplitude were increased at distal sites compared to a proximal site (near the pacing site). After apamin, the CM model had increased VF inducibility (paced vs control, 33/40 (82.5%) vs 7/20 (35%) P<0.001), and longer VF durations (124 vs 26 seconds, P<0.001). Conclusions Chronic ventricular pacing increases Ca2+ transients at late activation sites which activates IKAS to maintain repolarization reserve. IKAS blockade increases VF vulnerability in chronically paced rabbit ventricles

Molecular signature of clinical severity in recovering patients with severe acute respiratory syndrome coronavirus (SARS-CoV)

BACKGROUND: Severe acute respiratory syndrome (SARS), a recent epidemic human disease, is caused by a novel coronavirus (SARS-CoV). First reported in Asia, SARS quickly spread worldwide through international travelling. As of July 2003, the World Health Organization reported a total of 8,437 people afflicted with SARS with a 9.6% mortality rate. Although immunopathological damages may account for the severity of respiratory distress, little is known about how the genome-wide gene expression of the host changes under the attack of SARS-CoV. RESULTS: Based on changes in gene expression of peripheral blood, we identified 52 signature genes that accurately discriminated acute SARS patients from non-SARS controls. While a general suppression of gene expression predominated in SARS-infected blood, several genes including those involved in innate immunity, such as defensins and eosinophil-derived neurotoxin, were upregulated. Instead of employing clustering methods, we ranked the severity of recovering SARS patients by generalized associate plots (GAP) according to the expression profiles of 52 signature genes. Through this method, we discovered a smooth transition pattern of severity from normal controls to acute SARS patients. The rank of SARS severity was significantly correlated with the recovery period (in days) and with the clinical pulmonary infection score. CONCLUSION: The use of the GAP approach has proved useful in analyzing the complexity and continuity of biological systems. The severity rank derived from the global expression profile of significantly regulated genes in patients may be useful for further elucidating the pathophysiology of their disease

Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny

The relationships among the extant five gymnosperm groups—gnetophytes, Pinaceae, non-Pinaceae conifers (cupressophytes), Ginkgo, and cycads—remain equivocal. To clarify this issue, we sequenced the chloroplast genomes (cpDNAs) from two cupressophytes, Cephalotaxus wilsoniana and Taiwania cryptomerioides, and 53 common chloroplast protein-coding genes from another three cupressophytes, Agathis dammara, Nageia nagi, and Sciadopitys verticillata, and a non-Cycadaceae cycad, Bowenia serrulata. Comparative analyses of 11 conifer cpDNAs revealed that Pinaceae and cupressophytes each lost a different copy of inverted repeats (IRs), which contrasts with the view that the same IR has been lost in all conifers. Based on our structural finding, the character of an IR loss no longer conflicts with the “gnepines” hypothesis (gnetophytes sister to Pinaceae). Chloroplast phylogenomic analyses of amino acid sequences recovered incongruent topologies using different tree-building methods; however, we demonstrated that high heterotachous genes (genes that have highly different rates in different lineages) contributed to the long-branch attraction (LBA) artifact, resulting in incongruence of phylogenomic estimates. Additionally, amino acid compositions appear more heterogeneous in high than low heterotachous genes among the five gymnosperm groups. Removal of high heterotachous genes alleviated the LBA artifact and yielded congruent and robust tree topologies in which gnetophytes and Pinaceae formed a sister clade to cupressophytes (the gnepines hypothesis) and Ginkgo clustered with cycads. Adding more cupressophyte taxa could not improve the accuracy of chloroplast phylogenomics for the five gymnosperm groups. In contrast, removal of high heterotachous genes from data sets is simple and can increase confidence in evaluating the phylogeny of gymnosperms

Chloroplast Genomic Evoluion and Phylogeny of Extantymnosperms

現生的種子植物可分為五大群，蘇鐵植物(cycads)、銀杏(Ginkgo)、針葉樹植物(conifers)、買麻藤植物(gnetophytes)及被子植物(angiosperms)。然而，此五群植物間的親緣關係仍未有定論。為重新檢驗此一長久的爭議，本研究定序了台東蘇鐵(Cycas taitungensis)和小葉買麻藤（Gnetum parvifolium）的完整葉綠體基因組(chloroplast genome)。台東蘇鐵的葉綠體基因組為163,403 bp的圓形分子，其結構具有兩段25,074 bp的反向重複序列 (inverted repeat)。研究整理已知的37種陸生植物所共有的56個葉綠體基因組蛋白基因，以三種不同演算法重建親緣演化樹。所獲得之演化樹的樹形(topology)具一致性－皆支持現生所有種子植物、裸子植物、被子植物各為單系群(monophyly)。裸子植物單系群內，可再分成兩個次群組(subclade)，即蘇鐵–銀杏群組及買麻藤–松群組。以上結果與gnetifer及gnepines兩假說一致。此外，本研究亦提出cpDNA結構上突變的證據來支持上述的親緣分析結果。重建的演化樹中，買麻藤植物的分支(branch)明顯長於其他裸子植物，表示買麻藤植物有相對快速的演化速率。以相對速率檢驗法（relative rate test）分析，顯示買麻藤植物的快速演化速率主要發生在密碼子(codon)的第三位置，以及密碼子的第一與第二位置的transversion核苷酸位點。此外，蘇鐵的葉綠體基因組仍保存部份的tufA基因序列，稱為假tufA基因，此假基因亦存在於Anthoceros及銀杏的葉綠體基因組。以此假基因建構的演化樹，顯示tufA基因可能在種子植物的共同祖先就已遺失，推算此遺失事件應發生在距今約3億年前。本研究提出tRNAPro-GGG在被子植物的共同祖先(存在時間距今約1.5億年前)時已遺失的假說。另外，對松科植物如何遺失一段反向重複序列亦提出新的看法。本研究雖同時支持gnetifer及gnepines假說，但無法判定何者較正確。因此，需要分析更多非松科的針葉樹(non-Pinaceae conifers)葉綠體基因組的完整序列，以解決裸子植物的親緣演化。進一步探討導致買麻藤植物相對快速演化速率的因子，本研究另外定序了四種裸子植物之完整葉綠體基因組：三種買麻藤植物－Ephedra equisetina (木賊麻黃：109,518 bp)，Gnetum parvifolium (小葉買麻藤: 114,914 bp)，和Welwitschia mirabilis (千歲蘭: 118,919 bp)，以及一對照組植物：松科的台灣油杉（Keteleeria davidiana; 117,720 bp)。千歲蘭的葉綠體基因組在2008年已被完整定序，並為陸生光合作用植物中，最小且最緊密 (compact)的物種。然而，買麻藤綱之其他兩科－麻黃科 (Ephedrales) 及買麻藤科 (Gnetales) 的葉綠體基因組仍未被研究過，吾人對買麻藤綱植物的葉綠體基因組如何縮小(reduction)及緊密化(compaction)的機制仍未了解。研究發現Ephedra及Gnetum的葉綠體基因組比Welwitschia的更小且更緊密。買麻藤綱植物的葉綠體的共同特徵是: (1)遺失了18個在其他種子植物仍保留的基因；(2)基因間的序列 (spacer) 及基因的內顯子 (intron) 有明顯的序列刪除現象(sequence deletion)；又後者在操作組間 (inter-operon) 比在操作組內 (intra-operon) 明顯，且偏好刪除一整段長序列，而不是單一核苷酸。由此可推論在買麻藤綱植物的葉綠體演化過程中，有一選擇壓力 (selection) 迫使其葉綠體基因組縮小及緊密化。此外，買麻藤綱植物的快速演化速率與葉綠體基因組含高比率的腺嘌呤 (adenine: A) 及胸腺嘧啶 (thymine: T)有關，並在統計上具有顯著意義。綜合上述的發現，本研究推論買麻藤綱植物之葉綠體基因組的縮小及緊密化是一種減少資源消耗的演化策略 (a lower-cost strategy);其目的為: (1)對抗其惡劣的生存環境與(2)提高本身的競爭力來抗衡同生育地周遭的被子植物。此一演化策略導致買麻藤綱植物具有較快的演化速率。前人的研究已發現，買麻藤綱植物的核基因組為裸子植物中最小的，此一特性對本研究所作的演化推論，提供了一有力的證據。Phylogenetic relationships among the five groups of extant seed plants are presently unsettled. To re-examine this longstanding debate, we determined the complete chloroplast genomes (cpDNAs) of Cycas taitungensis and Gnetum parvifolium. The cpDNA of Cycas is a circular molecule of 163,403 bp with two typical large inverted repeats (IRs) of 25,074 bp each. e inferred phylogenetic relationships among major seed plant lineages using concatenated 56 protein-coding genes in 37 land plants. Phylogenies, generated by the use of 3 independent methods, provide concordant and robust support for the monophylies of extant seed plants, gymnosperms, and angiosperms, respectively. Within the modern gymnosperms are 2 highly supported sister clades: Cycas–Ginkgo and Gnetum–Pinus. This result agrees with both the ‘‘gnetifer’’ and ‘‘gnepines’’ hypotheses. The sister relationships in Cycas–Ginkgo and Gnetum–Pinus clades are further reinforced by cpDNA structural evidence. Branch lengths of Cycas–Ginkgo and Gnetum are consistently the shortest and the longest, respectively, in all separate analyses. However, the Gnetum relative rate test revealed this tendency only for the 3rd codon positions and the transversional sites of the first 2 codon positions. A pseudo tufA located between psbE and petL genes is here first detected in Anthoceros (a hornwort), cycads, and Ginkgo. We demonstrate that the pseudo tufA is a footprint descended from the chloroplast tufA of green algae. The duplication of ycf2 genes and their shift into IRs should have taken place at least in the common ancestor of seed plants more than 300 MYA, and the tRNAPro-GGG gene was lost from the angiosperm lineage at least 150 MYA. Additionally, from cpDNA structural comparison, we propose an alternative model for the loss of large IR regions in black pine. More cpDNA data from non-Pinaceae conifers are necessary to justify whether the gnetifer or gnepines hypothesis is valid and to generate solid structural evidence for the monophyly of extant gymnosperms.o comprehend the mechanisms driving the rapid evolutionary rates of gnetophytes, four additional cpDNAs, including one from each of the three gnetophyte orders, Ephedra equisetina, Gnetum parvifolium, and W. mirabilis, and one from the non-Pinus Pinaceae, Keteleeria davidiana were determined. The cpDNA of Welwitschia mirabilis (the only species of Welwitschiales) was recently reported to be the most reduced and compact among photosynthetic land plants. However, cpDNAs of the other two gnetophyte lineages (viz. Ephedrales and Gnetales) have not yet been studied. It remains unclear what underlining mechanisms have downsized the cpDNA. To pin down major factors for cpDNA reduction and compaction in gnetophytes, we have determined the cpDNAs of E. equisetina (109,518 bp) and G. parvifolium (114,914 bp). They are not only smaller but more compact than that of W. mirabilis (118,919 bp). The gnetophyte cpDNAs have commonly lost at least 18 genes that are retained in other seed plants. Furthermore, they have significantly biased usages of AT-rich codons and shorter introns and intergenic spaces, which are largely due to more deletions at inter-operon than intra-operon spaces and removal of segment sequences rather than single-nucleotides. We showed that the reduced gnetophyte cpDNAs clearly resulted from selection for economy by deletions of genes and non-coding sequences, which then led to the compactness and the accelerated substitution rates. The smallest C-values in gnetophyte nuclear DNAs and the competitive or resource-poor situations encountered by gnetophytes further suggest a critical need for an economic strategy.Contents文摘要…………………………………………………………………………. Ⅰ文摘要…………………………………………………………………………. Ⅲhapter 1. Introduction…………………………………………………………… 11.1 Backgrounds of cycads and gnetophytes………………………………… 11.2 The issue of the seed plant phylogeny…………………………………… 21.3 Effects of the long-branch attraction on phylogenetic studies…………... 31.4 Useful information from chloroplast genomes for addressing phylogenies……………………………………………………………… 31.5 The genetic background of chloroplast genomes………………………... 41.6 Evolution of genome reduction………………………………………….. 41.7 Aims of this study………………………………………………………... 5hapter 2. Materials and Methods………………………………………………... 72.1 CpDNA extraction of C. taitungensis and sequencing…………………... 72.2 Total DNA extraction, cpDNA amplification and sequencing…………... 72.3 Gene annotations and repeat sequence analyses………………………… 82.4 Sequencing of chloroplast ycf2 and tufA genes in other cycads and Ginkgo…………………………………………………………………… 82.5 Reverse transcriptase–polymerase chain reaction……………………….. 92.6 Sequence alignments and phylogenetic analyses ……………………….. 102.7 Dot-plot analyses………………………………………………………… 112.8 Estimations of substitution rates and effective number of codons (ENC).. 112.9 Statistic analyses…………………………………………………………. 12hapter 3. Results………………………………………………………………… 133.1 Characteristics of the C. taitungensis cpDNA…………………………… 133.2 Identification of the pseudo tufA gene…………………………………… 143.3 Only one RNA-editing site in the Cycas cpDNA predicted …………….. 153.4 Phylogenetic trees reconstructed by three different methods reveal consistent results………………………………………………………… 153.5 Comparative structural changes of cpDNAs support the cpDNA phylogeny ………………………………………………………………. 163.6 CpDNAs of Ephedra equisetina and Gnetum parvifolium are the top two smallest among known photosynthetic vascular plants…………………. 173.7 Two unusual RNA-editing sites in the Ephedra cpDNA………………... 183.8 Structural reorganizations in Keteleeria and gnetophyte cpDNAs……… 183.9 Reduction of the cpDNAs of Ephedra, Gnetum, and Welwitschia by multiple gene losses……………………………………………………... 193.10 CpDNA reduction by intron downsizing……………………………….. 193.11 Reduction and compaction by deletions of more inter-operon than intra-operon spaces and of more segments than single nucleotides…….. 203.12 Accelerated substitution rates have strong associations with elevated biased usage of AT-rich codons…………………………………………. 21hapter 4. Discussion…………………………………………………………….. 234.1 Evolution of cpDNA organizations in seed plants ……………………… 234.2 Synteny of an ancient tufA sequence in the cpDNAs of Cycads, Ginkgo, and a hornwort…………………………………………………………… 244.3 Reduction of RNA-editing sites in the cpDNA of Cycas………………... 254.4 CpDNA phylogeny suggests that extant gymnosperms and angiosperms are separate monophyletic clades………………………………………... 254.5 The deepest split in the evolution of extant gymnosperms is between the Cycas–Ginkgo and the Gnetales–Pinales clades………………………… 64.6 Substitution rates and long-branch attraction nearly equal rates in Cycas and Ginkgo………………………………………………………………. 274.7 Accelerated rates in Gnetum and LBA…………………………………... 274.8 Gene orders near IR/LSC junctions contain useful phylogenetic information………………………………………………………………. 294.9 Indels and gene loss/retention lend evidence to the phylogeny within gymnosperms……………………………………………………………. 304.10 Duplication of ycf2 gene in IRB regions predates the divergence of seed plants rather than leafy plants…………………………………………... 314.11 An alternative model for the loss of large IR regions in the Pinus cpDNA………………………………………………………………….. 314.12 CpDNA compaction is the consequence of selection for a reduced genome………………………………………………………………….. 334.13 Structural reorganization in the LSC region occurred before the divergence of the three gnetophyte lineages……………………………. 354.14 An alternative model for structural reorganizations in the SSC and IR regions of gnetophyte cpDNAs…………………………………………. 354.15 Accelerated substitution rates likely resulted from selection for economy or a lower-cost strategy………………………………………. 37hapter 5. Conclusions…………………………………………………………… 40eferences………………………………………………………………………… 42ppendix………………………………………………………………………….. 93ublications……………………………………………………………………….. 94igure listigure 1. The chloroplast genome of Cycas taitungensis…………………………9igure 2. Confirmation of the transcriptional ability of orf75……………………. 60igure 3. Phylogenies of 37 land plants based on 56 cpDNA protein-coding genes……………………………………………………………………. 61igure 4. A NJ tree of 37 land plants inferred from the first two codon positions of 56 cpDNA protein-coding genes……………………………………... 63igure 5. Comparison of the genes flanking the IR–LSC junctions (JLA and JLB) among 8 land plants……………………………………………………... 64igure 6. CpDNA maps of Ephedra equisetina, Gnetum parvifolium, Welwitschia mirabilis, and Keteleeria davidiana…………………………………….. 65igure 7. Alignments of trnR-CCG and trnI-GAU genes, respectively…………... 67igure 8. Dot-plot analyses of three sampled gnetophyte cpDNAs against the Cycas cpDNA…………………………………………………………… 68igure 9. A proposed secondary structure of the Ephedra rpl16 intron…………... 69igure 10. Relationships of mean sizes between two kinds of intergenic spaces in seven sampled gymnosperm cpDNAs…………………………………... 70igure 11. An alignment of pseudo chlL and functional chlL genes……………… 71igure 12. Comparisons of frequencies of AT-rich and GC-rich codons in the cpDNAs of seven elucidated gymnosperms…………………………... 73igure 13. A simplified phylogenetic tree with supports of cpDNA structural changes………………………………………………………………... 74igure 14. A NJ tree based on tufA genes from cyanobacteria, green algae, and land plants…………………………………………………………….. 75igure 15. Verification of the presence of two IR regions in the cpDNAs of Ginkgo biloba and Gnetum parvifolium, and a ycf2 in each IR………. 6igure 16. A 2-step model for the loss of the IRB region in the ancestral cpDNA of Pinus thunbergii……………………………………………………. 77igure 17. Two hypothetical models for the evolution of genomic reorganizations in the cpDNAs of gnetophytes………………………………………... 78 able Listable 1. Grouping of 56 protein-coding genes common to the cpDNAs sampled in the dataset…………………………………………………………….. 80able 2. Accession numbers and references for the taxa used in this study 81able 3. Comparisons of coding and pseudo genes among the cpDNAs of Cycas, Ephedra, Gnetum, Welwitschia, and Keteleeria………………………... 83able 4. Gene content of the C. taitungensis chloroplast genome………………... 85able 5. Position, length of a repetitive element, and sequence of each repeat found in the chloroplast genome of Cycas……………………………… 86able 6. Tajima''s relative rate tests between Cycas, Gnetum and other five seed plant lineages based on concatenated 56 chloroplast protein-coding genes…………………………………………………………………….. 87able 7. Comparisons of characteristics among 9 cpDNAs of photosynthetic vascular plants…………………………………………………………... 88able 8. Comparisons of intron lengths among 7 elucidated gymnosperm cpDNAs…………………………………………………………………. 90able 9. Substitution rates in 7 elucidated gymnosperm cpDNAs based on estimations of concatenated 58 common protein-coding genes………… 9

Graphene oxide–based nanomaterials: An insight into retinal prosthesis

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Retinal prosthesis has recently emerged as a treatment strategy for retinopathies, providing excellent assistance in the treatment of age-related macular degeneration (AMD) and retinitis pigmentosa. The potential application of graphene oxide (GO), a highly biocompatible nanomaterial with superior physicochemical properties, in the fabrication of electrodes for retinal prosthesis, is reviewed in this article. This review integrates insights from biological medicine and nanotechnology, with electronic and electrical engineering technological breakthroughs, and aims to highlight innovative objectives in developing biomedical applications of retinal prosthesis

Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes

Abstract Background Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus. Results We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots—mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT. Conclusions Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages