Lycophyte transcriptomes reveal two whole-genome duplications in Lycopodiaceae:Insights into the polyploidization of Phlegmariurus

Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds.They are an excellent study system for examining whole-genome duplications(WGDs),or polyploidization,in spore-dispersed vascular plants.However,a lack of genome sequence data limits the reliable detection of very ancient WGDs,small-scale duplications(SSDs),and recent WGDs.Here,we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites(Ks)of the transcriptomes of 13 species of lycophytes to identify,locate,and date multiple WGDs in the lycophyte family Lycopodiaceae.Additionally,we examined the genus Phlegmariurus for signs of genetic discordance,which can provide valuable insight into the underlying causes of such conflict(e.g.,hybridization,incomplete lineage sorting,or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae,with one occurring in the common ancestor of extant Phlegmariurus(Lycopodiaceae)approximately 22-23 million years ago(Mya)and the other occurring in the common ancestor of Lycopodiaceae around 206-214 Mya.Interestingly,we found significant genetic discordance in the genus Phlegmariurus,indicating that the genus has a complex evolutionary history.This study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.

Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species,Cyclocarya paliurus

Cyclocarya paliurus is a relict plant species that survived the last glacial period and shows a population expansion recently.Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B.Here,we presented three C.paliurus genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly.Comparative genomic analysis revealed two rounds of recent whole-genome duplication events and identified 691 genes with dosage effects that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of triterpenoids.Resequencing analysis of 45 C.paliurus individuals uncovered two bottlenecks,consistent with the known events of environmental changes,and many selectively swept genes involved in critical biological functions,including plant defense and secondary metabolite biosynthesis.We also proposed the biosynthesis pathway of cyclocaric acid B based on multi-omics data and identified key genes,in particular gibberellinrelated genes,associated with the heterodichogamy in C.paliurus species.Our study sheds light on evolutionary history of C.paliurus and provides genomic resources to study the medicinal herbs.

Effect of Whole-Genome Duplication on the Evolutionary Rescue of Sterile Hybrid Monkeyflowers

Hybridization is a creative evolutionary force,increasing genomic diversity and facilitating adaptation and even speciation.Hybrids often face significant challenges to establishment,including reduced fertility that arises from genomic incompatibilities between their parents.Whole-genome duplication in hybrids(allopolyploidy)can restore fertility,cause immediate phenotypic changes,and generate reproductive isolation.Yet the survival of polyploid lineages is uncertain,and few studies have compared the performance of recently formed allopolyploids and their parents under field conditions.Here,we use natural and synthetically produced hybrid and polyploid monkeyflowers(Mimulus spp.)to study how polyploidy contributes to the fertility,reproductive isolation,phenotype,and performance of hybrids in the field.We find that polyploidization restores fertility and that allopolyploids are reproductively isolated from their parents.The phenotype of allopolyploids displays the classic gigas effect of whole-genome duplication,in which plants have larger organs and are slower to flower.Field experiments indicate that survival of synthetic hybrids before and after polyploidization is intermediate between that of the parents,whereas natural hybrids have higher survival than all other taxa.We conclude that hybridization and polyploidy can act as sources of genomic novelty,but adaptive evolution is key in mediating the establishment of young allopolyploid lineages.

Phylotranscriptomics in Cucurbitaceae Reveal Multiple Whole-Genome Duplications and Key Morphological and Molecular Innovations

The ability of climbing plants to grow upward along others to reach the canopy for photosynthesis is hypothesized as a key innovation in flowering plants.Most members of the Cucurbitaceae,a family containing^1000 species and many important crops,are climbers and have characteristic tendrils and pepo fruits.Here,we present 127 newly sequenced transcdptomes and genomes along with other datasets for a total of 136 cucurbits representing all tribes to establish a robust Cucurbitaceae phylogeny containing eight highly resolved major clades.We analyzed whole-genome duplication,diversification dynamics,and ancestral morphologies,and found that after early genome duplication event(s),a burst of diversification and morphological innovations in flower,fruit,and root characters occurred under the climate optimum in the Early Eocene.Species radiation during the Mid-Eocene Climatic Optimum also coincided with several morphological changes shared by 80%of cucurbits.We found that the cucurbit-specific tendril identity gene TEN originated from a paleo-polyploidization event at the origin of the family.Our results support the hypothesis that cucurbit diversifications were probably driven by increased genetic diversity following polyploidizations and by trait morphological innovations under paleo-climate upheavals.Our study provides a phylogenetic framework and new insights into morphological and genomic changes underlying the adaptive evolution of Cucurbitaceae.

Multiple thoracic and abdominal foregut duplication cysts:A case report

BACKGROUND Congenital enteric duplication cysts are tubular or cystic structures that normally lie alongside the gastrointestinal(GI)tract.Enteric duplication cysts are typically solitary lesions that occur anywhere near the GI tract from the neck to the rectum,but having multiple duplication cysts is rare,and presentation within the pancreas is extremely rare.CASE SUMMARY We herein demonstrate a case of esophageal,gastric,and gastric-type duplication cyst of the pancreas in a seventeen-month-old girl who presented with failure to thrive,abdominal pain,vomiting,hematemesis,and melena since the age of three months.The cysts were excised by thoracoscopy and laparoscopy in the same setting.To our knowledge,no such case has been published.CONCLUSION Enteric duplications can occur throughout the entire alimentary tract.When they occur in the pancreas,they present a formidable challenge in both diagnosis and treatment.Due to the risk of complications and malignant transformation,surgical removal is the recommended treatment of all duplication cysts.

Inferring Mycobacterium Tuberculosis Drug Resistance and Transmission using Whole-genome Sequencing in a High TB-burden Setting in China

Objective China is among the 30 countries with a high burden of tuberculosis(TB)worldwide,and TB remains a public health concern.Kashgar Prefecture in the southern Xinjiang Autonomous Region is considered as one of the highest TB burden regions in China.However,molecular epidemiological studies of Kashgar are lacking.Methods A population-based retrospective study was conducted using whole-genome sequencing(WGS)to determine the characteristics of drug resistance and the transmission patterns.Results A total of 1,668 isolates collected in 2020 were classified into lineages 2(46.0%),3(27.5%),and 4(26.5%).The drug resistance rates revealed by WGS showed that the top three drugs in terms of the resistance rate were isoniazid(7.4%,124/1,668),streptomycin(6.0%,100/1,668),and rifampicin(3.3%,55/1,668).The rate of rifampicin resistance was 1.8%(23/1,290)in the new cases and 9.4%(32/340)in the previously treated cases.Known resistance mutations were detected more frequently in lineage 2 strains than in lineage 3 or 4 strains,respectively:18.6%vs.8.7 or 9%,P<0.001.The estimated proportion of recent transmissions was 25.9%(432/1,668).Multivariate logistic analyses indicated that sex,age,occupation,lineage,and drug resistance were the risk factors for recent transmission.Despite the low rate of drug resistance,drug-resistant strains had a higher risk of recent transmission than the susceptible strains(adjusted odds ratio,1.414;95%CI,1.023–1.954;P=0.036).Among all patients with drug-resistant tuberculosis(DR-TB),78.4%(171/218)were attributed to the transmission of DR-TB strains.Conclusion Our results suggest that drug-resistant strains are more transmissible than susceptible strains and that transmission is the major driving force of the current DR-TB epidemic in Kashgar.

Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs

Background Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones.Nevertheless,the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear.Results Here,we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical,high-altitude,and frigid regions.Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds.Analysis of selection signals revealed regions under selection for adaptation in tropical(55.5 Mb),high-altitude(43.6 Mb),and frigid(17.72 Mb)regions.The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments,including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments.Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation.These pathways included blood circulation,protein degradation,and inflammation for adaptation to tropical environments;heart and lung development,hypoxia response,and DNA damage repair for high-altitude adaptation;and thermogenesis,cold-induced vasodilation(CIVD),and the cell cycle for adaptation to frigid environments.By examining the chromatin state of the selection signatures,we identified the lung and ileum as two candidate functional tissues for environmental adaptation.Finally,we identified a mutation(chr1:G246,175,129A)in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments.Conclusions In this study,we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical,high-altitude,and frigid environments.Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.

Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper(Plectropomus leopardus)

The leopard coral grouper(Plectropomus leopardus)is a species of significant economic importance.Although artificial cultivation of P.leopardus has thrived in recent decades,the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data.In this study,we identified over 8.73 million single nucleotide polymorphisms(SNPs)through whole-genome resequencing of 326 individuals spanning six distinct groups.Furthermore,we categorized 226 individuals with high-coverage sequencing depth(≥14×)into eight clusters based on their genetic profiles and phylogenetic relationships.Notably,four of these clusters exhibited pronounced genetic differentiation compared with the other populations.To identify potentially advantageous loci for P.leopardus,we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity(θπ)and fixation index(FST)in these four clusters.Using these high-coverage resequencing data,we successfully constructed the first haplotype reference panel specific to P.leopardus.This achievement holds promise for enabling high-quality,cost-effectiveimputationmethods.Additionally,we combined low-coverage sequencing data with imputation techniques for a genome-wide association study,aiming to identify candidate SNP loci and genes associated with growth traits.A significant concentration of these genes was observed on chromosome 17,which is primarily involved in skeletal muscle and embryonic development and cell proliferation.Notably,our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs,showing potential for genetic selective breeding efforts.These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P.leopardus.

Duplication of the Urethra in Boys: A Case Report

Supernumerary urethra in boys is a very rare anatomical entity. Sagittal urethral duplications are classified into four groups: epispadias, hypospadias, fusiform and Y-shaped urethra. The most widely used classification is that of Effmann and Lebowitz, which describes 6 types, one of the rarest being the ‘Y’ subtype IIA2, which corresponds to a duplicated urethral path from the vesical neck to an ectopic perineal or anal outlet. We report here the case of a 4-year-old child presenting with subtype IIA2 with a perineal orifice and no other urinary disorders.

Segmental Duplications Are Common in Rice Genome

Segmental duplications on rice (Oryza sativa L.) chromosomes 8, 9, 11, and 12 were studied by examining the distributions of sequences resolved by 13 probes detecting multiple copies of DNA sequences. Four of the hybridization bands detected by a repetitive sequence probe, rTRS, were mapped to the ends of all the four chromosomes. Two or three of the bands detected by each of the other 12 probes were also mapped to different chromosomes. The bands detected by the same probe usually occurred in similar locations of different chromosomes. Loci detected by different DNA probes were often similarly arranged on different chromosomes. Chromosomes 8 and 9 showed colinearity of marker loci arrangement indicating a possible common origin. A segment on chromosome 9 was also very similar to the previously reported duplicated fragments on the ends of chromosomes 11 and 12 which were also detected in this study, indicating a likely common origin. Moreover, the various degrees of distributional similarity of the segments suggest a complex relationship among the chromosomes in the evolution of the rice genome. These results support the proposition that chromosome duplication and diversification may be a mechanism for the origin and evolution of the chromosomes in the rice genome.

基于Duplication Authority的TPM2.0密钥迁移协议

《TPM-Rev-2.0-Part-1-Architecture-01.38》国际标准允许用户基于密钥复制接口设计迁移协议,此复制接口通过innerwrap和outerwrap为密钥迁移提供机密性、完整性和认证性.但研究发现,基于该复制接口来设计密钥迁移协议存在3个问题:其一是缺少交互双方TPM的相互认证,会导致密钥能够在敌手和TPM间迁移;其二是当迁移密钥的属性encryptedDuplication=0且新父密钥的句柄newParentHandle=TPM_RH_NULL时,复制接口不能实施innerwrap和outerwrap,迁移密钥将以明文传输而造成泄露;其三当新父密钥是对称密钥时,innerwrap中的对称加密密钥以及outerwrap中的密钥种子如何在源TPM与目标TPM之间安全交换,《TPM-Rev-2.0-Part-1-Architecture-01.38》并没有给出具体的解决办法.针对上述问题,提出了基于Duplication Authority的密钥迁移协议.该协议以Duplication Authority为认证和控制中心,将密钥迁移过程分为初始化阶段、认证和属性获取阶段以及控制和执行阶段.Duplication Authority通过判定密钥的复制属性和类型、新父密钥的密钥类型和句柄类型来决定迁移流程.考虑了各种合理的属性组合,共设计了12种迁移流程.最后对该协议进行了安全分析和实验验证,结果显示,该协议不仅完全满足《TPM-Rev-2.0-Part-1-Architecture-01.38》规范,而且可以保证迁移密钥的完整性、机密性和认证性.

Rare adult gastric duplication cyst mimicking a gastrointestinal stromal tumor

Gastric duplication cyst is a very rare gastrointestinal tract malformation that accounts for 2%-4%of alimentary tract duplications.Most cases are diagnosed within the first year of life,following presentation of abdominal pain,vomiting,and weight loss and clinical discovery of an abdominal palpable mass.This case report describes a very uncommon symptomatic gastric duplication cyst diagnosed for the first time in adulthood.Only a few other case reports of similar condition exist,and all were identified by endosonography.The current case involves a 52-year-old male who presented with a onemonth history of progressive iron deficiency anemia without overt gastrointestinal bleeding.The patient underwent esophagogastroduodenoscopy,which revealed a 2.0 cm pinkish subepithelial lesion,suspected to be a gastrointestinal stromal tumor(GIST)and source of gastrointestinal bleeding.The endosonography showed inhomogeneous hypoechoic lesions with focal anechoic areas arising from a second and third layer of the gastric wall.Differential diagnoses of GIST,neuroendocrine tumor,or pancreatic heterotopia were made.The lesion was removed using an endoscopic submucosal resection technique.Histopathology revealed an erosive gastric mass composed of a complex structure of dilated gastric glands surrounded by fibro-muscular tissue,fibroblasts,and smooth muscle bundles,which led to the diagnosis of gastric duplication.

Partial intestinal obstruction secondary to multiple lipomas within jejunal duplication cyst: A case report

Lipoma within jejunal duplication presenting as abdominal bloating and partial intestinal obstruction is an exceptional clinical entity.We report a case of 68-year-old man complaining of abdominal bloating for 10 d due to multiple lipomas arising from jejunal duplication cysts.Only a few cases of a single lipoma within a Meckel’s diverticulum giving rise to this clinical scenario have been reported in the English language literature.However,no case of multiple lipomas within jejunal duplication cysts has been reported.We present a case in which doubleballoon endoscopy revealed a small intestinal structure changed into Meckel’s diverticulum-like cavities containing several lipomas.This case highlights intestinal lipoma as an uncommon cause of adult intussusceptions,which should be included in the differential diagnosis of small intestinal obstruction and appropriate examinations should be chosen.

Intestinal duplication in adulthood: A rare entity, difficult to diagnose

Duplications of the alimentary tract (ATD) are rare congenital anomalies often found early in life. They may occur anywhere in the intestinal tract but the ileum is the most frequently affected site. Clinical presentation of ATD in adults is variable and because these lesions occur so infrequently they are rarely suspected. In the present report we describe a case of ileal duplication in a 61-year-old patient with Crohn’s disease. Despite various radiological investigations and medical consultations, the diagnosis was only made on the surgical specimen.

Duplication of the transverse colon in an adult:Case report and review

Tubular duplication of the colon is very rare especially in adulthood,because it is frequently symptomatic earlier in newborn life,so only few cases are reported in literature.Several theories are proposed to explain the onset and the evolution of gut malformations as the aberrant lumen recanalization or the diverticular theory,the alteration of the lateral closure of the embryonal disk or finally the dorsal protrusion of the yolksac for herniation or adhesion to the ectoderm for an abnormality of the longitudinal line,but none clarifies the exact genesis of duplication.We present a case of "Y-shaped" tubular duplication of the transverse colon in a 21-year-old adult,with a history of chronic pain and constipation,referred to our department for abdominal pain with retrosternal irradiation,treated with the resection of the aberrant bowel.

A case of a duodenal duplication cyst presenting as melena

Duodenal duplication cysts are benign rare congenital anomalies reported mainly in the pediatric population,but seldom in adults.Symptoms depend on the type and location and can present as abdominal pain,distension,dysphagia or dyspepsia.They have been reported to be responsible for duodenal obstruction,pancreatitis and,in rare cases,gastrointestinal bleeding.We present a case of a duodenal duplication cyst in a 43-year-old man presenting as melena.Initial gastroduodenoscopy and colonoscopy did not reveal any bleeding focus.However,the patient began passing melena after 3 d,with an acute decrease in hemoglobin levels.Subsequent studies revealed a duplication cyst in the second portion of the duodenum which was surgically resected.Histology revealed a duodenal duplication cyst consisting of intestinal mucosa.There was no further bleeding and the patient recovered completely.In rare cases,duodenal duplication cysts might cause gastrointestinal bleeding and should be included in the differential diagnosis.

Total colorectal and terminal ileal duplication presenting as intussusception and intestinal obstruction

Colonic intussusception and gastrointestinal duplication are diseases that arise in young children. The clinical presentation of adult cases of intussusception and enteric duplication is non-specific and thus poses a diagnostic challenge. A computed tomography (CT) scan is recommended in adult cases as the most sensitive diagnostic tool and the pathognomonic finding of outer intussuscepiens and central intussusceptum is diagnostic. A septum of a duplicated colon in a non-intussuscepted segment has been rarely reported in the literature. With advancements in radiological imaging technology and the increased availability of CT scanners, the capacity for a correct pre-operative diagnosis has been significantly enhanced. Our current case report illustrates the importance of considering an uncommon etiology for enteric intussusception and duplication as a differential diagnosis of acute abdomen in an adult patient. Our analyses of this patient also highlight the successful use of CT scanning to make this diagnosis.

Foregut duplication cysts of the stomach with respiratory epithelium

Gastrointestinal duplication is a congenital rare disease entity. Gastric duplication cysts seem to appear even more rarely. Herein, two duplications cysts of the stomach in a 46 year-old female patient are presented. Abdominal computed tomography demonstrated a cystic lesion attached to the posterior aspect of the gastric fundus, while upper gastrointestinal endoscopy was negative. An exploratory laparotomy revealed a non-communicating cyst and a smaller similar cyst embedded in the gastrosplenic ligament. Excision of both cysts along with the spleen was performed and pathology reported two smooth muscle coated cysts with a pseudostratified ciliated epithelial lining (respiratory type).

Alimentary tract duplications in newborns and children: Diagnostic aspects and the role of laparoscopic treatment

Alimentary tract duplications are rare congenital lesions normally diagnosed in newborns and children that can occur anywhere from the mouth to the anus and have a reported incidence of approximately 1 in 4500 life births. Symptoms and clinical presentation vary greatly. The presentation varies according to age and location. The treatment finally is surgical; total resection when possible should be the aim of the intervention. In pediatric surgery minimally invasive surgical procedures became more and more important over the last decades. In consequence the operative procedure on alimentary tract duplications changed in this manner. We review on case reports and clinical reports on minimally invasive surgery in the treatment of alimentary tract duplications, determine the importance of minimally invasive techniques in the treatment of this rare entity and rule out that further studies in the field should be performed.

Laparoscopic resection of adult colon duplication causingintussusception

Gastrointestinal duplications are uncommon congenital malformations that can occur anywhere along the gastrointestinal tract. Most cases are recognized before the age of 2 years, and those encountered in adults are rare. We describe here a case of ascending colon duplication in a 20-year-old male that caused intussusception and was treated laparoscopically. Although computed tomography revealed a cystic mass filled with stool-like material, the preoperative diagnosis was a submucosal tumor of the ascending colon. We performed a laparoscopic right colectomy, and the postoperative pathological diagnosis was duplication of the ascending colon, both cystic and tubular components. We conclude that gastrointestinal duplications, although rare, should be considered in the differential diagnosis of all abdominal and submucosal cystic lesions and that laparoscopy is a preferred approach for the surgical treatment of gastrointestinal duplications.