Nannochloropsis artificial chromosomes(Nanno ACs)loom on the horizon

Species in genus Nannochloropsis,especially N.oceanica and N.gaditana,have been evolving as the model microalgae for both application and theory studies.The position effect of genome integration,the carrying capability limitation of integrative vectors and the instability of non-integrative vectors have hindered Nannochloropsis genetic modification with concatenate genes and extremely long DNA fragments.The molecular tools including genetic transformation,homologous recombination,gene edition,gene stacking and episome vectors for transient gene expression and diverse reporters and selection markers have been rapidly developing in Nannochloropsis species.The construction of animal and plant artificial chromosomes with“top down”strategy has set fine examples for the construction of Nannochloropsis artificial chromosomes(NannoACs).It seems that the methods and materials to set the foundation for constructing NannoACs are at hands.In this review,we outlined the current status of transgenes in Nannochloropsis species,summarized the limitations of both integrative and non-integrative vectors,and proposed a tentative approach to construct NannoACs by doubling and stabilizing the genome first,and then truncating the natural chromosomes.NannoACs once constructed will facilitate transferring the desired traits and concatenate genes into Nannochloropsis genetic backgrounds,thus contributing towards its genetic improvement and synthetic biological studies.

Research on the Construction of Bacterial Artificial Chromosome Vector DNA and the Potentials in Application

[ Objective] The aim of this study was to provide a method for solving the problems in preparing BAC vector with High-copy plasmid pUC119- Bluelox BAC. [ Method ] With selecting a proper single restriction site, sequences of a single copy BAC vector plasmid were inserted into proper site of High-copy plasmid pUC119 vector. [ Result] The gene sequence of BAC vector lost control function of single copy number in new plasmid pUC119-BAC and was copied through High-copy form. The gene sequence of BAC vector basic function was completely cutted off through single enzyme digestion and the control function of single copy could be recovered by auto-connection. [ Conclusion] The High-copy pUC119-BAC plasmid was used to copy and amplify high copy of basic function gene sequence in BAC vector, besides that it could be used to construct transfer vector of molecular cloned recombinant virus or BAC library.

Construction of a full bacterial artificial chromosome(BAC) library of Oryza sativa genome

We have constructed a full BAC library for the superior eaxly indica variety of OryZa sativa, Guang Lu Ai4. The MAX Efficiency DHlOB with increased stabilltyof inserts was used as BAC host cells. The potent pBelo BACII with double selection markers was used as cloning vector. The cloning efficiency we have reached was as high as 98%, and the transformation efficiency was raised up to 1Oo transformants / pg of large fragment DNA. The BAC recombinant transformants were picked at random and analyzed for the size of inserts, which turned out to be of 120 kb in length on average. We have obtained more than 20,000 such BAC clones. According to conventional probabillty equation, they covered the entire rice genome of 420,000 kb in length. The entire length of inserts of the library obtained has the 5- to 6- fold coverage of the genome. To our knowledge, this is the first reported full BAC library for a complex genome.

Bacterial artificial chromosome library construction of root-knot nematode resistant pepper genotype HDA149 and identification of clones linked to Me3 resistant locus

Pepper （Capsicum annuum. L.） is a widely cultivated vegetable crop worldwide and has the second largest planting area and the first largest vegetable output and value in China. Pepper root-knot nematode （Meloidogyne spp.） is one of the most serious pests of pepper, which caused huge losses every year. Previous studies showed that the Me3 gene is resistant to a wide range of Meloidogyne species, including M. arenaria, M. javanica, and M. incognita. HDA149, a double haploid pepper genotype, harboring the root-knot nematode resistance gene Me3, was used to construct bacterial artificial chro- mosome library （BAC） via the vector of CopyControFM pCC1 in this study. The library consists of 210 200 BAC clones and is equivalent to 5.3 pepper genomes. The average insert size is 95 kb, and most of them are 90-120 kb; but the empty clones are less than 3%. In order to screen the BAC library easily, 550 super pools with 384 BAC clones of each pool were further developed in this study. Specific primers from Me3 gene locus were used for BAC library screening, and more than 20 positive BAC clones were obtained. Then the selected positive BAC clones were analyzed by restriction enzyme digestion, BAC-end sequencing, marker development, and new positive BAC clones exploration, respectively. Finally, the contig with total length of about 300 kb linked to the Me3 locus was constructed based on chromosome walking strategy, which made a solid foundation for the cloning of the important root-knot nematode resistance gene Me3.

Transfer of disulfide bond formation modules via yeast artificial chromosomes promotes the expression of heterologous proteins in Kluyveromyces marxianus

Kluyveromyces marxianus is a food-safe yeast with great potential for producing heterologous proteins.Improving the yield in K.marxianus remains a challenge and incorporating large-scale functional modules poses a technical obstacle in engineering.To address these issues,linear and circular yeast artificial chromosomes of K.marxianus(KmYACs)were constructed and loaded with disulfide bond formation modules from Pichia pastoris or K.marxianus.These modules contained up to seven genes with a maximum size of 15 kb.KmYACs carried telomeres either from K.marxianus or Tetrahymena.KmYACs were transferred successfully into K.marxianus and stably propagated without affecting the normal growth of the host,regardless of the type of telomeres and configurations of KmYACs.KmYACs increased the overall expression levels of disulfide bond formation genes and significantly enhanced the yield of various heterologous proteins.In high-density fermentation,the use of KmYACs resulted in a glucoamylase yield of 16.8 g/l,the highest reported level to date in K.marxianus.Transcriptomic and metabolomic analysis of cells containing KmYACs suggested increased flavin adenine dinucleotide biosynthesis,enhanced flux entering the tricarboxylic acid cycle,and a preferred demand for lysine and arginine as features of cells overexpressing heterologous proteins.Consistently,supplementing lysine or arginine further improved the yield.Therefore,KmYAC provides a powerful platform for manipulating large modules with enormous potential for industrial applications and fundamental research.Transferring the disulfide bond formation module via YACs proves to be an efficient strategy for improving the yield of heterologous proteins,and this strategy may be applied to optimize other microbial cell factories.

Construction and Identification of Bacterial Artificial Chromosome Library for 0-613-2R in Upland Cotton

A bacterial artificial chromosome （BAC） library containing a large genomlc DNA insert is an important tool for genome physical mapping, map-based cloning, and genome sequencing. To Isolate genes via a map-based cloning strategy and to perform physical mapping of the cotton genome, a high-quality BAC library containing large cotton DNA Inserts Is needed. We have developed a BAC library of the restoring line 0-613-2R for Isolating the fertility restorer （Rf1） gene and genomic research in cotton （Gossypium hirsutum L.）. The BAC library contains 97 825 clones stored In 255 pieces of a 384-well mlcrotiter plate. Random samples of BACs digested with the Notl enzyme Indicated that the average Insert size Is approximately 130 kb, with a range of 80-275 kb, and 95.7% of the BAC clones in the library have an average insert size larger than 100 kb. Based on a cotton genome size of 2 250 Mb, library coverage is 5.7 × haploid genome equivalents. Four clones were selected randomly from the library to determine the stability of the BAC clones. There were no different fingerprints for 0 and 100 generations of each clone digested with Notl and Hlndiii enzymes. Thus, the atabiiity of a single BAC clone can be sustained at iesat for 100 generations. Eight simple sequence repeat （SSR） markers flanking the Rf; gene were chosen to screen the BAC library by pool using PCR method and 25 positive clones were identified with 3.1 positive clones per SSR marker.

Construction of a Bacterial Artificial Chromosome Library of TM-1,a Standard Line for Genetics and Genomics in Upland Cotton

A bacterial artificial chromosome （BAC） library was constructed for Gossypium hirsutum acc. TM-1, a genetic and genomic standard line for Upland cotton. The library consists of 147 456 clones with an average insert size of 122.8 kb ranging from 97 to 240 kb. About 96.0% of the clones have inserts over 100 kb. Therefore, this library represents theoretically 7.4 haploid genome equivalents based on an AD genome size of 2 425 Mb. Clones were stored in 384 384- well plates and arrayed into multiplex pools for rapid and reliable library screening. BAC screening was carried out by four-round poiymerase chain reactions using 23 simple sequence repeats （SSR） markers, three sequence-related amplified polymorphism markers and one pair of primers for a gene associated with fiber development to test the quality of the library. Correspondingly, in total 92 positive BAC clones were identified with an average four positive clones per SSR marker, ranging from one to eight hits. Additionally, since these SSR markers have been localized to chromosome 12 （A12） and 26 （D12） according to the genetic map, these BAC clones are expected to serve as seeds for the physical mapping of these two homologous chromosomes, sequentially map-based cloning of quantitative trait loci or genes associated with important agronomic traits.

Highly Efficient Base Editing in Viral Genome Based on Bacterial Artificial Chromosome Using a Cas9-Cytidine Deaminase Fused Protein

Viruses evolve rapidly and continuously threaten animal health and economy,posing a great demand for rapid and efficient genome editing technologies to study virulence mechanism and develop effective vaccine.We present a highly efficient viral genome manipulation method using CRISPR-guided cytidine deaminase.We cloned pseudorabies virus genome into bacterial artificial chromosome,and used CRISPR-guided cytidine deaminase to directly convert cytidine(C)to uridine(U)to induce premature stop mutagenesis in viral genes.The editing efficiencies were 100%.Comprehensive bioinformatic analysis revealed that a large number of editable sites exist in pseudorabies virus(PRV)genomes.Notably,in our study viral genome exists as a plasmid in E.coli,suggesting that this method is virus species-independent.This application of base-editing provided an alternative approach to generate mutant virus and might accelerate study on virulence and vaccine development.

Generation and expression analysis of BAC humanized mice carrying HLA-DP401 haplotype

Background:Human leukocyte antigen(HLA)-DP is much less studied than other HLA class Ⅱ antigens,that is,HLA-DR and HLA-DQ,etc.However,the accumulating data have suggested the important roles of DP-restricted responses in the context of cancer,allergy,and infectious disease.Lack of animal models expressing these genes as authentic cis-haplotypes blocks our understanding for the role of HLA-DP haplotypes in immunity.Methods:To explore the potential cis-acting control elements involved in the tran-scriptional regulation of the HLA-DPA1/DPB1 gene,we performed the expression analysis using bacterial artificial chromosome(BAC)-based transgenic humanized mice in the C57BL/6 background,which carried the entire HLA-DP401 gene locus.We further developed a mouse model of Staphylococcus aureus pneumonia in HLA-DP401 humanized transgenic mice,and performed the analysis on the expres-sion pattern of HLA-DP401 and immunological responses in the model.Results:In this study,we screened and identified a BAC clone spanning the entire HLA-DP gene locus.DNA from this clone was analyzed for integrity by pulsed-field gel electrophoresis and then microinjected into fertilized mouse oocytes to produce transgenic founder animals.Nine sets of PCR primers for regional markers with an average distance of 15 kb between each primer were used to confirm the integrity of the transgene in the five transgenic lines carrying the HLA-DPA1/DPB1 gene.Transgene copy numbers were determined by real-time PCR analysis.HLA-DP401 gene expression was analyzed at the mRNA and protein level.Although infection with S aureus Newman did not alter the percentage of immune cells in the spleen and thymus from the HLA-DP401-H2-Aβ1 humanized mice.Increased expression of HLA-DP401 was observed in the thymus of the humanized mice infected by S aureus.Conclusions:We generated several BAC transgenic mice,and analyzed the expres-sion of HLA-DPA1/DPB1 in those mice.A model of S aureus-induced pneumonia in the HLA-DP401-H2-Aβ1^(-/-)humanized mice was further developed,and S aureus in-fection upregulated the HLA-DP401 expression in thymus of those humanized mice.These findings demonstrate the potential of those HLA-DPA1/DPB1 transgenic humanized mice for developing animal models of infectious diseases and MHC-associated immunological diseases.

Transgenic Rice Plants Harboring Genomic DNA from Zizania latifolia Confer Bacterial Blight Resistance

Based on the sequence of a resistance gene analog FZ14 derived from Zizania latifolia （Griseb.）, a pair of specific PCR primers FZ14P1/FZ14P2was designed to isolate candidate disease resistance gene. The pooled-PCR approach was adopted using the primer pair to screen a genomic transformation-competent artificial chromosome （TAC） library derived from Z. latifolia. A positive TAC clone （ZR1） was obtained and confirmed by sequence analysis. The results indicated that ZR1 consisted of conserved motifs similar to P-loop （kinase la）, kinase 2, kinase 3a and GLPL （Gly-Leu-Pro-Leu）, suggesting that it could be a portion of NBS-LRR type of resistance gene. Using Agrobacterium-mediated transformation of Nipponbare mature embryo, a total of 48 independent transgenic To plants were obtained. Among them, 36 plants were highly resistant to the virulent bacterial blight strain PXO71. The results indicate that ZR1 contains at least one functional bacterial blight resistance gene.

Preparation of high molecular weight （HMW） genomic DNA from tea plant （Camellia sinensis） for BAC library construction

A bacterial artificial chromosome （BAC） library is an invaluable resource tool to initiate tea plant genomics research, and the preparation of high molecular weight （HMW） genomic DNA is a crucial first step for constructing a BAC Library. In order to construct a BAC library for enhancing tea plant genomics research, a new method for the preparation of tea pant high molecular weight （HMW） genomic DNA must be developed due to young tea plant leaves and shoots are notably rich in both tea polyphenols and tea polysaccharides. In this paper, a modified method for preparing high quality tea plant HMW genomi~ DNA was optimized, and the quality of tea plant genomic DNA was evaluated. The results were as follows： Critical indicators of HMW DNA preparation were the appearance of the smooth nuclei in solution （as opposed to sticky-gummy） before agarose plug solidification, non-dark colored nuclei plugs after lysis with an SDS/proteinase K solution, and the quality and quantity of HMW DNA fragments after restriction enzyme digestion. Importantly, 1% dissolved PVP-40 and 1% un-dissolved PVP-40 during the nuclei extraction steps, in conjunction with the removal of PVP-40 from the plug washing and nuclei lysis steps, were critical for achieving HWM tea plant DNA suitable for BAC library construction. Additionally, a third PFGE fraction selection step to eliminate contaminating small DNA fragments. The modifications provided parameters that may have prevented deleterious interactions from tea polyphenols and tea polysaccharides. The HMW genomic DNA produced by this new modified method has been used to successfully construct a large-insert tea plant BAC library, and thus may be suitable for BAC library construction from other plant species that contain similarly interfering compounds.

Diversity of Sodium Transporter HKT1;5 in Genus Oryza

Asian cultivated rice shows allelic variation in sodium transporter,OsHKT1;5,correlating with shoot sodium exclusion(salinity tolerance).These changes map to intra/extracellularly-oriented loops that occur between four transmembrane-P loop-transmembrane(MPM)motifs in OsHKT1;5.HKT1;5 sequences from more recently evolved Oryza species(O.sativa/O.officinalis complex species)contain two expansions that involve two intracellularly oriented loops/helical regions between MPM domains,potentially governing transport characteristics,while more ancestral HKT1;5 sequences have shorter intracellular loops.We compared homology models for homoeologous OcHKT 1;5-K and OcHKT1;5-L from halophytic O.coarctata to identify complementary amino acid residues in OcHKT1;5-L that potentially enhance affinity for Na+.Using haplotyping,we showed that Asian cultivated rice accessions only have a fraction of HKT1;5 diversity available in progenitor wild rice species(O.nivara and O.rufipogon).Progenitor HKT1;5 haplotypes can thus be used as novel potential donors for enhancing cultivated rice salinity tolerance.Within Asian rice accessions,10 non-synonymous HKT1;5 haplotypic groups occur.More HKT1;5 haplotypic diversities occur in cultivated indica gene pool compared to japonica.Predominant Haplotypes 2 and 10 occur in mutually exclusive japonica and indica groups,corresponding to haplotypes in O.sativa salt-sensitive and salt-tolerant landraces,respectively.This distinct haplotype partitioning may have originated in separate ancestral gene pools of indica and japonica,or from different haplotypes selected during domestication.Predominance of specific HKT1;5 haplotypes within the 3000 rice dataset may relate to eco-physiological fitness in specific geo-climatic and/or edaphic contexts.

Construction of Gpm6a/ReelinGFPCreERT2 by BAC recombination using a specific gene in hepatic mesothelial or stellate cells

AIM To prepare a Gpm6a/Reelin^(GFPCreERT2) construct with a rapid and reliable strategy using a bacterial artificial chromosome(BAC). METHODS Gpm6 a and Reelin BACs were purified and transformed into SW102 E. coli by electroporation. The GFPCreE RT2 fragment was prepared from a shuttle vector and transformed into SW102 E. coli carrying a BAC. Homologous recombination was induced in SW102 E. coli. Recombinant clones were screened and confirmed by PCR and restriction enzyme digestion. Recombinant clones were transformed into SW102 E. coli to remove the kanamycin unit.RESULTS A complete BAC was successfully transformed into SW102 E. coli by electroporation because BAC purified from SW102 E. coli showed the same pattern as the original BAC with Bam H I digestion. The GFPCre ERT2 fragment was deemed to have been prepared successfully because we obtained the same size fragment as expected. Homologous recombination was induced, and GFPCre ERT2 was deemed to have been inserted into the correct site of the BAC because we found the band change was the same as the expected pattern after restriction enzyme digestion. The kanamycin unit was deemed to have been removed successfully because we obtained different sizes of bands that were consistent with the results expected by PCR with different primers. CONCLUSION The construct of Gpm6 a^(GFPCreERT2) or Reelin^(GFPCreERT2) was prepared successfully, which will establish a foundation for tracing the hepatic stellate cell lineage and studying its function.

Machine learning-aided scoring of synthesis difficulties for designer chromosomes

Designer chromosomes are artificially synthesized chromosomes.Nowadays,these chromosomes have numerous applications ranging from medical research to the development of biofuels.However,some chromosome fragments can interfere with the chemical synthesis of designer chromosomes and eventually limit the widespread use of this technology.To address this issue,this study aimed to develop an interpretable machine learning framework to predict and quantify the synthesis difficulties of designer chromosomes in advance.Through the use of this framework,six key sequence features leading to synthesis difficulties were identified,and an e Xtreme Gradient Boosting model was established to integrate these features.The predictive model achieved high-quality performance with an AUC of 0.895 in cross-validation and an AUC of 0.885 on an independent test set.Based on these results,the synthesis difficulty index(S-index)was proposed as a means of scoring and interpreting synthesis difficulties of chromosomes from prokaryotes to eukaryotes.The findings of this study emphasize the significant variability in synthesis difficulties between chromosomes and demonstrate the potential of the proposed model to predict and mitigate these difficulties through the optimization of the synthesis process and genome rewriting.

Exogenous artificial DNA forms chromatin structure with active transcription in yeast

Yeast artificial chromosomes(YACs) are important tools for sequencing,gene cloning,and transferring large quantities of genetic information.However,the structure and activity of YAC chromatin,as well as the unintended impacts of introducing foreign DNA sequences on DNA-associated biochemical events,have not been widely explored.Here,we showed that abundant genetic elements like TATA box and transcription factor-binding motifs occurred unintentionally in a previously reported datacarrying chromosome(d Chr).In addition,we used state-of-the-art sequencing technologies to comprehensively profile the genetic,epigenetic,transcriptional,and proteomic characteristics of the exogenous d Chr.We found that the data-carrying DNA formed active chromatin with high chromatin accessibility and H3K4 tri-methylation levels.The d Chr also displayed highly pervasive transcriptional ability and transcribed hundreds of noncoding RNAs.The results demonstrated that exogenous artificial chromosomes formed chromatin structures and did not remain as naked or loose plasmids.A better understanding of the YAC chromatin nature will improve our ability to design better data-storage chromosomes.

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

Arabidopsis thaliana is an important and long-established model species for plant molecular biology,genetics,epigenetics,and genomics.However,the latest version of reference genome still contains a significant number of missing segments.Here,we reported a high-quality and almost complete Col-0 genome assembly with two gaps(named Col-XJTU)by combining the Oxford Nanopore Technologies ultra-long reads,Pacific Biosciences high-fidelity long reads,and Hi-C data.The total genome assembly size is 133,725,193 bp,introducing 14.6 Mb of novel sequences compared to the TAIR10.1 reference genome.All five chromosomes of the Col-XJTU assembly are highly accurate with consensus quality(QV)scores>60(ranging from 62 to 68),which are higher than those of the TAIR10.1 reference(ranging from 45 to 52).We completely resolved chromosome(Chr)3 and Chr5 in a telomere-to-telomere manner.Chr4 was completely resolved except the nucleolar organizing regions,which comprise long repetitive DNA fragments.The Chrl centromere(CEN1),reportedly around 9 Mb in length,is particularly challenging to assemble due to the presence of tens of thousands of CEN180 satellite repeats.Using the cutting-edge sequencing data and novel computational approaches,we assembled a 3.8-Mb-long CEN1 and a 3.5-Mb-long CEN2.We also investigated the structure and epigenetics of centromeres.Four clusters of CEN180 monomers were detected,and the centromere-specific histone H3-like protein(CENH3)exhibited a strong preference for CEN180 Cluster 3.Moreover,we observed hypomethylation patterns in CENH3-enriched regions.We believe that this high-quality genome assembly,Col-XJTU,would serve as a valuable reference to better understand the global pattern of centromeric polymorphisms,as well as the genetic and epigenetic features in plants.

Genome-wide screening and transcriptional profile analysis of desaturase genes in the European corn borer moth

Acyl-coenzyme A （Acyl-CoA） desaturases play a key role in the biosynthesis of female moth sex pheromones. Desaturase genes are encoded by a large multigene family, and they have been divided into five subgroups on the basis of biochemical functionality and phylogenetic affinity. In this study both copy numbers and transcriptional levels of desaturase genes in the European corn borer （ECB）, Ostrinia nubilalis, were investigated. The results from genome-wide screening of ECB bacterial artificial chromosome （BAC） library indicated there are many copies of some desaturase genes in the genome. An open reading frame （ORF） has been isolated for the novel desaturase gene ECB ezi-A11~ from ECB gland complementary DNA and its functionality has been analyzed by two yeast expression systems. No functional activities have been detected for it. The expression levels of the four desaturase genes both in the pheromone gland and fat body of ECB and Asian corn borer （ACB）, O. furnacalis, were determined by real-time polymerase chain reaction. In the ECB gland, All is the most abundant, although the amount of A14 is also considerable. In the ACB gland, A14 is the most abundant and is 100 times more abundant than all the other three combined. The results from the analysis of evolution of desaturase gene transcription in the ECB, ACB and other moths indicate that the pattern of A 11 gene transcription is significantly different from the transcriptional patterns of other desaturase genes and this difference is tied to the underlying nucleotide composition bias of the genome.

A Puzzle-Based Genetic Algorithm with Block Mining and Recombination Heuristic for the Traveling Salesman Problem

In this research, we introduce a new heuristic approach using the concept of ant colony optimization （ACO） to extract patterns from the chromosomes generated by previous generations for solving the generalized traveling salesman problem. The proposed heuristic is composed of two phases. In the first phase the ACO technique is adopted to establish an archive consisting of a set of non-overlapping blocks and of a set of remaining cities （nodes） to be visited. The second phase is a block recombination phase where the set of blocks and the rest of cities are combined to form an artificial chromosome. The generated artificial chromosomes （ACs） will then be injected into a standard genetic algorithm （SGA） to speed up the convergence. The proposed method is called ＂Puzzle-Based Genetic Algorithm＂ or ＂p-ACGA＂. We demonstrate that p-ACGA performs very well on all TSPLIB problems, which have been solved to optimality by other researchers. The proposed approach can prevent the early convergence of the genetic algorithm （GA） and lead the algorithm to explore and exploit the search space by taking advantage of the artificial chromosomes.

Expression of recombinant human butyrylcholinesterase in the milk of transgenic mice

Butyrylcholinesterase(BCHE)is a natural bioscavenger that protects humans against organophosphate toxicity.Due to the limited yield of human BCHE(hBCHE)when purifying from human plasma,it is necessary to find an alternative method to produce this protein.One potential method is to produce transgenic livestock that make modified milk containing high concentration of hBCHE.In this study,we cloned the hBCHEgene into a human lactoferrin(hLF)bacterial artificial chromosome(BAC)construct to make a hLFhBCHE BAC construct.Subsequently,we injected the BAC construct into pronuclei of mouse fertilized embryos and generated transgenic mice.Expression analysis showed that recombinant hBCHE(rhBCHE)was expressed efficiently in the mammary gland of the transgenic mice and the concentration of rhBCHE in the milk of individual mice ranged from 76
12 to 159
28 mg·L^(–1).Protein function tests showed that rhBCHE has the same enzymatic activity as the native hBCHE.Our results pave the way for making transgenic livestock to produce large quantities of rhBCHE.