RESUMEN
Current source and mask optimization (SMO) research tends to focus on advanced inverse optimization algorithms to accelerate SMO procedures. However, innovations of forward imaging models currently attract little attention, which impacts computational efficiency more significantly. A sampling-based imaging model is established with the innovation of an inverse point spread function to reduce computational dimensions, which can provide an advanced framework for fast inverse lithography. Simulations show that the proposed SMO method with the help of the proposed model can further speed up the algorithm-accelerated SMO procedure by a factor of 3.
RESUMEN
BACKGROUND: The Stephania tetrandra S. Moore (S. tetrandra) is a medicinal plant belonging to the family Menispermaceae that has high medicinal value and is well worth doing further exploration. The wild resources of S. tetrandra were widely distributed in tropical and subtropical regions of China, generating potential genetic diversity and unique population structures. The geographical origin of S. tetrandra is an important factor influencing its quality and price in the market. In addition, the species relationship within Stephania genus still remains uncertain due to high morphological similarity and low support values of molecular analysis approach. The complete chloroplast (cp) genome data has become a promising strategy to determine geographical origin and understand species evolution for closely related plant species. Herein, we sequenced the complete cp genome of S. tetrandra from Zhejiang Province and conducted a comparative analysis within Stephania plants to reveal the structural variations, informative markers and phylogenetic relationship of Stephania species. RESULTS: The cp genome of S. tetrandra voucher ZJ was 157,725 bp, consisting of a large single copy region (89,468 bp), a small single copy region (19,685 bp) and a pair of inverted repeat regions (24,286 bp each). A total of 134 genes were identified in the cp genome of S. tetrandra, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes and 2 pseudogene copies (ycf1 and rps19). The gene order and GC content were highly consistent in the Stephania species according to the comparative analysis results, with the highest RSCU value in arginine (1.79) and lowest RSCU value in serine of S. tetrandra, respectively. A total of 90 SSRs have been identified in the cp genome of S. tetrandra, where repeats that consisting of A or T bases were much higher than that of G or C bases. In addition, 92 potential RNA editing sites were identified in 25 protein-coding genes, with the most predicted RNA editing sites in ndhB gene. The variations on length and expansion extent to the junction of ycf1 gene were observed between S. tetrandra vouchers from different regions, indicating potential markers for further geographical origin discrimination. Moreover, the values of transition to transversion ratio (Ts/Tv) in the Stephania species were significantly higher than 1 using Pericampylus glaucus as reference. Comparative analysis of the Stephania cp genomes revealed 5 highly variable regions, including 3 intergenic regions (trnH-psbA, trnD-trnY, trnP) and two protein coding genes (rps16 and ndhA). The identified mutational hotspots of Stephania plants exhibited multiple SNP sites and Gaps, as well as different Ka/Ks ratio values. In addition, five pairs of specific primers targeting the divergence regions were accordingly designed, which could be utilized as potential molecular markers for species identification, population genetic and phylogenetic analysis in Stephania species. Phylogenetic tree analysis based on the conserved chloroplast protein coding genes indicated a sister relationship between S. tetrandra and the monophyletic group of S. japonica and S. kwangsiensis with high support values, suggesting a close genetic relationship within Stephania plants. However, two S. tetrandra vouches from different regions failed to cluster into one clade, confirming the occurrences of genetic diversities and requiring further investigation for geographical tracing strategy. CONCLUSIONS: Overall, we provided comprehensive and detailed information on the complete chloroplast genome and identified nucleotide diversity hotspots of Stephania species. The obtained genetic resource of S. tetrandra from Zhejiang Province would facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of Stephania plants.
Asunto(s)
Genoma del Cloroplasto , Menispermaceae , Stephania tetrandra , Estructura Molecular , FilogeniaRESUMEN
Recently, a single vectorial pupil optimization (VPO) was proposed to compensate for the polarization effect induced by thick mask and image optics at one field point in a lithography system, which does not work at full field points. In this paper, we propose a multi-objective VPO (MOVPO) method to obtain a universal vectorial pupil that can compensate for the polarization aberration at full field points. A novel multi-objective cost function, to the best of our knowledge, is built and includes uneven image pattern errors causing by polarization aberration (PA) at full field points in the MOVPO method. Comprehensive simulations demonstrate that the proposed MOVPO method can effectively improve the consistency of imaging and enlarge the overlapped process window at full field points.
RESUMEN
Ramie (Boehmeria nivea L. Gaud) is a traditional fiber crop and important medicinal plant belonging to the family Urticaceae. In this study, we determine the complete chloroplast genome sequence of B. nivea. The assembled chloroplast genome is 156065 bp in length and shares the conserved quadripartite structure as other cp genomes in Boehmeria. The genome contains 131 genes, including 84 protein genes, 8 rRNA genes, 37 tRNA genes and 2 pseudo genes. There are 17 duplicated genes in the IR region. The overall GC content of B. nivea is 36.33%, with the highest GC content of 42.72% in IR region. A total of 67 simple sequence repeats are identified in the cp genome of B. nivea. Phylogenetic analysis demonstrated that B. nivea clustered together with B. tomentosa, further forming a monophyletic group with the species of Debregeasia and Pipturus. This work provides basic genetic resources for developing robust markers and investigating the population genetics diversities for B. nivea.
RESUMEN
Lysimachia hemsleyana Maxim. is an important medical plant in the Family Primulaceae. In this study, we determined the complete chloroplast genome of L. hemsleyana. It is 155,618 bp in length, containing a large single copy (LSC) region of 85,615 bp, a small single copy (SSC) region of 17,861 bp, which were separated by a pair of inverted repeat (IR) regions of 26,071bp. The complete chloroplast genome of L. hemsleyana encoded a total of 134 genes, including 89 protein-coding genes with the pseudogene of ycf1, 8 ribosomal RNA genes and 37 transfer RNA genes. Phylogenetic analysis revealed that L. hemsleyana was most closely related to the Korea endemic plant Lysimachia coreana with high bootstrap support value. This work provides basic molecular information that would be useful for further investigation on conservation genetics and evolutionary relationships of L. hemsleyana.
RESUMEN
In this study, the complete mitogenome sequence of great seahorse Hippocampus kelloggi (Gasterosteiformes: Syngnathidae) has been amplified and sequenced employing the polymerase chain reaction-based method. The total length of mitochondrial DNA is 16 536 bp and includes 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA genes, and a control region. The mitochondrial gene arrangement of H. kelloggi was similar to that observed in most vertebrate creatures. The overall base composition of H. kelloggi is 32.19% for A, 23.68% for C, 29.30% for T, and 14.82% for G, with a slight AT bias of 61.49%. Phylogenetic analyses based on complete mitochondrial genome sequence showed that H. kelloggi has a close genetic relationship to H. reidi, H. ingens, and H. kuda.