We demonstrate highly compact optical add-drop filters based on silicon-on-insulator microring resonators. The microring resonators have a small radius of 2.5 mu m and a very large free spectral ...range ~ 32 nm at the 1.55 mu m communication band. The propagation loss in such small micoring resonators was experimentally determined and shown to be extremely important in designing microring add-drop filters with low add-drop crosstalk, low drop loss, and maximally flat drop passband. For box-like channel dropping responses, second-order optical add-drop filters with two coupled microring resonators are designed and demonstrated, and the simulation matches well with the experiment. Devices were patterned with electron-beam lithography. Two fabrication procedures utilizing different polarity of resists were introduced and compared, and the process with negative resist resulted in much smaller sidewall roughness of waveguides, thus reducing the propagation loss in microring resonators.
Eukaryotic genomes are generally organized in multiple chromosomes. Here we have created a functional single-chromosome yeast from a Saccharomyces cerevisiae haploid cell containing sixteen linear ...chromosomes, by successive end-to-end chromosome fusions and centromere deletions. The fusion of sixteen native linear chromosomes into a single chromosome results in marked changes to the global three-dimensional structure of the chromosome due to the loss of all centromere-associated inter-chromosomal interactions, most telomere-associated inter-chromosomal interactions and 67.4% of intra-chromosomal interactions. However, the single-chromosome and wild-type yeast cells have nearly identical transcriptome and similar phenome profiles. The giant single chromosome can support cell life, although this strain shows reduced growth across environments, competitiveness, gamete production and viability. This synthetic biology study demonstrates an approach to exploration of eukaryote evolution with respect to chromosome structure and function.
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KISLJ, NUK, SBMB, UL, UM, UPUK
The advances of sequencing technology accelerate the development of theory of molecular quantitative genetics such as QTL mapping, genome-wide association study and genomic selection. This paper was ...designed to study genomic selection in large yellow croaker breeding. The aims of this study were: (i) to estimate heritability values of traits in large yellow croaker; (ii) to assess feasibility of genomic selection in the traits of growth rate and meat quality; (iii) to compare predictive accuracies affected by different algorithms and training sizes, and to find what training sizes could reach ideal accuracies; (iv) to compare results of GWAS with genomic prediction, and to assess feasibility of pre-selection of significant SNPs in genomic selection. 500 individuals were tested in the trait of body weight and body length, while 176 were tested in the percentage of n-3 highly unsaturated fatty acids (n-3HUFA) in muscle. GBLUP and emBayesB were used to perform genomic prediction.
Genotyping-By-Sequencing method was used to construct the libraries for the NGS sequencing and find ~30,000 SNPs. Heritability estimates were 0.604, 0.586 and 0.438 for trait of body weight, body length and n-3HUFA, respectively. The predictive abilities estimated by GBLUP showed higher than that by emBayesB in traits of body weight and body length. However, the result was just the opposite in n-3HUFA. According to fit the curve of predictive accuracy, we estimated that at least 1000 individuals in training set could reach an accuracy of 0.8 in body weight and body length. GBLUP, emBayesB and GWAS could not always find significant SNPs associated with phenotypes consistently. Significant SNPs were selected by emBayesB could obtain the largest proportions to explain total additive genetic variances.
This research showed that genomic selection was feasible in large yellow croaker breeding. We suggest doing a test before deciding to use which algorithm in specific trait in genomic prediction. We estimated required training sizes to reach ideal predictive accuracies and assessed feasibility of pre-selection of SNPs successfully. Because of high mortality rate of fish and high cost in genomic sequencing, genomic selection may be more suitable for applying on some traits which cannot be measured on candidates directly.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Ultrabroad-bandwidth radiofrequency pulses offer significant applications potential, such as increased data transmission rate and multipath tolerance in wireless communications. Such ...ultrabroad-bandwidth pulses are inherently difficult to generate with chip-based electronics due to limits in digital-to-analog converter technology and high timing jitter. Photonic means of radiofrequency waveform generation, for example, by spectral shaping and frequency-time mapping, can overcome the bandwidth limit in electronic generation. However, previous bulk optic systems for radiofrequency arbitrary waveform generation do not offer the integration advantage of electronics. Here, we report a chip-scale, fully programmable spectral shaper consisting of cascaded multiple-channel microring resonators, on a silicon photonics platform that is compatible with electronic integrated circuit technology. Using such a spectral shaper, we demonstrate the generation of burst radiofrequency waveforms with programmable time-dependent amplitude, frequency and phase profiles, for frequencies up to 60 GHz. Our demonstration suggests potential for chip-scale photonic generation of ultrabroad-bandwidth arbitrary radiofrequency waveforms.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Abstract
Sweet cherry (
Prunus avium
) is an economically significant fruit species in the genus
Prunus
. However, in contrast to other important fruit trees in this genus, only one draft genome ...assembly is available for sweet cherry, which was assembled using only Illumina short-read sequences. The incompleteness and low quality of the current sweet cherry draft genome limit its use in genetic and genomic studies. A high-quality chromosome-scale sweet cherry reference genome assembly is therefore needed. A total of 65.05 Gb of Oxford Nanopore long reads and 46.24 Gb of Illumina short reads were generated, representing ~190x and 136x coverage, respectively, of the sweet cherry genome. The final de novo assembly resulted in a phased haplotype assembly of 344.29 Mb with a contig N50 of 3.25 Mb. Hi-C scaffolding of the genome resulted in eight pseudochromosomes containing 99.59% of the bases in the assembled genome. Genome annotation revealed that more than half of the genome (59.40%) was composed of repetitive sequences, and 40,338 protein-coding genes were predicted, 75.40% of which were functionally annotated. With the chromosome-scale assembly, we revealed that gene duplication events contributed to the expansion of gene families for salicylic acid/jasmonic acid carboxyl methyltransferase and ankyrin repeat-containing proteins in the genome of sweet cherry. Four auxin-responsive genes (two GH3s and two SAURs) were induced in the late stage of fruit development, indicating that auxin is crucial for the sweet cherry ripening process. In addition, 772 resistance genes were identified and functionally predicted in the sweet cherry genome. The high-quality genome assembly of sweet cherry obtained in this study will provide valuable genomic resources for sweet cherry improvement and molecular breeding.
Subcutaneous fat (SCF) and intramuscular fat (IMF) deposition is relevant to health in humans, as well as meat production and quality in pigs. In this study, we generated RNA sequence data for 122 ...SCF, 120 IMF, and 87 longissimus dorsi muscle (LDM) samples using 155 F
pigs from a specially designed heterogeneous population generated by intercrossing four highly selected European commercial breeds and four indigenous Chinese pig breeds. The phenotypes including waist back fat thickness and intramuscular fat content were also measured in the 155 F
pigs. We found that the genes in SCF and IMF differed largely in both expression levels and network connectivity, and highlighted network modules that exhibited strongest gain of connectivity in SCF and IMF, containing genes that were associated with the immune process and DNA double-strand repair, respectively. We identified 215 SCF genes related to kinase inhibitor activity, mitochondrial fission, and angiogenesis, and 90 IMF genes related to lipolysis and fat cell differentiation, displayed a tissue-specific association with back fat thickness and IMF content, respectively. We found that cis-expression QTL for trait-associated genes in the two adipose tissues tended to have tissue-dependent predictability for the two adipose traits. Alternative splicing of genes was also found to be associated with SCF or IMF deposition, but the association was much less extensive than that based on expression levels. This study provides a better understanding of SCF and IMF gene transcription and network organization and identified critical genes and network modules that displayed tissue-specific associations with subcutaneous and intramuscular fat deposition. These features are helpful for designing breeding programs to genetically improve the two adipose traits in a balanced way.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Ganoderma tsugae
is an endemic medicinal mushroom in Northeast China, providing important source of pharmaceutical product. Comparing with other
Ganoderma
species, wild
G. tsugae
can utilize ...coniferous wood. However, functional genes related to medicinal component synthesis and the genetic mechanism of conifer substrate utilization is still obscure. Here, we assembled a high-quality
G. tsugae
genome with 18 contigs and 98.5% BUSCO genes and performed the comparative genomics with other
Ganoderma
species.
G. tsugae
diverged from their common ancestor of
G. lingzhi
and
G. sinense
about 21 million years ago. Genes in
G. tsugae
-specific and
G. tsugae
-expanded gene families, such as
salh
,
phea
,
cyp53a1
, and
cyp102a
, and positively selected genes, such as
glpk
and
amie
, were functionally enriched in plant-pathogen interaction, benzoate degradation, and fanconi anemia pathway. Those functional genes might contribute to conifer substrate utilization of
G. tsugae
. Meanwhile, gene families in the terpene synthesis were identified and genome-wide SNP variants were detected in population. Finally, the study provided valuable genomic resources and offered useful hints for the functional gene mapping and investigation of key gene contributing to conifer cultivation substrate utilization and medicinal component biosynthesis.
Lentinula edodes (Berk.) is the second most productive mushroom in the world. It contains compounds effective for antiviral, antitumor, antioxidant and immune regulation. Although genomes have ...previously been reported for this species, a high-quality chromosome-level reference for L. edodes is unavailable. This hinders detailed investigation of population genetics, breeding history of strains and genes related to environmental stress responses.
A high-quality chromosome-level genome was constructed. We separated a monokaryon from protoplasts of the commercial L. edodes strain L808 and assembled the genome of L. edodes using PacBio long-read and Illumina short-read sequencing, along with the high-throughput chromatin conformation capture (Hi-C) technique. We assembled a 45.87 Mb genome, and 99% of the sequences were anchored onto 10 chromosomes. The contig and scaffold N50 length were 2.17 and 4.94 Mb, respectively. Over 96% of the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) were identified, and 9853 protein-coding genes were predicted. We performed population genome resequencing using 34 wild strains and 65 commercial cultivars of L. edodes originating from China, Japan, the United States and Australia. Based on whole-genome variants, we showed substantial differences in the Chinese wild population, which divided into different branches according to the main areas of their geographical distribution. We also determined the breeding history of L. edodes at the molecular level, and demonstrated that the cultivated strains in China mainly originated from wild strains from China and Northeast Asia. Phenotypic analysis showed that 99 strains exhibited differences on the Cd accumulation. Three significant loci in the of L. edodes genome were identified using the genome-wide association study (GWAS) of Cd accumulation traits. Functional genes associated with Cd accumulation traits were related to DNA ligase and aminoacyl tRNA synthetase, indicating that DNA damage repair and in vivo protein translation may be responses to Cd stress.
A high-quality chromosome-level genome and population genetic data of L. edodes provide genetic resources for functional genomic, evolutionary and artificial breeding studies for L. edodes.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Genomic selection is widely applied for genetic improvement in livestock crossbreeding systems to select excellent nucleus purebred (PB) animals and to improve the performance of commercial crossbred ...(CB) animals. Most current predictions are based solely on PB performance. Our objective was to explore the potential application of genomic selection of PB animals using genotypes of CB animals with extreme phenotypes in a three-way crossbreeding system as the reference population. Using real genotyped PB as ancestors, we simulated the production of 100,000 pigs for a Duroc x (Landrace x Yorkshire) DLY crossbreeding system. The predictive performance of breeding values of PB animals for CB performance using genotypes and phenotypes of (1) PB animals, (2) DLY animals with extreme phenotypes, and (3) random DLY animals for traits of different heritabilities (Formula: see text = 0.1, 0.3, and 0.5) was compared across different reference population sizes (500 to 6500) and prediction models (genomic best linear unbiased prediction (GBLUP) and Bayesian sparse linear mixed model (BSLMM)).
Using a reference population consisting of CB animals with extreme phenotypes showed a definite predictive advantage for medium- and low-heritability traits and, in combination with the BSLMM model, significantly improved selection response for CB performance. For high-heritability traits, the predictive performance of a reference population of extreme CB phenotypes was comparable to that of PB phenotypes when the effect of the genetic correlation between PB and CB performance (Formula: see text) on the accuracy obtained with a PB reference population was considered, and the former could exceed the latter if the reference size was large enough. For the selection of the first and terminal sires in a three-way crossbreeding system, prediction using extreme CB phenotypes outperformed the use of PB phenotypes, while the optimal design of the reference group for the first dam depended on the percentage of individuals from the corresponding breed that the PB reference data comprised and on the heritability of the target trait.
A commercial crossbred population is promising for the design of the reference population for genomic prediction, and selective genotyping of CB animals with extreme phenotypes has the potential for maximizing genetic improvement for CB performance in the pig industry.
Carcass length is very important for body size and meat production for swine, thus understanding the genetic mechanisms that underly this trait is of great significance in genetic improvement ...programs for pigs. Although many quantitative trait loci (QTL) have been detected in pigs, very few have been fine-mapped to the level of the causal mutations. The aim of this study was to identify potential causal single nucleotide polymorphisms (SNPs) for carcass length by integrating a genome-wide association study (GWAS) and functional assays.
Here, we present a GWAS in a commercial Duroc × (Landrace × Yorkshire) (DLY) population that reveals a prominent association signal (P = 4.49E-07) on pig chromosome 17 for carcass length, which was further validated in two other DLY populations. Within the detected 1 Mb region, the BMP2 gene stood out as the most likely causal candidate because of its functions in bone growth and development. Whole-genome gene expression studies showed that the BMP2 gene was differentially expressed in the cartilage tissues of pigs with extreme carcass length. Then, we genotyped an additional 267 SNPs in 500 selected DLY pigs, followed by further whole-genome SNP imputation, combined with deep genome resequencing data on multiple pig breeds. Reassociation analyses using genotyped and imputed SNP data revealed that the rs320706814 SNP, located approximately 123 kb upstream of the BMP2 gene, was the strongest candidate causal mutation, with a large association with carcass length, with a ~ 4.2 cm difference in length across all three DLY populations (N = 1501; P = 3.66E-29). This SNP segregated in all parental lines of the DLY (Duroc, Large White and Landrace) and was also associated with a significant effect on body length in 299 pure Yorkshire pigs (P = 9.2E-4), which indicates that it has a major value for commercial breeding. Functional assays showed that this SNP is likely located within an enhancer and may affect the binding affinity of transcription factors, thereby regulating BMP2 gene expression.
Taken together, these results suggest that the rs320706814 SNP on pig chromosome 17 is a putative causal mutation for carcass length in the widely used DLY pigs and has great value in breeding for body size in pigs.
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