The chordate ancestor possessed a single copy of the Brachyury gene for notochord acquisition

Most currently available bioreactors have some defects in the expression, activity, or purification of target protein and peptide molecules, whereas the mucus gland of fish can overcome these defects to become a novel bioreactor for the biopharmaceutical industry. In this study, we have evaluated the practicability of developing a mucus gland bioreactor in loach (Paramisgurnus dabryanus). A transgenic construct pT2-krt8-IFN1 was obtained by subcloning the promoter of zebrafish keratin 8 gene and the type I interferon (IFN1) cDNA of grass carp into the SB transposon. The IFN1 expressed in CIK cells exhibited an antiviral activity against the replication of GCRV873 and activated two genes downstream of JAK-STAT signaling pathway. A transgenic loach line was then generated by microinjection of the pT2-krt8-IFN1 plasmids and in vitro synthesized capped SB11 mRNA. Southern blots indicated that a single copy of IFN1 gene was stably integrated into the genome of transgenic loach. The expression of grass carp IFN1 in transgenic loaches was detected with RT-PCR and Western blots. About 0.0825 µg of grass carp IFN1 was detected in 20 µL mucus from transgenic loaches. At a viral titer of 1 × 103 PFU/mL, plaque numbers on plates containing mucus from transgenic loaches reduced by 18% in comparison with those of the control, indicating that mucus of IFN1-transgenic loaches exhibited an antiviral activity. Thus, we have successfully created a mucus gland bioreactor that has great potential for the production of various proteins and peptides.

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The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab009 ◽

2021 ◽

Vol 11 (2) ◽

Author(s):

James G Baldwin-Brown ◽

Scott M Villa ◽

Anna I Vickrey ◽

Kevin P Johnson ◽

Sarah E Bush ◽

...

Keyword(s):

Low Cost ◽

Single Copy ◽

Odorant Receptors ◽

Rna Seq ◽

Pediculus Humanus ◽

Final Assembly ◽

Oxford Nanopore ◽

Genes Encoding ◽

Host Parasite ◽

G Protein Coupled

Abstract The pigeon louse Columbicola columbae is a longstanding and important model for studies of ectoparasitism and host-parasite coevolution. However, a deeper understanding of its evolution and capacity for rapid adaptation is limited by a lack of genomic resources. Here, we present a high-quality draft assembly of the C. columbae genome, produced using a combination of Oxford Nanopore, Illumina, and Hi-C technologies. The final assembly is 208 Mb in length, with 12 chromosome-size scaffolds representing 98.1% of the assembly. For gene model prediction, we used a novel clustering method (wavy_choose) for Oxford Nanopore RNA-seq reads to feed into the MAKER annotation pipeline. High recovery of conserved single-copy orthologs (BUSCOs) suggests that our assembly and annotation are both highly complete and highly accurate. Consistent with the results of the only other assembled louse genome, Pediculus humanus, we find that C. columbae has a relatively low density of repetitive elements, the majority of which are DNA transposons. Also similar to P. humanus, we find a reduced number of genes encoding opsins, G protein-coupled receptors, odorant receptors, insulin signaling pathway components, and detoxification proteins in the C. columbae genome, relative to other insects. We propose that such losses might characterize the genomes of obligate, permanent ectoparasites with predictable habitats, limited foraging complexity, and simple dietary regimes. The sequencing and analysis for this genome were relatively low cost, and took advantage of a new clustering technique for Oxford Nanopore RNAseq reads that will be useful to future genome projects.

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The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

Plants ◽

10.3390/plants10081517 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1517

Author(s):

Se-Hwan Cheon ◽

Min-Ah Woo ◽

Sangjin Jo ◽

Young-Kee Kim ◽

Ki-Joong Kim

Keyword(s):

Northeast Asia ◽

Single Copy ◽

Rrna Genes ◽

Bootstrap Support ◽

Trna Genes ◽

Protein Coding ◽

Tropical Regions ◽

Relationship Of ◽

The Relationship ◽

Simple Sequence

The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

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STRONG: metagenomics strain resolution on assembly graphs

Genome Biology ◽

10.1186/s13059-021-02419-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Christopher Quince ◽

Sergey Nurk ◽

Sebastien Raguideau ◽

Robert James ◽

Orkun S. Soyer ◽

...

Keyword(s):

Time Series ◽

De Novo ◽

Single Copy ◽

Bayesian Algorithm ◽

Anaerobic Digestor ◽

Core Genes

AbstractWe introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.

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Genome Assembly of the Canadian Two-row Malting Barley Cultivar AAC Synergy

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab031 ◽

2021 ◽

Author(s):

Wayne Xu ◽

James R Tucker ◽

Wubishet A Bekele ◽

Frank M You ◽

Yong-Bi Fu ◽

...

Keyword(s):

Reference Genome ◽

Single Copy ◽

Barley Cultivar ◽

Malting Barley ◽

Orthologous Genes ◽

Hordeum Vulgare L ◽

Chromosome Conformation ◽

Mate Pair ◽

Genome Assemblies ◽

First Time

Abstract Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cultivar AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, N50 of 2.32 Mb and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single-copy orthologous genes). After removal of small scaffolds (< 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with the updated version of six-row Morex and recently released two-row Golden Promise genome assemblies.

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A Mouse Single-Copy Gene,Gtf2i,the Homolog of HumanGTF2I,That Is Duplicated in the Williams–Beuren Syndrome Deletion Region

Genomics ◽

10.1006/geno.1997.5182 ◽

1998 ◽

Vol 48 (2) ◽

pp. 163-170 ◽

Cited By ~ 28

Author(s):

Yu-Ker Wang ◽

Luis A. Pérez-Jurado ◽

Uta Francke

Keyword(s):

Single Copy ◽

Single Copy Gene ◽

Deletion Region ◽

Copy Gene

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Phylogenetic comparison and splice site conservation of eukaryotic U1 snRNP-specific U1-70K gene family

Scientific Reports ◽

10.1038/s41598-021-91693-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Tao Fan ◽

Yu-Zhen Zhao ◽

Jing-Fang Yang ◽

Qin-Lai Liu ◽

Yuan Tian ◽

...

Keyword(s):

Gene Family ◽

Splice Site ◽

Messenger Rna ◽

Expression Patterns ◽

Protein Structures ◽

Single Copy ◽

Central Component ◽

Animal Kingdom ◽

Functional Studies ◽

U1 Snrnp

AbstractEukaryotic cells can expand their coding ability by using their splicing machinery, spliceosome, to process precursor mRNA (pre-mRNA) into mature messenger RNA. The mega-macromolecular spliceosome contains multiple subcomplexes, referred to as small nuclear ribonucleoproteins (snRNPs). Among these, U1 snRNP and its central component, U1-70K, are crucial for splice site recognition during early spliceosome assembly. The human U1-70K has been linked to several types of human autoimmune and neurodegenerative diseases. However, its phylogenetic relationship has been seldom reported. To this end, we carried out a systemic analysis of 95 animal U1-70K genes and compare these proteins to their yeast and plant counterparts. Analysis of their gene and protein structures, expression patterns and splicing conservation suggest that animal U1-70Ks are conserved in their molecular function, and may play essential role in cancers and juvenile development. In particular, animal U1-70Ks display unique characteristics of single copy number and a splicing isoform with truncated C-terminal, suggesting the specific role of these U1-70Ks in animal kingdom. In summary, our results provide phylogenetic overview of U1-70K gene family in vertebrates. In silico analyses conducted in this work will act as a reference for future functional studies of this crucial U1 splicing factor in animal kingdom.

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