Mb In Length Research Articles

A Chromosome-Level Genome Assembly Identifies the Origin of Neo-Y Chromosome to the Unique X <sub>1</sub>X <sub>2</sub>Y System

The barred knifejaw, Oplegnathus fasciatus (Teleostei: Centrarchiformes Oplegnathidae), is an important species in marine cage culture and fish stocking for marine ranching in East Asia. The males of Oplegnathidae (O. fasciatus and O. punctatus) species are characterized by an X1X2Y system with a neo-Y chromosome based on male karyotype analyses. Release of the chromosome-level reference genome of female O. fasciatus has facilitated insights into the origin of the unique X1X2Y system of male O. fasciatus. In the present study, we applied PacBio long-read sequencing and high-throughput chromosome interaction mapping (Hi-C) to assemble a chromosome-level genome of male O. fasciatus. A highly contiguous genome with a size of 795 Mb, 2,295 contigs, and a contig N50 of 2.13 Mb was obtained. The 1,355 ordered contigs combined with the draft genome were further assembled into 23 chromosomes approximately 762 Mb in length with a contig N50 of 2.18 Mb and a scaffold N50 of 32.43 Mb. A large neo-chromosome (Ch9) of 94.2 Mb was assembled from 444 contigs, and found to be more than three times larger than the rest chromosomes of male O. fasciatus. In addition, 63.4 Mb of the Ch9 sequences of male O. fasciatus had high identity (~99.0%) to the Ch8 (31.4 Mb/37.5 Mb) and Ch10 (32.0 Mb/35.3 Mb) sequences of female O. fasciatus based on a whole-genome synteny analysis, showing that the neo-Y chromosome shared significant homology with Ch8 and Ch10 based on male/female genome comparison. Significant fission tracks at the terminal point of the chromosomes were also identified between Ch9 and Ch8/Ch10 using synteny analyses, which showed chromosome rearrangements events had happened in the neo-chromosome Ch9. Our present results accurately demonstrated that the X1X2Y system of male O. fasciatus originated from the fusions of the non-homologous chromosomes Ch8 and Ch10. According to the synteny analyses and previous karyotypes results, which characterized acrocentric chromosomes, we suggested that a centric fusion of Ch8 and Ch10 was responsible for the formation of the X1X2Y system of male O. fasciatus.

Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula.

The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome‐scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single‐molecule real‐time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi‐C‐based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein‐coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.

Discerning three novel chromate reduce and transport genes of highly efficient Pannonibacter phragmitetus BB: From genome to gene and protein

Here, Pannonibacter phragmitetus BB was investigated at genomic, genetic and protein levels to explore molecular mechanisms of chromium biotransformation, respectively. The results of Miseq sequencing uncovered that a high-qualified bacterial genome draft was achieved with 5.07 Mb in length. Three novel genes involved in chromate reduce and transport, named nitR, chrA1 and chrA2, were identified by alignment, annotation and phylogenetic tree analyses, which encode a chromate reductase (NitR) and two chromate transporters (ChrA1 and ChrA2). Reverse transcription real-time polymerase chain reaction (RT-qPCR) analyses showed that the relative quantitative transcription of the three genes as the maximum reduction rate of Cr(VI) were significantly up-regulated with the increasing initial Cr(VI) concentrations. However, at the maximum cell growth points nitR was in a low transcription level, while the transcription of chrA1 and chrA2 were hold at a relatively high level and decreased with the increasing initial Cr(VI) concentrations. The ex-situ chromate reducing activity of NitR was revealed a Vmax of 34.46 µmol/min/mg enzyme and Km of 14.55 µmol/L, suggesting feasibility of the reaction with Cr(VI) as substrate. The multiple alignment demonstrates that NitR is potentially a nicotinamide adenine dinucleotide phosphate (NADPH) dependent flavin mononucleotide (FMN) reductase of Class I chromate reductases. Our results will prompt a large-scaled bioremediation on the contaminated soils and water by Pannonibacter phragmitetus BB, taking advantage of uncovering its molecular mechanisms of chromium biotransformation.

Draft Genome Sequence of Bifidobacterium longum UMA026, Isolated from Holstein Dairy Cow Feces.

ABSTRACTThe draft genome sequence of an isolate identified as Bifidobacterium longum is communicated herein. This strain was isolated from the feces of a 1-week-old Holstein dairy cow. The draft genome of this Bifidobacterium longum isolate is 2.39 Mb in length, with a G+C content of 60.1%.

Minimap2: pairwise alignment for nucleotide sequences.

Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment. https://github.com/lh3/minimap2. Supplementary data are available at Bioinformatics online.

Genome Sequence of Bacillus halotolerans Strain MS50-18A with Antifungal Activity against Phytopathogens, Isolated from Saline Soil in San Luís Potosí, Mexico.

ABSTRACTBacillus halotolerans strain MS50-18A, isolated from saline soil, possesses antifungal activity toward root rot causal phytopathogens and has friendly interactions with the chili pepper plant. The draft genome sequence is 4.06 Mb in length and contains 4,215 genes. Genes related to glycine/betaine uptake and bacilysin biosynthesis are present, supporting its saline stress tolerance and antifungal activity.

Comparative genomics and transcriptome analysis of Lactobacillus rhamnosus ATCC 11443 and the mutant strain SCT-10-10-60 with enhanced L-lactic acid production capacity.

Mechanisms for high L-lactic acid production remain unclear in many bacteria. Lactobacillus rhamnosus SCT-10-10-60 was previously obtained from L. rhamnosus ATCC 11443 via mutagenesis and showed improved L-lactic acid production. In this study, the genomes of strains SCT-10-10-60 and ATCC 11443 were sequenced. Both genomes are a circular chromosome, 2.99Mb in length with a GC content of approximately 46.8%. Eight split genes were identified in strain SCT-10-10-60, including two LytR family transcriptional regulators, two Rex redox-sensing transcriptional repressors, and four ABC transporters. In total, 60 significantly up-regulated genes (log2fold-change ≥ 2) and 39 significantly down-regulated genes (log2fold-change ≤ - 2) were identified by a transcriptome comparison between strains SCT-10-10-60 and ATCC 11443. KEGG pathway enrichment analysis revealed that "pyruvate metabolism" was significantly different (P < 0.05) between the two strains. The split genes and the differentially expressed genes involved in the "pyruvate metabolism" pathway are probably responsible for the increased L-lactic acid production by SCT-10-10-60. The genome and transcriptome sequencing information and comparison of SCT-10-10-60 with ATCC 11443 provide insights into the anabolism of L-lactic acid and a reference for improving L-lactic acid production using genetic engineering.

Genome sequence of the small brown planthopper, Laodelphax striatellus.

Background Laodelphax striatellus Fallén (Hemiptera: Delphacidae) is one of the most destructive rice pests. L. striatellus is different from 2 other rice planthoppers with a released genome sequence, Sogatella furcifera and Nilaparvata lugens, in many biological characteristics, such as host range, dispersal capacity, and vectoring plant viruses. Deciphering the genome of L. striatellus will further the understanding of the genetic basis of the biological differences among the 3 rice planthoppers.FindingsA total of 190 Gb of Illumina data and 32.4 Gb of Pacbio data were generated and used to assemble a high-quality L. striatellus genome sequence, which is 541 Mb in length and has a contig N50 of 118 Kb and a scaffold N50 of 1.08 Mb. Annotated repetitive elements account for 25.7% of the genome. A total of 17 736 protein-coding genes were annotated, capturing 97.6% and 98% of the BUSCO eukaryote and arthropoda genes, respectively. Compared with N. lugens and S. furcifera, L. striatellus has the smallest genome and the lowest gene number. Gene family expansion and transcriptomic analyses provided hints to the genomic basis of the differences in important traits such as host range, migratory habit, and plant virus transmission between L. striatellus and the other 2 planthoppers.ConclusionsWe report a high-quality genome assembly of L. striatellus, which is an important genomic resource not only for the study of the biology of L. striatellus and its interactions with plant hosts and plant viruses, but also for comparison with other planthoppers.

Insights from the Genome Sequence of Mycobacterium lepraemurium: Massive Gene Decay and Reductive Evolution.

ABSTRACTMycobacterium lepraemurium is the causative agent of murine leprosy, a chronic, granulomatous disease similar to human leprosy. Due to the similar clinical manifestations of human and murine leprosy and the difficulty of growing both bacilli axenically, Mycobacterium leprae and M. lepraemurium were once thought to be closely related, although it was later suggested that M. lepraemurium might be related to Mycobacterium avium. In this study, the complete genome of M. lepraemurium was sequenced using a combination of PacBio and Illumina sequencing. Phylogenomic analyses confirmed that M. lepraemurium is a distinct species within the M. avium complex (MAC). The M. lepraemurium genome is 4.05 Mb in length, which is considerably smaller than other MAC genomes, and it comprises 2,682 functional genes and 1,139 pseudogenes, which indicates that M. lepraemurium has undergone genome reduction. An error-prone repair homologue of the DNA polymerase III α-subunit was found to be nonfunctional in M. lepraemurium, which might contribute to pseudogene formation due to the accumulation of mutations in nonessential genes. M. lepraemurium has retained the functionality of several genes thought to influence virulence among members of the MAC.

Hydrogenophaga crassostreae sp. nov., isolated from a Pacific oyster.

A Gram-negative, motile, rod-shaped, and aerobic bacterial strain, designated LPB0072T, was isolated from a Pacific oyster (Crassostrea gigas). Autotrophic growth with hydrogen gas was not observed. Cells oxidized thiosulfate to sulfate and reduced nitrate to nitrite. The complete genome sequence of strain LPB0072T (CP017476) is 4.94 Mb in length and contains 4459 protein-coding genes, with a G+C content of 61.3 mol%. Analysis of the 16S rRNA gene sequence indicated that strain LPB0072T belongs to the genus Hydrogenophaga, with greatest sequence similarity to the type strain of Hydrogenophaga taeniospiralis (97.5 %). The isoprenoid quinone (Q-8) and the major cellular fatty acids (C16 : 1ω7c and/or C16 : 1ω6c, C16 : 0 and C17 : 1ω6c) identified were concordant with the chemotaxonomic properties of the genus Hydrogenophaga. The average nucleotide identities with closely related species were below the suggested boundary for species delineation, indicating that the isolate is a novel species. Numerous physiological and biochemical features also distinguished the isolate from other known Hydrogenophaga species. Based on the polyphasic data presented in this study, strain LPB0072T should be classified as a novel species in the genus Hydrogenophaga, and the name Hydrogenophaga crassostreae sp. nov. is proposed. The type strain is LPB0072T (=KACC 18705T=JCM 31188T).

Copy number veriation regions detection in Qinchuan cattle

Abstract Copy number variation (CNV) is a main and prevalent structural alterations underlying evolution of animal, which is considered to affect gene expression and complex traits. In this study, we analyzed genomic characteristics of CNV regions (CNVRs) in 254 Qinchuan cattle using GeneSeek HD 77k BeadChip. PennCNV algorithm was utilized for CNVs detection with strict quality criteria. A total of 255 CNVRs were identified based on 2076 CNVs detected, containing 215 loss events, 31 gain events, and 9 mix events. These regions were 184 Mb in length corresponding to 7.3% of the bovine genome. Our function enrichment analysis showed that the CNVRs overlapping with protein coding genes were significantly enriched with multiple biological functions and pathways. These CNVRs were also related with many economic traits of beef cattle including meat and carcass (57 QTLs), reproduction (36 QTLs), and growth (12 QTLs). In conclusion, our results enriched the information of CNVR maps of Qinchuan cattle which will be helpful for breeding of this cattle breed.

The draft genome sequence of a desert tree Populus pruinosa.

Populus pruinosa is a large tree that grows in deserts and shows distinct differences in both morphology and adaptation compared to its sister species, P. euphratica. Here we present a draft genome sequence for P. pruinosa and examine genomic variations between the 2 species. A total of 60 Gb of clean reads from whole-genome sequencing of a P. pruinosa individual were generated using the Illumina HiSeq2000 platform. The assembled genome is 479.3 Mb in length, with an N50 contig size of 14.0 kb and a scaffold size of 698.5 kb; 45.47% of the genome is composed of repetitive elements. We predicted 35 131 protein-coding genes, of which 88.06% were functionally annotated. Gene family clustering revealed 224 unique and 640 expanded gene families in the P. pruinosa genome. Further evolutionary analysis identified numerous genes with elevated values for pairwise genetic differentiation between P. pruinosa and P. euphratica. We provide the genome sequence and gene annotation for P. pruinosa. A large number of genetic variations were recovered by comparison of the genomes between P. pruinosa and P. euphratica. These variations will provide a valuable resource for studying the genetic bases for the phenotypic and adaptive divergence of the 2 sister species.

Draft Genome Sequences of Alloscardovia macacae UMA81211 and UMA81212, Isolated from the Feces of a Rhesus Macaque (Macaca mulatta).

ABSTRACTHere, we provide the draft genome sequences of two isolates identified as Alloscardovia macacae. These bacteria originated from the feces of a rhesus macaque. The draft genomes of both Alloscardovia macacae isolates are ~1.8 Mb in length, with a G+C content of 56.1%.

Draft Genome Sequence of Leifsonia sp. Strain NCR5, a Rhizobacterium Isolated from Cadmium-Contaminated Soil.

ABSTRACTWe report here the draft genome sequence of Leifsonia sp. strain NCR5, a Gram-positive actinomycete isolated from Carpobrotus rossii (Haw.) Schwantes rhizosphere. The de novo genome of Leifsonia sp. strain NCR5 was assembled with 69 scaffolds and a G+C content of 69%, was 4.2 Mb in length, and contained 3,952 coding sequences.

Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600\u2009K SNP array

Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs. Subsequently, ten novel CNVRs were randomly chosen for further quantitative real-time PCR (qPCR) confirmation, and eight were successfully validated. Gene functional enrichment revealed that these CNVRs cluster into Gene Ontology (GO) categories of homeobox and embryonic skeletal system morphogenesis. One CNVR overlapping with the homeobox transcription factor DLX3 and previously shown to be associated with curly hair in sheep was identified as the candidate CNV for the special curly fleece phenotype in Tan sheep. We constructed a Chinese indigenous sheep genomic CNV map based on the Illumina Ovine SNP 600 K BeadChip array, providing an important addition to published sheep CNVs, which will be helpful for future investigations of the genomic structural variations underlying traits of interest in sheep.

Draft genome and SNPs associated with carotenoid accumulation in adductor muscles of bay scallop (Argopecten irradians).

Carotenoids are commonly deposited in the gonads of marine bivalves but rarely in their adductor muscles. An orange-adductor variant was identified in our breeding program for the bay scallop Argopecten irradians. In the present study, bay scallop genome survey sequencing was conducted, followed by genotyping by sequencing (GBS)-based case-control association analysis in a selfing family that exhibited segregation in adductor color. K-mer analysis (K=17) revealed that the bay scallop genome is about 990 Mb in length. De novo assembly produced 217,310 scaffold sequences, which provided 72.1% coverage of the whole genome and covered 72,187 transcripts, thereby yielding the most informative sequence resource for bay scallop to date. The average carotenoid content of the orange-adductor progenies was significantly higher than that of the white-adductor progenies. Thus, 20 individuals of each subgroup were sampled for case-control analysis. As many as 15,224 heterozygous loci were identified in the parent, among which 9280 were genotyped in at least 10 individuals of each of the two sub-groups. Association analysis indicated that 126 SNPs were associated with carotenoid accumulation in the adductor muscle and that 88 of these were significantly enriched on 28 scaffolds (FDR controlled P < 0.05). The SNPs and genes located on these scaffolds can serve as valuable candidates for further research into the mechanisms by which marine bivalves accumulate carotenoids in their adductor muscles.

Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions

Bitter gourd (Momordica charantia) is an important vegetable and medicinal plant in tropical and subtropical regions globally. In this study, the draft genome sequence of a monoecious bitter gourd inbred line, OHB3-1, was analyzed. Through Illumina sequencing and de novo assembly, scaffolds of 285.5 Mb in length were generated, corresponding to ∼84% of the estimated genome size of bitter gourd (339 Mb). In this draft genome sequence, 45,859 protein-coding gene loci were identified, and transposable elements accounted for 15.3% of the whole genome. According to synteny mapping and phylogenetic analysis of conserved genes, bitter gourd was more related to watermelon (Citrullus lanatus) than to cucumber (Cucumis sativus) or melon (C. melo). Using RAD-seq analysis, 1507 marker loci were genotyped in an F2 progeny of two bitter gourd lines, resulting in an improved linkage map, comprising 11 linkage groups. By anchoring RAD tag markers, 255 scaffolds were assigned to the linkage map. Comparative analysis of genome sequences and predicted genes determined that putative trypsin-inhibitor and ribosome-inactivating genes were distinctive in the bitter gourd genome. These genes could characterize the bitter gourd as a medicinal plant.

Draft genome sequence of pectic polysaccharide-degrading moderate thermophilic bacterium Geobacillus thermodenitrificans DSM 101594.

Geobacillus thermodenitrificans DSM 101594 was isolated as a producer of extracellular thermostable pectic polysaccharide degrading enzymes. The completely sequenced genome was 3.6 Mb in length with GC content of 48.86%. A number of genes encoding enzymatic active against the high molecular weight polysaccharides of potential biotechnological importance were identified in the genome.

Draft genome sequence of subterranean clover, a reference for genus Trifolium.

Clovers (genus Trifolium) are widely cultivated across the world as forage legumes and make a large contribution to livestock feed production and soil improvement. Subterranean clover (T. subterraneum L.) is well suited for genomic and genetic studies as a reference species in the Trifolium genus, because it is an annual with a simple genome structure (autogamous and diploid), unlike the other economically important perennial forage clovers, red clover (T. pratense) and white clover (T. repens). This report represents the first draft genome sequence of subterranean clover. The 471.8 Mb assembled sequence covers 85.4% of the subterranean clover genome and contains 42,706 genes. Eight pseudomolecules of 401.1 Mb in length were constructed, based on a linkage map consisting of 35,341 SNPs. The comparative genomic analysis revealed that different clover chromosomes showed different degrees of conservation with other Papilionoideae species. These results provide a reference for genetic and genomic analyses in the genus Trifolium and new insights into evolutionary divergence in Papilionoideae species.

Evaluation of artificial selection in Standard Poodles using whole-genome sequencing.

Identifying regions of artificial selection within dog breeds may provide insights into genetic variation that underlies breed-specific traits or diseases-particularly if these traits or disease predispositions are fixed within a breed. In this study, we searched for runs of homozygosity (ROH) and calculated the d i statistic (which is based upon F ST) to identify regions of artificial selection in Standard Poodles using high-coverage, whole-genome sequencing data of 15 Standard Poodles and 49 dogs across seven other breeds. We identified consensus ROH regions ≥1Mb in length and common to at least ten Standard Poodles covering 0.6% of the genome, and d i regions that most distinguish Standard Poodles from other breeds covering 3.7% of the genome. Within these regions, we identified enriched gene pathways related to olfaction, digestion, and taste, as well as pathways related to adrenal hormone biosynthesis, T cell function, and protein ubiquitination that could contribute to the pathogenesis of some Poodle-prevalent autoimmune diseases. We also validated variants related to hair coat and skull morphology that have previously been identified as being under selective pressure in Poodles, and flagged additional polymorphisms in genes such as ITGA2B, CBX4, and TNXB that may represent strong candidates for other common Poodle disorders.