Genome Length Research Articles

The complete chloroplast genome of Calohypnum plumiforme (Wilson) (hypanceae, bryophyta)

Calohypnum plumiforme is a widely distributed moss in East Asia. In this study, Illumina sequencing data was used to assemble the complete chloroplast genome of C. plumiforme. The length of the circular genome is 124,037 bp. It contains a total of 121 genes, including 81 protein-coding, 36 tRNA, and 4 rRNA genes. The GC content of the chloroplast genome of C. plumiforme is 29.07%. The phylogenetic analysis suggested that C. plumiforme is sister to Calliergonella cuspidata. This study provides important sequence information for species identification and its phylogenetic relationship in the Bryopsida.

Characterization of the complete chloroplast genome of Rumex dentatus L. (Polygonaceae)

Rumex dentatus L. is a flowering plant with promising therapeutic effects. Here, we reported the complete chloroplast genome sequence of R. dentatus. The length of the complete genome is 159,103 bp, with a pair of inverted repeat regions (IRb/IRa, 30,628 bp) separated by a large single-copy (LSC, 84,848 bp) region and a small single-copy (SSC, 12,999 bp) region. The overall GC content of the genome was 37.6%, and the corresponding values in the LSC, SSC, and IR regions were 35.8%, 32.6%, and 41.1%, respectively. There are 129 genes, including 84 protein coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic tree showed that R. dentatus was most relative to the species of R. nepalensis and R. crispus.

The complete chloroplast genome sequence of Tussilago farfara (Asteraceae)

Tussilago farfara is a member of the family Asteraceae. In this paper, we reported the complete chloroplast (cp) genome sequence of T. farfara. The results showed that T. farfara complete chloroplast genome comprises 151,325 bp, containing a largen single copy (LSC) region of 83,370 bp, a small single copy (SSC) region of 18,273 bp, and a pair of inverted repeats (IRs) region of 24,841 bp. The genome has a GC content of 37.4%. The LSC, SSC, and IR regions represent 35.5%, 30.6%, and 43.0% of the T. farfara chloroplast genome length. We annotated 132 genes, comprising 87 protein-coding genes (PCGs), eight rRNA genes, and 36 tRNA genes. A phylogenetic analysis based on 31 cpDNA genomes suggested that the T. farfara is closely related to Farfugium japonicum.

Chromosome-scale Cerasus humilis genome assembly reveals gene family evolution and possible genomic basis of calcium accumulation in fruits

Chinese dwarf cherry (Cerasus humilis), which is well known as “calcium fruit” for its high calcium content, is widely utilized in North China for its ecological and economical value. Understanding the evolutionary history and genetic basis underlying the calcium accumulation in this fruit is a fundamental goal in comparative genomics. In this study, we obtained a full phased chromosome-scale C. humilis genome for the cultivar “zhisha” using PacBio circular consensus sequencing reads and Phase genomics Proximo Hi-C technologies. The final assembled genome lengths were 235.41 and 237.35 Mb for primary assembly (p0) and alternate haplotig (p1), respectively, with an N50 contig length of 3.23 Mb. The genome contained 26,800 protein-coding genes, while 41.33% of the genome length consisted of TEs. Phylogenetic analysis revealed that C. humilis displayed a close relationship with Prunus and phylogenetically diverged from its common ancestor ∼23.2 million years ago (MYA). Functional enrichment of expanded gene families in C. humilis genome highlighted genes involved in signal transduction, antiporter activity, polygalacturonase activity, auxin efflux transmembrane transporter activity, and auxin efflux, which is related to calcium transport and distribution. Phylogenetic analysis coupled with tissue-specific expression patterns indicated that PSGs WAK2 and CBL10, may also be responsible for the high Ca2+accumulation ability in C. humilis. These results glean tremendous insight into the fundamental genetic basis of the high calcium content in C. humilis fruit. In addition, the reference C. humilis genome we present in this study will be valuable resources for molecular breeding and genetic research of this fruit species.

Novel characteristics of Chinese NADC34-like PRRSV during 2020-2021.

NADC34-like porcine reproductive and respiratory syndrome virus (PRRSV) strains were first detected in China in 2017, with epidemic potential. In this study, the phylogenetic, epidemic, and recombinant properties of NADC34-like PRRSV in China were evaluated comprehensively. From 2020 to October 2021, 82 NADC34-like PRRSV isolates were obtained from 433 PRRSV-positive clinical samples. These strains accounted for 11.5% and 28.6% of positives in 2020 and 2021, respectively, and have spread to eight provinces. We selected 15 samples for whole-genome sequencing, revealing genome lengths of 15,009-15,113nt. Phylogenetic analysis revealed that Chinese NADC34-like strains cluster with American sublineage 1.5 strains and do not form an independent branch. Recombination analysis revealed that six of fifteen complete genome sequences were derived from recombination between NADC34-like and NADC30-like or HP-PRRSV; all of the strains recombined with local strains in China, exhibiting a complex recombination pattern. Partial Nsp2 sequence alignment showed that nine of fifteen isolates had a 100 aa continuous deletion (similar to that in IA/2014/NADC34); other isolates had a 131 aa discontinuous deletion (similar to that in NADC30). Five of them also had additional amino acid deletions, all of which are reported for the first time here. In the last 2 years, NADC34-like PRRSV has become one of the main epidemic strains in some areas of China; it has changed significantly, its homology has decreased significantly, and it has undergone complex recombination with local Chinese strains. These results are of great significance for understanding the current epidemic situation of PRRSV in China.

Genomic architecture of three newly isolated unclassified Butyrivibrio species elucidate their potential role in the rumen ecosystem.

One cellulose-degrading strain CB08 and two xylan-degrading strains XB500-5 and X503 were isolated from buffalo rumen. All the strains were designated as putative novel species of Butyrivibrio based on phylogeny, phylogenomy, digital DNA-DNA hybridization, and average nucleotide identity with their closest type strains. The draft genome length of CB08 was ~3.54Mb, while X503 and XB500-5 genome sizes were ~3.24 Mb and ~3.27 Mb, respectively. Only 68.28% of total orthologous clusters were shared among three genomes, and 40-44% of genes were identified as hypothetical proteins. The presence of genes encoding diverse carbohydrate-active enzymes (CAZymes) exhibited the lignocellulolytic potential of these strains. Further, the genome annotations revealed the metabolic pathways for monosaccharide fermentation to acetate, butyrate, lactate, ethanol, and hydrogen. The presence of genes for chemotaxis, antibiotic resistance, antimicrobial activity, synthesis of vitamins, and essential fatty acid suggested the versatile metabolic nature of these Butyrivibrio strains in the rumen environment.

Using networks to analyze and visualize the distribution of overlapping genes in virus genomes.

Gene overlap occurs when two or more genes are encoded by the same nucleotides. This phenomenon is found in all taxonomic domains, but is particularly common in viruses, where it may increase the information content of compact genomes or influence the creation of new genes. Here we report a global comparative study of overlapping open reading frames (OvRFs) of 12,609 virus reference genomes in the NCBI database. We retrieved metadata associated with all annotated open reading frames (ORFs) in each genome record to calculate the number, length, and frameshift of OvRFs. Our results show that while the number of OvRFs increases with genome length, they tend to be shorter in longer genomes. The majority of overlaps involve +2 frameshifts, predominantly found in dsDNA viruses. Antisense overlaps in which one of the ORFs was encoded in the same frame on the opposite strand (-0) tend to be longer. Next, we develop a new graph-based representation of the distribution of overlaps among the ORFs of genomes in a given virus family. In the absence of an unambiguous partition of ORFs by homology at this taxonomic level, we used an alignment-free k-mer based approach to cluster protein coding sequences by similarity. We connect these clusters with two types of directed edges to indicate (1) that constituent ORFs are adjacent in one or more genomes, and (2) that these ORFs overlap. These adjacency graphs not only provide a natural visualization scheme, but also a novel statistical framework for analyzing the effects of gene- and genome-level attributes on the frequencies of overlaps.

A scalable artificial intelligence platform that automatically finds copy number variations (CNVs) in journal articles and transforms them into a database: CNV extraction, transformation, and loading AI (CNV-ETLAI)

BackgroundAlthough copy number variations (CNVs) are infrequent, each anomaly is unique, and multiple CNVs can appear simultaneously. Growing evidence suggests that CNVs contribute to a wide range of diseases. When CNVs are detected, assessment of their clinical significance requires a thorough literature review. This process can be extremely time-consuming and may delay disease diagnosis. Therefore, we have developed CNV Extraction, Transformation, and Loading Artificial Intelligence (CNV-ETLAI), an innovative tool that allows experts to classify and interpret CNVs accurately and efficiently. MethodsWe combined text, table, and image processing algorithms to develop an artificial intelligence platform that automatically extracts, transforms, and organizes CNV information into a database. To validate CNV-ETLAI, we compared its performance to ground truth datasets labeled by a human expert. In addition, we analyzed the CNV data, which was collected using CNV-ETLAI via a crowdsourcing approach. ResultsIn comparison to a human expert, CNV-ETLAI improved CNV detection accuracy by 4% and performed the analysis 60 times faster. This performance can improve even further with upscaling of the CNV-ETLAI database as usage increases. 5,800 CNVs from 2,313 journal articles were collected. Total CNV frequency for the whole chromosome was highest for chromosome X, whereas CNV frequency per 1 Mb of genomic length was highest for chromosome 22. ConclusionsWe have developed, tested, and shared CNV-ETLAI for research and clinical purposes (https://lmic.mgh.harvard.edu/CNV-ETLAI). Use of CNV-ETLAI is expected to ease and accelerate diagnostic classification and interpretation of CNVs.

Gymnodinialimonas ceratoperidinii gen. nov., sp. nov., isolated from rare marine dinoflagellate Ceratoperidinium margalefii.

A bacterial strain, designated J12C1-MA-4T, was isolated from liquid culture of the dinoflagellate Ceratoperidinium margalefii. The bacterium was Gram-negative, aerobic, and rod-shaped. Oxidase and catalase were positive. Optimal growth was observed at30°C, pH 7.0, in the presence of 1% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene and a 92 core gene set suggested that the strain J12C1-MA-4T belongs to the family Rhodobacteraceae in the class Alphaproteobacteria and represents a taxon separated from other genera. 16S rRNA gene sequence of the strain J12C1-MA-4T showed high similarities to Loktanella ponticola KCTC 42133T (95.7%), Pseudooctadecabacter jejudonensis KCTC 32525T (95.5%) and Jannaschia helgolandensis KCTC 12191T (95.3%). The genome length of strain J12C1-MA-4T was 3,621,968bp with a DNA G + C content of 64.48mol%. The major cellular fatty acids of strain J12C1-MA-4T were summed feature 8 (comprising C18:1ω7c and/or C18:1ω6c) (> 10%). Phosphatidylglycerol (PG), phosphatidylcholine (PC), phospholipids (PL), lipids 1 (L1) and aminolipid (AL) were shown to be the major polar lipids. The sole predominant isoprenoid quinone was Q-10. Based on phylogenetic, phenotypic, chemotaxonomic and genomic features, we propose that strain J12C1-MA-4T represent a novel species in the novel genus of the family Rhodobacteraceae, with the proposed name Gymnodinialimonas ceratoperidinii gen. nov., sp. nov.. The type strain is J12C1-MA-4T (=KCTC 82770T =GDMCC 1.2729T).

Complete Genome Sequence of Aeromonas hydrophila Bacteriophage BUCT552

ABSTRACTWe report the complete genome sequence of Aeromonas hydrophila bacteriophage BUCT552 whose full length of the linear dsDNA genome is 59,685 bp and G+C content is 60.0%. It contains 74 open reading frames but no tRNA. The results of TEM showed BUCT552 is a member of the family Siphoviridae.

Assembly and Annotation of Escherichia coli Bacteriophage U115.

ABSTRACTWe present the annotated genome sequence of Escherichia coli bacteriophage U115, a T4-like bacteriophage. Phage U115 has a genome length of 166,986 bp and has 286 predicted genes.

Neiella holothuriorum sp. nov., isolated from the gut of a sea cucumber Apostichopus japonicus.

A Gram-stain negative, aerobic, rod-shaped bacterium, designated 126T, was isolated from the intestinal content of a sea cucumber, Apostichopus japonicus, in China. Strain 126T was found to grow optimally at 25-28°C and pH 7.5-8.0 in marine 2216 E medium, with tolerance of 1-7% (w/v) NaCl. Strain 126T is motile by means of one to several polar flagella. The dominant fatty acids of strain 126T were identified as C16:1 ω7c/C16:1 ω6c (29.5%), C18:1 ω7c/C18:1 ω6c (19.8%) and C16:0 (16.7%). The respiratory quinone was found to be Q-8. The polar lipid profile was found to be mainly composed of phosphatidylglycerol and phosphatidylethanolamine. The total length of the draft genome is approximately 4.2 × 106bp, encoding 3655 genes and 3576 coding sequences. The G + C content of the genomic DNA is 48.0%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 126T belongs to the genus Neiella and is closely related to Neiella marina J221T (96.5%). Genomic comparisons of 126T to N. marina J221T revealed that they had similar genome size, G + C content and complement of clusters of orthologous groups. However, average nucleotide identity and digital DNA-DNA hybridization values between strains126T and N. marina J221T was 75.5% and 19.7%, which could distinguish the strains. On the basis of these phenotypic and genotypic data, strain 126T is concluded to represent a novel species, for which the name Neiella holothuriorum sp. nov. is proposed. The type strain is 126T (= GDMCC 1.2530T = KCTC 82829T).

Comparative Analysis the Complete Chloroplast Genomes of Nine Musa Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications.

Musa (family Musaceae) is monocotyledonous plants in order Zingiberales, which grows in tropical and subtropical regions. It is one of the most important tropical fruit trees in the world. Herein, we used next-generation sequencing technology to assemble and perform in-depth analysis of the chloroplast genome of nine new Musa plants for the first time, including genome structure, GC content, repeat structure, codon usage, nucleotide diversity and etc. The entire length of the Musa chloroplast genome ranged from 167,975 to 172,653 bp, including 113 distinct genes comprising 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. In comparative analysis, we found that the contraction and expansion of the inverted repeat (IR) regions resulted in the doubling of the rps19 gene. The several non-coding sites (psbI–atpA, atpH–atpI, rpoB–petN, psbM–psbD, ndhf–rpl32, and ndhG–ndhI) and three genes (ycf1, ycf2, and accD) showed significant variation, indicating that they have the potential of molecular markers. Phylogenetic analysis based on the complete chloroplast genome and coding sequences of 77 protein-coding genes confirmed that Musa can be mainly divided into two groups. These genomic sequences provide molecular foundation for the development and utilization of Musa plants resources. This result may contribute to the understanding of the evolution pattern, phylogenetic relationships as well as classification of Musa plants.

Draft Genome Sequence of Legionella Species Isolated from Drinking Water in an Italian Industry.

ABSTRACTWe report the draft genome sequences of an environmental Legionella strain isolated from an industrial water distribution system in Italy. Macrophage infectivity potentiator (mip) and β-subunit of RNA polymerase (rpoB) genes were used to perform the species identification. Whole-genome sequencing (WGS) and average nucleotide identity (ANI) identified the isolate as belonging to a presumptive novel Legionella species, with a genome length of 3,281,851 bp.

Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes.

Lentinula edodes is a tetrapolar basidiomycete with two haploid nuclei in each cell during most of their life cycle. Understanding the two haploid nuclei genome structures and their interactions on growth and fruiting body development has significant practical implications, especially for commercial cultivars. In this study, we isolated and assembled the two haploid genomes from a commercial strain of L. edodes using Illumina, HiFi, and Hi-C technologies. The total genome lengths were 50.93 Mb and 49.80 Mb for the two monokaryons SP3 and SP30, respectively, with each assembled into 10 chromosomes with 99.63% and 98.91% anchoring rates, respectively, for contigs more than 100 Kb. Genome comparisons suggest that two haploid nuclei likely derived from distinct genetic ancestries, with ~30% of their genomes being unique or non-syntenic. Consistent with a tetrapolar mating system, the two mating-type loci A (matA) and B (matB) of L. edodes were found located on two different chromosomes. However, we identified a new but incomplete homeodomain (HD) sublocus at ~2.8 Mb from matA in both monokaryons. Our study provides a solid foundation for investigating the relationships among cultivars and between cultivars and wild strains and for studying how two genetically divergent nuclei coordinate to regulate fruiting body formation in L. edodes.

The complete mitochondrial genome of Hyalomma rufipes (Acari: Ixodidae) from China and comparative analysis of mitogenomes in genus Hyalomma

ABSTRACT The coarse-legged tick Hyalomma rufipes (Koch, 1844), a two-host tick and an important vector for multiple pathogens, can cause severe damage to humans and domestic animals. Here, we provide the complete mitochondrial genome (mitogenome) of H. rufipes from China obtained by next-generation sequencing (NGS) methods. The 14,761 bp long mitogenome of H. rufipes had a high A + T content (79.7%) and contained a typical set of 37 genes, with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes (rRNAs). The genome also included two control regions (CRs) and three tick-boxes. We compared the mitogenomes of H. rufipes from China and South Africa. The results showed that the gene arrangement, CRs location, and incomplete secondary structures of trnC and trnS1 were similar. However, several differences presented in the two isolates, including the gene length and the termination codons of PCGs. Also, the comparison of the mitogenomes of Hyalomma species revealed differences in genome length, A + T content, and initiation and termination codons. Furthermore, gene rearrangement existed in the tick mitogenomes, with a unique arrangement in Amblyomma transversale. Additionally, our phylogenetic analyses clearly clarified the phylogenetic relationships within ticks, H. rufipes being clustered with other Hyalomma species and more closely related to H. marginatum.

Sequencing and analysis of the complete mitochondrial genome of Jacobiasca formosana (Hemiptera: Cicadellidae: Typhlocybinae: Empoascini)

In this study, the whole mitochondrial genome of Jacobiasca formosana was sequenced and annotated. The mitogenome is 16,353bp in length, including 37 typical genes and a control region. The 13 length of protein genomes (PCGs) is 10,980bp in size, which encode 3,649 amino acids. All PCGs started with ATN codon and most of PCGs stopped with TAN, except for COX1, COX2 and ND5 used incomplete T as stop codon. The phylogenetic tree results showed that J. formosana belonged to the Empoascini of subfamily Typhlocybinae but different from other species in the subfamily.

Chromosome-level assembly of the common vetch (Vicia sativa) reference genome.

Vicia sativa L. (common vetch, n =6) is an annual, herbaceous, climbing legume, originating in the Fertile Crescent of the Middle East and now widespread in the Mediterranean basin, West, Central and Eastern Asia, North and South America. V.sativa is of economic importance as a forage legume in countries such as Australia, China, and the USA, and contributes valuable nitrogen to agricultural rotation cropping systems. To accelerate precision genome breeding and genomics-based selection of this legume, we present a chromosome-level reference genome sequence for V.sativa, constructed using a combination of long-read Oxford Nanopore sequencing, short-read Illumina sequencing, and high-throughput chromosome conformation data (CHiCAGO and Hi-C) analysis. The chromosome-level assembly of six pseudo-chromosomes has a total genome length of 1.65Gbp, with a median contig length of 684Kbp. BUSCO analysis of the assembly demonstrated very high completeness of 98% of the dicotyledonous orthologs. RNA-seq analysis and gene modelling enabled the annotation of 53,218 protein-coding genes. This V.sativa assembly will provide insights into vetch genome evolution and be a valuable resource for genomic breeding, genetic diversity and for understanding adaption to diverse arid environments.

Slag: A program for seeded local assembly of genes in complex genomes.

Although finished genomes have become more common, there is still a need for assemblies of individual genes or chromosomal regions when only unassembled reads are available. slag (Seeded Local Assembly of Genes) fulfils this need by performing iterative local assembly based on cycles of matching‐read retrieval with blast and assembly with cap3, phrap, spades, canu or unicycler. The target sequence can be nucleotide or protein. Read fragmentation allows slag to use phrap or cap3 to assemble long reads at lower coverage (e.g., 5×) than is possible with canu or unicycler. In simple, nonrepetitive genomes, a slag assembly can cover a whole chromosome, but in complex genomes the growth of target‐matching contigs is limited as additional reads are consumed by consensus contigs consisting of repetitive elements. Apart from genomic complexity, contig length and correctness depend on read length and accuracy. With pyrosequencing or Illumina reads, slag‐assembled contigs are accurate enough to allow design of PCR primers, while contigs assembled from Oxford Nanopore or pre‐HiFi Pacific Biosciences long reads are generally only accurate enough to design baiting sequences for further targeted sequencing. In an application with real reads, slag successfully extended sequences for four wheat genes, which were verified by cloning and Sanger sequencing of overlapping amplicons. slag is a robust alternative to atram 2 for local assemblies, especially for read sets with less than 20× coverage. slag is freely available at https://github.com/cfcrane/SLAG.

Assessment of Heterozygosity and Genome-Wide Analysis of Heterozygosity Regions in Two Duroc Pig Populations.

Heterozygosity can effectively reflect the diverse models of population structure and demographic history. However, the genomic distribution of heterozygotes and the correlation between regions of heterozygosity (runs of heterozygosity, ROHet) and phenotypes are largely understudied in livestock. The objective of this study was to identify ROHet in the Duroc pig genome, and investigate the relationships between ROHet and eight important economic traits. Here, we genotyped 3,770 American Duroc (S21) and 2,096 Canadian Duroc (S22) pigs using 50 K single nucleotide polymorphism array to analyze heterozygosity. A total of 145,010 and 84,396 ROHets were characterized for S21 and S22 populations, respectively. ROHet segments were mostly enriched in 1–2 Mb length classification (75.48% in S21 and 72.25% in S22). The average genome length covered by ROHet was 66.53 ± 12.20 Mb in S21 and 73.32 ± 13.77 Mb in S22 pigs. Additionally, we detected 20 and 13 ROHet islands in S21 and S22 pigs. Genes in these genomic regions were mainly involved in the biological processes of immunity and reproduction. Finally, the genome-wide ROHet-phenotypes association analysis revealed that 130 ROHets of S21 and 84 ROHets of S22 were significantly associated with eight economic traits. Among the candidate genes in the significant ROHet regions, 16 genes related to growth, metabolism, and meat quality were considered as candidate genes for important economic traits of pigs. This work preliminarily explores the effect of heterozygosity-rich regions in the pig genome on production performance and provides new insights for subsequent research on pig genetic improvement.