The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)

AbstractThe basidiomycete fungus Lentinula novae-zelandiae is endemic to New Zealand and is a sister taxon to Lentinula edodes, the second most cultivated mushroom in the world. To explore the biology of this organism, a high-quality chromosome level reference genome of L. novae-zelandiae was produced. Macrosyntenic comparisons between the genome assembly of L. novae-zelandiae, L. edodes and a set of three genome assemblies of diverse species from the Agaricomycota reveal a high degree of macrosyntenic restructuring within L. edodes consistent with signal of domestication. These results show L. edodes has undergone significant genomic change during the course of its evolutionary history, likely a result of its cultivation and domestication over the last 1000 years.

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Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology

Genes ◽

10.3390/genes12091336 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1336

Author(s):

Azamat Totikov ◽

Andrey Tomarovsky ◽

Dmitry Prokopov ◽

Aliya Yakupova ◽

Tatiana Bulyonkova ◽

...

Keyword(s):

Genetic Diversity ◽

Conservation Biology ◽

Threatened Species ◽

Mammalian Species ◽

Draft Genome ◽

Chromosome Length ◽

Chromosome Conformation ◽

Genome Wide ◽

Genome Assemblies ◽

Chromosome Level

Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.

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Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

10.21203/rs.3.rs-796229/v1 ◽

2021 ◽

Author(s):

Ulrich Technau ◽

Sophia Robb ◽

Grigory Genikhovich ◽

Juan Montenegro ◽

Witney Fropf ◽

...

Keyword(s):

Gene Regulation ◽

Draft Genome ◽

Gene Clusters ◽

Sea Anemone ◽

Gene Repertoire ◽

Sea Anemones ◽

Animal Evolution ◽

Topologically Associated Domains ◽

Genome Assemblies ◽

Chromosome Level

Abstract Draft genome sequences of non-bilaterian species have provided important insights into the evolution of the metazoan gene repertoire. However, there is little information about the evolution of gene clusters, genome architectures and karyotypes during animal evolution. Here we report chromosome-level genome assemblies of two related anthozoan cnidarians, the sea anemones, Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence of the chromosomes between the two species. We show that, in contrast to Bilateria, Hox and NK clusters of investigated cnidarians are disintegrated, indicating that microsynteny conservation is largely lost. In line with that, we find no evidence for topologically associated domains, suggesting fundamental difference in long-range gene regulation compared to vertebrates. However, both sea anemone genomes show remarkable chromosomal conservation with other cnidarians, several bilaterians and the sponge Ephydatia muelleri, allowing us to reconstruct the putative cnidarian and metazoan chromosomes, consisting of 19 and 16 ancestral linkage groups, respectively. These data suggest that large parts of the ancestral metazoan genome have been retained in chromosomes of some extant lineages, yet, higher order gene regulation may have evolved only after the cnidarian-bilaterian split.

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Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication

Nature Communications ◽

10.1038/s41467-021-26272-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Feng Zhu ◽

Zhong-Tao Yin ◽

Zheng Wang ◽

Jacqueline Smith ◽

Fan Zhang ◽

...

Keyword(s):

Mutant Cell ◽

Genomic Variation ◽

Pekin Duck ◽

Genomic Databases ◽

Protein Coding ◽

Avian Evolution ◽

Almost All ◽

Genome Assemblies ◽

High Quality Genome ◽

Chromosome Level

AbstractDomestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed “missing genes” in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck.

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An improved pig reference genome sequence to enable pig genetics and genomics research

GigaScience ◽

10.1093/gigascience/giaa051 ◽

2020 ◽

Vol 9 (6) ◽

Cited By ~ 12

Author(s):

Amanda Warr ◽

Nabeel Affara ◽

Bronwen Aken ◽

Hamid Beiki ◽

Derek M Bickhart ◽

...

Keyword(s):

Reference Genome ◽

Genomic Research ◽

Biomedical Model ◽

Model Species ◽

Domestic Pig ◽

Genomics Research ◽

Long Read ◽

Genetics And Genomics ◽

Genome Assemblies ◽

Chromosome Level

Abstract Background The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete, and unresolved redundancies, short-range order and orientation errors, and associated misassembled genes limited its utility. Results We present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

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Chromosome‐level hybrid de novo genome assemblies as an attainable option for nonmodel insects

Molecular Ecology Resources ◽

10.1111/1755-0998.13176 ◽

2020 ◽

Vol 20 (5) ◽

pp. 1277-1293 ◽

Cited By ~ 1

Author(s):

Coline C. Jaworski ◽

Carson W. Allan ◽

Luciano M. Matzkin

Keyword(s):

De Novo ◽

Genome Assemblies ◽

Chromosome Level

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Chromosome-Level Genome Assemblies: Expanded Capabilities for Conservation Biology Research

Proceedings ◽

10.3390/iecge-07149 ◽

2020 ◽

Vol 76 (1) ◽

pp. 10

Author(s):

Azamat Totikov ◽

Andrey Tomarovsky ◽

Lorena Derezanin ◽

Olga Dudchenko ◽

Erez Lieberman-Aiden ◽

...

Keyword(s):

Genetic Diversity ◽

High Throughput ◽

Conservation Biology ◽

Threatened Species ◽

Draft Genome ◽

Chromosome Conformation ◽

Genome Wide ◽

Genome Assemblies ◽

Biology Research ◽

Chromosome Level

Genome assemblies are becoming increasingly important for understanding genetic diversity in threatened species. However, due to limited budgets in the area of conservation biology, genome assemblies, when available, tend to be highly fragmented with tens of thousands of scaffolds. The recent advent of high throughput chromosome conformation capture (Hi-C) makes it possible to generate more contiguous assemblies containing scaffolds that are length of entire chromosomes. Such assemblies greatly facilitate analyses and visualization of genome-wide features. We compared genetic diversity in seven threatened species that had both draft genome assemblies and newer chromosome-level assemblies available. Chromosome-level assemblies allowed better estimation of genetic diversity, localization, and, especially, visualization of low heterozygosity regions in the genomes.

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Chromosome-level genome assemblies of Channa argusandChanna maculata and comparative analysis of their temperature adaptability

GigaScience ◽

10.1093/gigascience/giab070 ◽

2021 ◽

Vol 10 (10) ◽

Author(s):

Mi Ou ◽

Rong Huang ◽

Cheng Yang ◽

Bin Gui ◽

Qing Luo ◽

...

Keyword(s):

Comparative Analysis ◽

Low Temperature ◽

Gene Families ◽

Temperature Adaptation ◽

Fish Family ◽

Transcription Factor Genes ◽

Immune Related Genes ◽

Genome Assemblies ◽

Temperature Adaptability ◽

Chromosome Level

Abstract Background Channa argus and Channa maculata are the main cultured species of the snakehead fish family, Channidae. The relationship between them is close enough that they can mate; however, their temperature adaptability is quite different. Results In this study, we sequenced and assembled the whole genomes of C. argus and C. maculata and obtained chromosome-level genome assemblies of 630.39 and 618.82 Mb, respectively. Contig N50 was 13.20 and 21.73 Mb, and scaffold N50 was 27.66 and 28.37 Mb, with 28,054 and 24,115 coding genes annotated for C. argus and C. maculata, respectively. Our analyses showed that C. argus and C. maculata have 24 and 21 chromosomes, respectively. Three pairs of chromosomes in C. argus correspond to 3 chromosomes in C. maculata, suggesting that 3 chromosomal fusion events occurred in C. maculata. Comparative analysis of their gene families showed that some immune-related genes were unique or expandable to C. maculata, such as genes related to herpes simplex infection. Analysis of the transcriptome differences related to temperature adaptation revealed that the brain and liver of C. argus rapidly produced more differentially expressed genes than C. maculata. Genes in the FoxO signalling pathway were significantly enriched in C. argus during the cooling process (P < 0.05), and the expression of 3 transcription factor genes in this pathway was significantly different between C. argus and C. maculata (P < 0.01). Conclusions C. maculata may have higher resistance to certain diseases, whereas C. argus has a faster and stronger response to low-temperature stress and thus has better adaptability to a low-temperature environment. This study provides a high-quality genome research platform for follow-up studies of Channidae and provides important clues regarding differences in the low-temperature adaptations of fish.

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The salmon louse genome may be much larger than sequencing suggests

10.1101/2022.01.14.476287 ◽

2022 ◽

Author(s):

Grace Wyngaard ◽

Rasmus Skern-Mauritzen ◽

Ketil Malde ◽

Rachel Prendergast ◽

Stefano Peruzzi

Keyword(s):

Genome Size ◽

North Atlantic ◽

Single Copy ◽

Bay Of Fundy ◽

Lepeophtheirus Salmonis ◽

The North ◽

Salmon Lice ◽

The North Atlantic ◽

Genome Assemblies ◽

Chromosome Level

The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding over 92% of expected genes and transcriptome datasets routinely mapping over 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements in the range of 1.3 to 1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up approx. 60% of the genome assemblies.

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Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

10.1101/2021.07.13.451380 ◽

2021 ◽

Author(s):

Hollis A Dahn ◽

Jacquelyn Mountcastle ◽

Jennifer Balacco ◽

Sylke Winkler ◽

Iliana Bista ◽

...

Keyword(s):

Molecular Weight ◽

High Molecular Weight ◽

Long Range ◽

High Quality ◽

High Molecular Weight Dna ◽

Preservation Methods ◽

Long Read ◽

Genome Assemblies ◽

Ultra High Molecular Weight ◽

Chromosome Level

Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for Phase 1 of the Vertebrate Genomes Project (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all ~70,000 extant vertebrate species.

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