The highly continuous reference genome of a leaf-chimeric red pineapple (Ananas comosus var. bracteatus f. tricolor) provides insights into elaboration of leaf color

Abstract Ananas comosus var. bracteatus f. tricolor (GL1) is a red pineapple accession whose mostly green leaves with chimeric white leaf margins turn red in spring and autumn and during flowering. It is an important ornamental plant and ideal plant research model for anthocyanin metabolism, chimeric leaf development, and photosynthesis. Here, we generated a highly contiguous chromosome-scale genome assembly for GL1 and compared it with other 3 published pineapple assemblies (var. comosus accessions MD2 and F153, and var. bracteatus accession CB5). The GL1 assembly has a total size of ∼461 Mb, with a contig N50 of ∼2.97 Mb and Benchmarking Universal Single-Copy Ortholog score of 97.3%. More than 99% of the contigs are anchored to 25 pseudochromosomes. Compared with the other 3 published pineapple assemblies, the GL1 assembly was confirmed to be more continuous. Our evolutionary analysis showed that the Bromeliaceae and Poaceae diverged from their nearest common ancestor ∼82.36 million years ago (MYA). Population structure analysis showed that while GL1 has not undergone admixture, bracteatus accession CB5 has resulted from admixture of 3 species of Ananas. Through classification of orthogroups, analysis of genes under positive selection, and analysis of presence/absence variants, we identified a series of genes related to anthocyanin metabolism and development of chimeric leaves. The structure and evolution of these genes were compared among the published pineapple assemblies with reveal candidate genes for these traits. The GL1 genome assembly and its comparisons with other 3 pineapple genome assemblies provide a valuable resource for the genetic improvement of pineapple and serve as a model for understanding the genomic basis of important traits in different pineapple varieties and other pan-cereal crops.

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A chromosome-anchored genome assembly for Lake Trout (Salvelinus namaycush)

10.22541/au.161792605.50398568/v1 ◽

2021 ◽

Author(s):

Seth Smith ◽

Eric Normandeau ◽

Haig Djambazian ◽

Pubudu Nawarathna ◽

Pierre Berube ◽

...

Keyword(s):

Genome Assembly ◽

Lake Trout ◽

Single Copy ◽

Salvelinus Namaycush ◽

Genomic Research ◽

Total Size ◽

Salmonid Species ◽

Long Read ◽

Potential Applications ◽

Conservation Concern

Here we present an annotated, chromosome-anchored, genome assembly for Lake Trout (Salvelinus namaycush) – a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation. We leveraged Pacific Biosciences long-read sequencing, paired-end Illumina sequencing, proximity ligation (Hi-C), and a previously published linkage map to produce a highly contiguous assembly composed of 7,378 contigs (contig N50 = 1.8 mb) assigned to 4,120 scaffolds (scaffold N50 = 44.975 mb). 84.7% of the genome was assigned to 42 chromosome-sized scaffolds and 93.2% of Benchmarking Universal Single Copy Orthologs were recovered, putting this assembly on par with the best currently available salmonid genomes. Estimates of genome size based on k-mer frequency analysis were highly similar to the total size of the finished genome, suggesting that the entirety of the genome was recovered. A mitome assembly was also produced. Self-vs-self synteny analysis allowed us to identify homeologs resulting from the Salmonid specific autotetraploid event (Ss4R) and alignment with three other salmonid species allowed us to identify homologous chromosomes in other species. We also generated multiple resources useful for future genomic research on Lake Trout including a repeat library and a sex averaged recombination map. A novel RNA sequencing dataset was also used to produce a publicly available set of gene annotations using the National Center for Biotechnology Information Eukaryotic Genome Annotation Pipeline. Potential applications of these resources to population genetics and the conservation of native populations are discussed.

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Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica

Frontiers in Plant Science ◽

10.3389/fpls.2021.625416 ◽

2021 ◽

Vol 12 ◽

Author(s):

Nataliya V. Melnikova ◽

Elena N. Pushkova ◽

Ekaterina M. Dvorianinova ◽

Artemy D. Beniaminov ◽

Roman O. Novakovskiy ◽

...

Keyword(s):

Genome Assembly ◽

Single Copy ◽

Dioecious Species ◽

Male And Female ◽

Male Genome ◽

Oxford Nanopore ◽

Genome Assemblies ◽

First Time ◽

High Quality Genome ◽

Y Haplotype

The genus Populus is presented by dioecious species, and it became a promising object to study the genetics of sex in plants. In this work, genomes of male and female Populus × sibirica individuals were sequenced for the first time. To achieve high-quality genome assemblies, we used Oxford Nanopore Technologies and Illumina platforms. A protocol for the isolation of long and pure DNA from young poplar leaves was developed, which enabled us to obtain 31 Gb (N50 = 21 kb) for the male poplar and 23 Gb (N50 = 24 kb) for the female one using the MinION sequencer. Genome assembly was performed with different tools, and Canu provided the most complete and accurate assemblies with a length of 818 Mb (N50 = 1.5 Mb) for the male poplar and 816 Mb (N50 = 0.5 Mb) for the female one. After polishing with Racon and Medaka (Nanopore reads) and then with POLCA (Illumina reads), assembly completeness was 98.45% (87.48% duplicated) for the male and 98.20% (76.77% duplicated) for the female according to BUSCO (benchmarking universal single-copy orthologs). A high proportion of duplicated BUSCO and the increased genome size (about 300 Mb above the expected) pointed at the separation of haplotypes in a large part of male and female genomes of P. × sibirica. Due to this, we were able to identify two haplotypes of the sex-determining region (SDR) in both assemblies; and one of these four SDR haplotypes, in the male genome, contained partial repeats of the ARR17 gene (Y haplotype), while the rest three did not (X haplotypes). The analysis of the male P. × sibirica SDR suggested that the Y haplotype originated from P. nigra, while the X haplotype is close to P. trichocarpa and P. balsamifera species. Moreover, we revealed a Populus-specific repeat that could be involved in translocation of the ARR17 gene or its part to the SDR of P. × sibirica and other Populus species. The obtained results expand our knowledge on SDR features in the genus Populus and poplar phylogeny.

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The Draft Genome of a Flat Peach (Prunus persica L. cv. ‘124 Pan’) Provides Insights into Its Good Fruit Flavor Traits

Plants ◽

10.3390/plants10030538 ◽

2021 ◽

Vol 10 (3) ◽

pp. 538

Author(s):

Aidi Zhang ◽

Hui Zhou ◽

Xiaohan Jiang ◽

Yuepeng Han ◽

Xiujun Zhang

Keyword(s):

Genome Assembly ◽

Prunus Persica ◽

Sugar Content ◽

Draft Genome ◽

Single Copy ◽

Terpene Biosynthesis ◽

Total Size ◽

Protein Coding ◽

Draft Genome Assembly ◽

Fruit Flavor

The flat peach has become more and more popular worldwide for its fruit quality with relatively low acidity, high sugar content and rich flavor. However, the draft genome assembly of flat peach is still unavailable and the genetic basis for its fruit flavor remains unclear. In this study, the draft genome of a flat peach cultivar ‘124 Pan’ was assembled by using a hybrid assembly algorithm. The final assembly resulted in a total size of 206 Mb with a N50 of 26.3 Mb containing eight chromosomes and seven scaffolds. Genome annotation revealed that a total of 25,233 protein-coding genes were predicted with comparable gene abundance among the sequenced peach species. The phylogenetic tree and divergence times inferred from 572 single copy genes of 13 plant species confirmed that Prunus ferganensis was the ancestor of the domesticated peach. By comparing with the genomes of Prunus persica (Lovell) and Prunus ferganensis, the expansion of genes encoding enzymes involved in terpene biosynthesis was found, which might contribute to the good fruit flavor traits of ‘124 Pan’. The flat peach draft genome assembly obtained in this study will provide a valuable genomic resource for peach improvement and molecular breeding.

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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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Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus

Scientific Reports ◽

10.1038/s41598-021-89091-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Guilherme B. Dias ◽

Musaad A. Altammami ◽

Hamadttu A. F. El-Shafie ◽

Fahad M. Alhoshani ◽

Mohamed B. Al-Fageeh ◽

...

Keyword(s):

Genome Assembly ◽

Control Strategies ◽

Insect Pest ◽

Single Copy ◽

Gene Content ◽

Rhynchophorus Ferrugineus ◽

Red Palm Weevil ◽

Transcriptomic Data ◽

Palm Trees ◽

Palm Weevil

AbstractThe red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function in R. ferrugineus has the potential to inform pest control strategies and thereby mitigate economic and biodiversity losses caused by this species. Using 10x Genomics linked-read sequencing, we produced a haplotype-resolved diploid genome assembly for R. ferrugineus from a single heterozygous individual with modest sequencing coverage ($$\sim$$ ∼ 62x). Benchmarking against conserved single-copy Arthropod orthologs suggests both pseudo-haplotypes in our R. ferrugineus genome assembly are highly complete with respect to gene content, and do not suffer from haplotype-induced duplication artifacts present in a recently published hybrid assembly for this species. Annotation of the larger pseudo-haplotype in our assembly provides evidence for 23,413 protein-coding loci in R. ferrugineus, including over 13,000 predicted proteins annotated with Gene Ontology terms and over 6000 loci independently supported by high-quality Iso-Seq transcriptomic data. Our assembly also includes 95% of R. ferrugineus chemosensory, detoxification and neuropeptide-related transcripts identified previously using RNA-seq transcriptomic data, and provides a platform for the molecular analysis of these and other functionally-relevant genes that can help guide management of this widespread insect pest.

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Classification of hepatitis C virus into major types and subtypes based on molecular evolutionary analysis

Virus Research ◽

10.1016/0168-1702(95)00007-d ◽

1995 ◽

Vol 36 (2-3) ◽

pp. 201-214 ◽

Cited By ~ 21

Author(s):

Ken-ichi Ohba ◽

Masashi Mizokami ◽

Tomoyoshi Ohno ◽

Kaoru Suzuki ◽

Etsuro Orito ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Evolutionary Analysis ◽

Molecular Evolutionary Analysis

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A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause

Insects ◽

10.3390/insects12020167 ◽

2021 ◽

Vol 12 (2) ◽

pp. 167

Author(s):

John H. Boyle ◽

Pasi M. A. Rastas ◽

Xin Huang ◽

Austin G. Garner ◽

Indra Vythilingam ◽

...

Keyword(s):

Linkage Map ◽

Aedes Albopictus ◽

Dna Sequences ◽

Genome Assembly ◽

Single Copy ◽

Health Concern ◽

Candidate Snps ◽

Single Location ◽

Asian Tiger ◽

Photoperiodic Diapause

The Asian tiger mosquito, Aedes albopictus, is an invasive vector mosquito of substantial public health concern. The large genome size (~1.19–1.28 Gb by cytofluorometric estimates), comprised of ~68% repetitive DNA sequences, has made it difficult to produce a high-quality genome assembly for this species. We constructed a high-density linkage map for Ae. albopictus based on 111,328 informative SNPs obtained by RNAseq. We then performed a linkage-map anchored reassembly of AalbF2, the genome assembly produced by Palatini et al. (2020). Our reassembled genome sequence, AalbF3, represents several improvements relative to AalbF2. First, the size of the AalbF3 assembly is 1.45 Gb, almost half the size of AalbF2. Furthermore, relative to AalbF2, AalbF3 contains a higher proportion of complete and single-copy BUSCO genes (84.3%) and a higher proportion of aligned RNAseq reads that map concordantly to a single location of the genome (46%). We demonstrate the utility of AalbF3 by using it as a reference for a bulk-segregant-based comparative genomics analysis that identifies chromosomal regions with clusters of candidate SNPs putatively associated with photoperiodic diapause, a crucial ecological adaptation underpinning the rapid range expansion and climatic adaptation of A. albopictus.

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Four distinct and unusual linker proteins in a mitotically dividing nucleus are derived from a 71-kilodalton polyprotein, lack p34cdc2 sites, and contain protein kinase A sites

Molecular and Cellular Biology ◽

10.1128/mcb.14.1.10-20.1994 ◽

1994 ◽

Vol 14 (1) ◽

pp. 10-20

Author(s):

M Wu ◽

C D Allis ◽

M T Sweet ◽

R G Cook ◽

T H Thatcher ◽

...

Keyword(s):

Protein Kinase ◽

Protein Kinase A ◽

Phosphorylation Site ◽

High Mobility ◽

Single Copy ◽

Amino Acid Sequences ◽

Evolutionary Analysis ◽

Associated Proteins ◽

Kinase Phosphorylation ◽

Kinase A

Tetrahymena thermophila micronuclei contain four linker-associated proteins, alpha, beta, gamma, and delta. Synthetic oligonucleotides based on N-terminal protein sequences of beta and gamma were used to clone the micronuclear linker histone (MLH) gene. The MLH gene is single copy and is transcribed into a 2.4-kb message encoding all four linker-associated proteins. The message is translated into a polypeptide (Mic LH) that is processed at the sequence decreases RTK to give proteins whose amino acid sequences differ markedly from each other, from the sequence of macronuclear H1, and from sequences of typical H1s of other organisms. This represents the first example of multiple chromatin proteins derived from a single polyprotein. The delta protein consists largely of two high-mobility-group (HMG) boxes. An evolutionary analysis of HMG boxes indicates that the delta HMG boxes are similar to the HMG boxes of tsHMG, a protein that appears in elongating mouse spermatids when they condense and cease transcription, suggesting that delta could play a similar role in the micronucleus. The micronucleus divides mitotically, while the macronucleus divides amitotically. Surprisingly, macronuclear H1 but not Mic LH contains sequences resembling p34cdc2 kinase phosphorylation sites, while each of the Mic LH-derived proteins contains a typical protein kinase A phosphorylation site in its carboxy terminus.

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A highly contiguous nuclear genome assembly of the mandarinfish Synchiropus splendidus (Syngnathiformes: Callionymidae)

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab306 ◽

2021 ◽

Author(s):

Martin Stervander ◽

William A Cresko

Keyword(s):

Genome Assembly ◽

Nuclear Genome ◽

Phylogenetic Position ◽

Blue Color ◽

Long Reads ◽

The Family ◽

Commercially Important ◽

Genomic Resource ◽

Genome Assemblies ◽

Important Fish

Abstract The fish order Syngnathiformes has been referred to as a collection of misfit fishes, comprising commercially important fish such as red mullets as well as the highly diverse seahorses, pipefishes, and seadragons—the well-known family Syngnathidae, with their unique adaptations including male pregnancy. Another ornate member of this order is the species mandarinfish. No less than two types of chromatophores have been discovered in the spectacularly colored mandarinfish: the cyanophore (producing blue color) and the dichromatic cyano-erythrophore (producing blue and red). The phylogenetic position of mandarinfish in Syngnathiformes, and their promise of additional genetic discoveries beyond the chromatophores, made mandarinfish an appealing target for whole genome sequencing. We used linked sequences to create synthetic long reads, producing a highly contiguous genome assembly for the mandarinfish. The genome assembly comprises 483 Mbp (longest scaffold 29 Mbp), has an N50 of 12 Mbp, and an L50 of 14 scaffolds. The assembly completeness is also high, with 92.6% complete, 4.4% fragmented, and 2.9% missing out of 4,584 BUSCO genes found in ray-finned fishes. Outside the family Syngnathidae, the mandarinfish represents one of the most contiguous syngnathiform genome assemblies to date. The mandarinfish genomic resource will likely serve as a high-quality outgroup to syngnathid fish, and furthermore for research on the genomic underpinnings of the evolution of novel pigmentation.

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The hormone neuroparsin seems essential in Lepidoptera but not in domesticated silkworms

10.1101/716746 ◽

2019 ◽

Author(s):

Jan A. Veenstra

Keyword(s):

Bombyx Mori ◽

Genome Assembly ◽

Galleria Mellonella ◽

Sequence Similarity ◽

Neuroendocrine Cells ◽

Primary Sequence ◽

Genome Assemblies ◽

Limited Sequence ◽

Wax Moth

AbstractThe primary sequence of the Arthropod neurohormone neuroparsin is so variable that so far no orthologs from moths and butterflies have been characterized, even though classical neurosecretory stains identify cells that are homologous to those producing this hormone in other insect species. Here Lepidopteran cDNAs showing limited sequence similarity to other insect neuroparsins are described. That these cDNAs do indeed code for authentic neuroparsins was confirmed by in situ hybridization in the wax moth, Galleria mellonella, which labeled the neuroparsin neuroendocrine cells. Although in virtually all genome assemblies from Lepidoptera a neuroparsin gene could be identified, the genome assembly from the silkworm, Bombyx mori, has a neuroparsin gene containing a 16 nucleotide deletion that renders this gene nonfunctional. Although only a small number of all silkworm strains carry this deletion, it suggests that the domestication of the silkworm has rendered the function of this neurohormone dispensable.

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