Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map

Abstract Background The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. Results The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92–94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. Conclusions The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.

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Improved chromosome level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) based on SMRT Sequencing and linkage map

10.1101/2020.11.03.364950 ◽

2020 ◽

Author(s):

Daniel Blande ◽

Olli-Pekka Smolander ◽

Virpi Ahola ◽

Pasi Rastas ◽

Jaakko Tanskanen ◽

...

Keyword(s):

Linkage Map ◽

Model System ◽

Metapopulation Dynamics ◽

Melitaea Cinxia ◽

Smrt Sequencing ◽

Final Assembly ◽

Glanville Fritillary Butterfly ◽

Gene Models ◽

Chromosome Level

AbstractThe Glanville fritillary (Melitaea cinxia) butterfly is a long-term model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome level assembly of the butterfly’s genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO, indicates that the genome contains 93 - 95% of the BUSCO genes in complete and single copies. We predicted 14,830 gene models using the MAKER pipeline and manually curated 1,232 of these gene models. The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome and genetics studies on this species.

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A chromosome-level genome assembly and annotation of the humpback grouper Cromileptes altivelas

10.1101/2020.06.22.164277 ◽

2020 ◽

Author(s):

Yun Sun ◽

Dongdong Zhang ◽

Jianzhi Shi ◽

Guisen Chen ◽

Ying Wu ◽

...

Keyword(s):

Genome Assembly ◽

Chromosome Conformation ◽

Protein Coding ◽

Market Values ◽

Final Assembly ◽

Long Reads ◽

High Gene ◽

Food Fish ◽

High Quality Genome ◽

Chromosome Level

AbstractCromileptes altivelas that belongs to Serranidae in the order Perciformes, is widely distributed throughout the tropical waters of the Indo-West Pacific regions. Due to their excellent food quality and abundant nutrients, it has become a popular marine food fish with high market values. Here, we reported a chromosome-level genome assembly and annotation of the humpback grouper genome using more than 103X PacBio long-reads and high-throughput chromosome conformation capture (Hi-C) technologies. The N50 contig length of the assembly is as large as 4.14 Mbp, the final assembly is 1.07 Gb with N50 of scaffold 44.78 Mb, and 99.24% of the scaffold sequences were anchored into 24 chromosomes. The high-quality genome assembly also showed high gene completeness with 27,067 protein coding genes and 3,710 ncRNAs. This high accurate genome assembly and annotation will not only provide an essential genome resource for C. altivelas breeding and restocking, but will also serve as a key resource for studying fish genomics and genetics.

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Recovering individual haplotypes and a contiguous genome assembly from pooled long read sequencing of the diamondback moth (Lepidoptera: Plutellidae)

10.1101/867879 ◽

2019 ◽

Author(s):

Samuel Whiteford ◽

Arjen E. van’t Hof ◽

Ritesh Krishna ◽

Thea Marubbi ◽

Stephanie Widdison ◽

...

Keyword(s):

Linkage Map ◽

Diamondback Moth ◽

Reference Sequence ◽

Final Assembly ◽

Long Reads ◽

Long Read ◽

Divergent Haplotype ◽

Map Integration ◽

Related Individuals ◽

Methodological Approaches

AbstractBackgroundRecent advances in genomics have addressed the challenge that divergent haplotypes pose to the reconstruction of haploid genomes. However for many organisms, the sequencing of either field-caught individuals or a pool of heterogeneous individuals is still the only practical option. Here we present methodological approaches to achieve three outcomes from pooled long read sequencing: the generation of a contiguous haploid reference sequence, the sequences of heterozygous haplotypes; and reconstructed genomic sequences of individuals related to the pooled material.ResultsPacBio long read sequencing, Dovetail Hi-C scaffolding and linkage map integration yielded a haploid chromosome-level assembly for the diamondback moth (Plutella xylostella), a global pest of Brassica crops, from a pool of related individuals. The final assembly consisted of 573 scaffolds, with a total assembly size of 343.6Mbp a scaffold N50 value of 11.3Mbp (limited by chromosome size) and a maximum scaffold size of 14.4Mbp. This assembly was then integrated with an existing RAD-seq linkage map, anchoring 95% of the assembled sequence to defined chromosomal positions.ConclusionsWe describe an approach to resolve divergent haplotype sequences and describe multiple validation approaches. We also reconstruct individual genomes from pooled long-reads, by applying a recently developed k-mer binning method.

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Chromosome-level genome construction of a Japanese stickleback species using ultra-dense linkage analysis using single-cell sequencing of sperms

10.1101/2020.05.12.092221 ◽

2020 ◽

Author(s):

Kazutoshi Yoshitake ◽

Asano Ishikawa ◽

Ryo Yonezawa ◽

Shigeharu Kinoshita ◽

Jun Kitano ◽

...

Keyword(s):

Linkage Analysis ◽

Single Cell ◽

Linkage Map ◽

Analysis Tool ◽

Causal Genes ◽

Order Of Magnitude ◽

Cell Genome ◽

High Density Linkage Map ◽

Chromosome Level ◽

Single Cell Genome

AbstractThe presence of high quality genomes at the chromosome level is very useful in the search for the causal genes of mutants and in genetic breeding. The advent of next-generation sequencers has made it easier to decode genomes, but it is still difficult to construct the genomes of higher organisms. In order to construct the genome of a higher organism, the genome sequence of the organism is extended to the length of the chromosome by linkage analysis after assembly and scaffolding. However, in the past linkage analysis, it was difficult to make a high-density linkage map, and it was not possible to analyze organisms without an established breeding system. As an innovative alternative to conventional linkage analysis, we devised a method for genotyping sperm using 10x single-cell genome (CNV) sequencing libraries to generate a linkage map without interbreeding individuals. The genome was constructed using sperm from Gasterosteus nipponicus, and single-cell genotyping yielded 1,864,430 very dense hetero-SNPs. The average coverage per sperm cell is 0.13x. The number of sperm used is 1,738, which is an order of magnitude higher than the number of sperm used for conventional linkage analysis. We have improved the linkage analysis tool SELDLA (Scaffold Extender with Low Depth Linkage Analysis) so that we can analyze the data in accordance with the characteristics of single-cell genotyping data. Finally, we were able to determine the location and orientation on the chromosome for 85.6% of the contigs in the 456 Mbase genome of Gasterosteus nipponicus sequenced in nanopores. A total of 95.6% of the contigs in which a cross-reaction was detected within the contigs.

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High-density linkage map around the root aerenchyma locus Qaer1.06 in the backcross populations of maize Mi29 × teosinte “Zea nicaraguensis”

Breeding Science ◽

10.1270/jsbbs.59.427 ◽

2009 ◽

Vol 59 (4) ◽

pp. 427-433 ◽

Cited By ~ 27

Author(s):

Yoshiro Mano ◽

Fumie Omori

Keyword(s):

Linkage Map ◽

High Density ◽

Root Aerenchyma ◽

Backcross Populations ◽

High Density Linkage Map

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High-density linkage map construction and identification of loci regulating fruit quality traits in blueberry

Horticulture Research ◽

10.1038/s41438-021-00605-z ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Molla F. Mengist ◽

Hamed Bostan ◽

Elisheba Young ◽

Kristine L. Kay ◽

Nicholas Gillitt ◽

...

Keyword(s):

Linkage Map ◽

Fruit Quality ◽

Titratable Acidity ◽

Fruit Weight ◽

High Density ◽

Soluble Solids ◽

Quality Traits ◽

Total Soluble Solids ◽

Fruit Quality Traits ◽

High Density Linkage Map

AbstractFruit quality traits play a significant role in consumer preferences and consumption in blueberry (Vaccinium corymbosum L). The objectives of this study were to construct a high-density linkage map and to identify the underlying genetic basis of fruit quality traits in blueberry. A total of 287 F1 individuals derived from a cross between two southern highbush blueberry cultivars, ‘Reveille’ and ‘Arlen’, were phenotyped over three years (2016–2018) for fruit quality-related traits, including titratable acidity, pH, total soluble solids, and fruit weight. A high-density linkage map was constructed using 17k single nucleotide polymorphisms markers. The linkage map spanned a total of 1397 cM with an average inter-loci distance of 0.08 cM. The quantitative trait loci interval mapping based on the hidden Markov model identified 18 loci for fruit quality traits, including seven loci for fruit weight, three loci for titratable acidity, five loci for pH, and three loci for total soluble solids. Ten of these loci were detected in more than one year. These loci explained phenotypic variance ranging from 7 to 28% for titratable acidity and total soluble solid, and 8–13% for pH. However, the loci identified for fruit weight did not explain more than 10% of the phenotypic variance. We also reported the association between fruit quality traits and metabolites detected by Proton nuclear magnetic resonance analysis directly responsible for these fruit quality traits. Organic acids, citric acid, and quinic acid were significantly (P < 0.05) and positively correlated with titratable acidity. Sugar molecules showed a strong and positive correlation with total soluble solids. Overall, the study dissected the genetic basis of fruit quality traits and established an association between these fruit quality traits and metabolites.

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Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome

Genome Biology and Evolution ◽

10.1093/gbe/evaa161 ◽

2020 ◽

Vol 12 (11) ◽

pp. 1953-1960

Author(s):

Andrey A Yurchenko ◽

Hans Recknagel ◽

Kathryn R Elmer

Keyword(s):

Linkage Map ◽

Single Copy ◽

Phenotypic Traits ◽

Sequencing Data ◽

High Coverage ◽

Squamate Reptiles ◽

Common Lizard ◽

Zootoca Vivipara ◽

The Common ◽

Chromosome Level

Abstract Squamate reptiles exhibit high variation in their phenotypic traits and geographical distributions and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46-Gb genome assembly has a scaffold N50 of 11.52 Mb with N50 contig size of 220.4 kb and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total, 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.

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