Marsupial chromosomics: bridging the gap between genomes and chromosomes

2019 ◽  
Vol 31 (7) ◽  
pp. 1189 ◽  
Author(s):  
Janine E. Deakin ◽  
Sally Potter
Keyword(s):  
Dna Sequence ◽  
Genome Assembly ◽  
Genome Architecture ◽  
Sequence Information ◽  
Full Potential ◽  
Tasmanian Devil ◽  
Sequencing Technology ◽  
A Genome ◽  
Devil Facial Tumour Disease ◽  
Chromosome Level

Marsupials have unique features that make them particularly interesting to study, and sequencing of marsupial genomes is helping to understand their evolution. A decade ago, it was a huge feat to sequence the first marsupial genome. Now, the advances in sequencing technology have made the sequencing of many more marsupial genomes possible. However, the DNA sequence is only one component of the structures it is packaged into: chromosomes. Knowing the arrangement of the DNA sequence on each chromosome is essential for a genome assembly to be used to its full potential. The importance of combining sequence information with cytogenetics has previously been demonstrated for rapidly evolving regions of the genome, such as the sex chromosomes, as well as for reconstructing the ancestral marsupial karyotype and understanding the chromosome rearrangements involved in the Tasmanian devil facial tumour disease. Despite the recent advances in sequencing technology assisting in genome assembly, physical anchoring of the sequence to chromosomes is required to achieve a chromosome-level assembly. Once chromosome-level assemblies are achieved for more marsupials, we will be able to investigate changes in the packaging and interactions between chromosomes to gain an understanding of the role genome architecture has played during marsupial evolution.

scholarly journals A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 144 ◽  
Author(s):  
Laís Coelho ◽  
Lukas Musher ◽  
Joel Cracraft
Keyword(s):  
Genome Assembly ◽  
High Throughput Sequencing ◽  
Population Genomics ◽  
De Novo ◽  
Structural Difference ◽  
Whole Genome ◽  
Sequencing Technology ◽  
A Genome ◽  
Avian Genomes ◽  
Chromosome Level

Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.

scholarly journals Chromosome-level genome assembly of a regenerable maize inbred line A188

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guifang Lin ◽  
Cheng He ◽  
Jun Zheng ◽  
Dal-Hoe Koo ◽  
Ha Le ◽  
...  
Keyword(s):  
Inbred Line ◽  
Genome Assembly ◽  
Gene Function ◽  
Maize Inbred Line ◽  
Carotenoid Cleavage Dioxygenase ◽  
Structural Variations ◽  
Embryonic Callus ◽  
Network Analyses ◽  
A Genome ◽  
Chromosome Level

Abstract Background The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. Results Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. Conclusions The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

scholarly journals A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

2019 ◽  
Vol 11 (11) ◽  
pp. 3144-3157 ◽  
Author(s):  
Yutaka Satou ◽  
Ryohei Nakamura ◽  
Deli Yu ◽  
Reiko Yoshida ◽  
Mayuko Hamada ◽  
...  
Keyword(s):  
Genome Size ◽  
Inbred Line ◽  
Genome Assembly ◽  
Ciona Intestinalis ◽  
Type A ◽  
Chromosomal Evolution ◽  
Sequence Information ◽  
A Genome ◽  
Biological Studies ◽  
Wide Range

Abstract Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114–120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.

scholarly journals Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano, and Hi-C analysis

GigaScience ◽  
2020 ◽  
Vol 9 (2) ◽  
Author(s):  
De-Lu Ning ◽  
Tao Wu ◽  
Liang-Jun Xiao ◽  
Ting Ma ◽  
Wen-Liang Fang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Juglans Regia ◽  
Future Research ◽  
High Quality ◽  
Illumina Hiseq ◽  
A Genome ◽  
Contact Frequency ◽  
Juglans Sigillata ◽  
Chromosome Level

Abstract Background Juglans sigillata, or iron walnut, belonging to the order Juglandales, is an economically important tree species in Asia, especially in the Yunnan province of China. However, little research has been conducted on J. sigillata at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to its plateau environment. To address these issues, a high-quality reference genome of J. sigillata would be useful. Findings To construct a high-quality reference genome for J. sigillata, we first generated 38.0 Gb short reads and 66.31 Gb long reads using Illumina and Nanopore sequencing platforms, respectively. The sequencing data were assembled into a 536.50-Mb genome assembly with a contig N50 length of 4.31 Mb. Additionally, we applied BioNano technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with scaffold N50 length of 16.43 Mb and contig N50 length of 4.34 Mb. To obtain a chromosome-level genome assembly, we constructed 1 Hi-C library and sequenced 79.97 Gb raw reads using the Illumina HiSeq platform. We anchored ∼93% of the scaffold sequences into 16 chromosomes and evaluated the quality of our assembly using the high contact frequency heat map. Repetitive elements account for 50.06% of the genome, and 30,387 protein-coding genes were predicted from the genome, of which 99.8% have been functionally annotated. The genome-wide phylogenetic tree indicated an estimated divergence time between J. sigillata and Juglans regia of 49 million years ago on the basis of single-copy orthologous genes. Conclusions We provide the first chromosome-level genome for J. sigillata. It will lay a valuable foundation for future research on the genetic improvement of J. sigillata.

scholarly journals Chromosomal-level reference genome of the neotropical tree Jacaranda mimosifolia D. Don

2021 ◽  
Author(s):  
Mingcheng Wang ◽  
Lei Zhang ◽  
Zhiqiang Wang
Keyword(s):  
Genome Assembly ◽  
Morphological Characteristics ◽  
Gene Families ◽  
Deciduous Tree ◽  
Protein Coding ◽  
Neotropical Tree ◽  
A Genome ◽  
Genomic Resource ◽  
Jacaranda Mimosifolia ◽  
Chromosome Level

Abstract Jacaranda mimosifolia D. Don is a deciduous tree widely cultivated in the tropics and subtropics of the world. It is famous for its beautiful blue flowers and pinnate compound leaves. In addition, this tree has great potential in environmental monitoring, soil quality improvement, and medicinal applications. However, a genome resource for J. mimosifolia has not been reported to date. In this study, we constructed a chromosome-level genome assembly of J. mimosifolia using PacBio sequencing, Illumina sequencing, and Hi-C technology. The final genome assembly was ∼707.32 Mb in size, 688.76 Mb (97.36%) of which could be grouped into 18 pseudochromosomes, with contig and scaffold N50 values of 16.77 and 39.98 Mb, respectively. A total of 30,507 protein-coding genes were predicted, 95.17% of which could be functionally annotated. Phylogenetic analysis among 12 plant species confirmed the close genetic relationship between J. mimosifolia and Handroanthus impetiginosus. Gene family clustering revealed 481 unique, 103 significantly expanded, and 16 significantly contracted gene families in the J. mimosifolia genome. This chromosome-level genome assembly of J. mimosifolia will provide a valuable genomic resource for elucidating the genetic bases of the morphological characteristics, adaption evolution, and active compounds biosynthesis of J. mimosifolia.

scholarly journals Chromosome-level genome assembly and annotation of the loquat (Eriobotrya japonica) genome

GigaScience ◽  
2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Shuang Jiang ◽  
Haishan An ◽  
Fangjie Xu ◽  
Xueying Zhang
Keyword(s):  
Genome Assembly ◽  
High Throughput Sequencing ◽  
Chromosome Rearrangement ◽  
Flowering Plant ◽  
Eriobotrya Japonica ◽  
Sequencing Data ◽  
African Countries ◽  
Short Reads ◽  
A Genome ◽  
Chromosome Level

Abstract Background The loquat (Eriobotrya japonica) is a species of flowering plant in the family Rosaceae that is widely cultivated in Asian, European, and African countries. It blossoms in the winter and ripens in the early summer. The genome of loquat has to date not been published, which limits the study of molecular biology in this cultivated species. Here, we used the third-generation sequencing technology of Nanopore and Hi-C technology to sequence the genome of Eriobotrya. Findings We generated 100.10 Gb of long reads using Oxford Nanopore sequencing technologies. Three types of Illumina high-throughput sequencing data, including genome short reads (47.42 Gb), transcriptome short reads (11.06 Gb), and Hi-C short reads (67.25 Gb), were also generated to help construct the loquat genome. All data were assembled into a 760.1-Mb genome assembly. The contigs were mapped to chromosomes by using Hi-C technology based on the contacts between contigs, and then a genome was assembled exhibiting 17 chromosomes and a scaffold N50 length of 39.7 Mb. A total of 45,743 protein-coding genes were annotated in the Eriobotrya genome, and we investigated the phylogenetic relationships between the Eriobotrya and 6 other Rosaceae species. Eriobotrya shows a close relationship with Malus and Pyrus, with the divergence time of Eriobotrya and Malus being 6.76 million years ago. Furthermore, chromosome rearrangement was found in Eriobotrya and Malus. Conclusions We constructed the first high-quality chromosome-level Eriobotrya genome using Illumina, Nanopore, and Hi-C technologies. This work provides a valuable reference genome for molecular studies of the loquat and provides new insight into chromosome evolution in this species.

scholarly journals Devil women

2018 ◽  
Vol 24 (3) ◽  
pp. 271
Author(s):  
Samantha Fox ◽  
Carolyn J. Hogg ◽  
Catherine E. Grueber ◽  
Katherine Belov
Keyword(s):  
At Risk ◽  
Government Agencies ◽  
Full Potential ◽  
Tasmanian Devil ◽  
Common Goal ◽  
Personal Stories ◽  
Devil Facial Tumour Disease ◽  
Risk Of Extinction ◽  
Carnivorous Marsupial ◽  
The Devil

The Tasmanian devil, an iconic carnivorous marsupial, is at risk of extinction due to a contagious cancer called devil facial tumour disease. Saving any species from extinction requires strong partnerships between government agencies, zoo bodies and academia. The Devil Tools & Tech project brought these groups together under a single banner to achieve a common goal. The project has strong leadership from women. Here we tell our personal stories as to how we came to be involved in saving the devil and emphasise the importance of strong networks for women to reach their full potential.

scholarly journals A chromosomal-level genome assembly and the diet habit-specific amino acid mutation identification of the Cyprinidae fish Ancherythroculter nigrocauda

2020 ◽  
Author(s):  
Yanhong Sun ◽  
Guiying Wang ◽  
Jianfang Gui ◽  
Jian Chen ◽  
Pei Li ◽  
...  
Keyword(s):  
Amino Acid ◽  
Single Molecule ◽  
Genome Assembly ◽  
High Efficiency ◽  
Expression Patterns ◽  
Amino Acid Mutation ◽  
Specific Amino Acid ◽  
Genetic Breeding ◽  
A Genome ◽  
Chromosome Level

Abstract Background Ancherythroculter nigrocauda is an endemic Cyprinidae fish in China, it has many desirable traits for genetic breeding, including strong disease resistance, unusual stress tolerance and high efficiency in nutrition update, which have made it an emerging commercial aquaculture fish. With the publication of its close-related species’ genome sequence, we can study the diet-specific genomic mutations within Cyprinidae. Results Here we report whole genome assembly of a female A. nigrocauda individual constructed using the single molecule DNA sequencing platform PacBio Sequel. With the help of Hi-C anchoring, we successfully placed contigs to chromosome level (2n = 48), yielding a genome size of 1054.05 Mb with contig N50 of 3.40 Mb and scaffold N50 of 42.68 Mb. This genome assembly, which has reached a high base-level accuracy of 99.999%, harboring 33,606 annotated protein-coding genes. We also found 582 genes hold diet-specific amino acid mutation between herbivorous and carnivorous fishes and 26 of them showed significant different expression patterns in liver tissue of these two types of fishes. Conclusions The availability of the chromosome-level genome assembly of A. nigrocauda provides valuable resources for future in-depth comparative genomics studies and applications including genetic breeding. The diet-specific amino acid mutation can be used in breeding of new strains of carnivorous fishes which feed on herbivorous fodder.

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