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

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.

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Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

10.1101/2020.09.09.289611 ◽

2020 ◽

Author(s):

Guifang Lin ◽

Cheng He ◽

Jun Zheng ◽

Dal-Hoe Koo ◽

Ha Le ◽

...

Keyword(s):

Inbred Line ◽

Genome Assembly ◽

Single Copy ◽

Maize Inbred Line ◽

Genome Comparison ◽

Carotenoid Cleavage Dioxygenase ◽

Elevated Expression ◽

Enhanced Expression ◽

Low Expression ◽

Chromosome Level

ABSTRACTThe highly embryogenic and transformable maize inbred line A188 is an attractive model for analyzing maize gene function. Here we constructed a chromosome-level genome assembly of A188 using long reads and optical maps. Genome comparison of A188 with the reference line B73 identified pervasive structural variation, including a 1.8 Mb duplication on the Gametophyte factor1 locus for unilateral cross-incompatibility and six inversions of 0.7 Mb or greater. Increased copy number of the gene, carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression together with low expression of yellow endosperm 1 (y1) condition reduced carotenoid accumulation, which accounts for the white seed phenotype of A188 that contrasts with the yellow seed of B73 that has high expression of y1 and low expression of the single-copy ccd1. Further, transcriptome and epigenome analyses with the A188 reference genome revealed enhanced expression of defense pathways and altered DNA methylation patterns of embryonic callus.

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Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

10.1101/2021.03.15.435372 ◽

2021 ◽

Author(s):

Fei Ge ◽

Jingtao Qu ◽

Peng Liu ◽

Lang Pan ◽

Chaoying Zou ◽

...

Keyword(s):

Single Molecule ◽

Inbred Line ◽

Genome Mapping ◽

Maize Inbred Line ◽

Sequencing Data ◽

Structural Variations ◽

Single Molecule Sequencing ◽

Maize Genetic ◽

Induction Ratio ◽

Phenotypic Variations

Heretofore, little is known about the mechanism underlying the genotype-dependence of embryonic callus (EC) induction, which has severely inhibited the development of maize genetic engineering. Here, we report the genome sequence and annotation of a maize inbred line with high EC induction ratio, A188, which is assembled from single-molecule sequencing and optical genome mapping. We assembled a 2,210 Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to those of 9.73 Mb for B73 and 10.2 Mb for Mo17. Comparative analysis revealed that ~30% of the predicted A188 genes had large structural variations to B73, Mo17 and W22 genomes, which caused considerable protein divergence and might lead to phenotypic variations between the four inbred lines. Combining our new A188 genome, previously reported QTLs and RNA sequencing data, we reveal 8 large structural variation genes and 4 differentially expressed genes playing potential roles in EC induction.

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

Genome Biology and Evolution ◽

10.1093/gbe/evz228 ◽

2019 ◽

Vol 11 (11) ◽

pp. 3144-3157 ◽

Cited By ~ 12

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.

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Marsupial chromosomics: bridging the gap between genomes and chromosomes

Reproduction Fertility and Development ◽

10.1071/rd18201 ◽

2019 ◽

Vol 31 (7) ◽

pp. 1189 ◽

Cited By ~ 1

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.

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

Diversity ◽

10.3390/d11090144 ◽

2019 ◽

Vol 11 (9) ◽

pp. 144 ◽

Cited By ~ 4

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.

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Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

The Crop Journal ◽

10.1016/j.cj.2021.08.002 ◽

2021 ◽

Author(s):

Fei Ge ◽

Jingtao Qu ◽

Peng Liu ◽

Lang Pan ◽

Chaoying Zou ◽

...

Keyword(s):

Functional Genomics ◽

Inbred Line ◽

Genome Assembly ◽

Reference Genome ◽

Maize Inbred Line

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A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus)

Genomics ◽

10.1016/j.ygeno.2021.04.007 ◽

2021 ◽

Author(s):

Paulino Martínez ◽

Diego Robledo ◽

Xoana Taboada ◽

Andrés Blanco ◽

Michel Moser ◽

...

Keyword(s):

Genome Assembly ◽

Genome Wide Association Study ◽

Scophthalmus Maximus ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Main Driver ◽

Turbot Scophthalmus Maximus ◽

Chromosome Level

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Chromosome Level Assembly of Homozygous Inbred Line ‘Wongyo 3115’ Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria × ananassa)

Frontiers in Plant Science ◽

10.3389/fpls.2021.696229 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hye-Eun Lee ◽

Abinaya Manivannan ◽

Sun Yi Lee ◽

Koeun Han ◽

Jun-Geol Yeum ◽

...

Keyword(s):

Linkage Map ◽

Inbred Line ◽

High Density ◽

Genetic Maps ◽

Fruit Firmness ◽

Sequencing Technologies ◽

A Genome ◽

Genetic Mechanisms ◽

Trait Locus ◽

Chromosome Level

Strawberry is an allo-octoploid crop with high genome heterozygosity and complexity, which hinders the sequencing and the assembly of the genome. However, in the present study, we have generated a chromosome level assembly of octoploid strawberry sourced from a highly homozygous inbred line ‘Wongyo 3115’, using long- and short-read sequencing technologies. The assembly of ‘Wongyo 3115’ produced 805.6 Mb of the genome with 323 contigs scaffolded into 208 scaffolds with an N50 of 27.3 Mb after further gap filling. The whole genome annotation resulted in 151,892 genes with a gene density of 188.52 (genes/Mb) and validation of a genome, using BUSCO analysis resulted in 94.10% complete BUSCOs. Firmness is one of the vital traits in strawberry, which facilitate the postharvest shelf-life qualities. The molecular and genetic mechanisms that contribute the firmness in strawberry remain unclear. We have constructed a high-density genetic map based on the ‘Wongyo 3115’ reference genome to identify loci associated with firmness in the present study. For the quantitative trait locus (QTL) identification, the ‘BS F2’ populations developed from two inbred lines were genotyped, using an Axiom 35K strawberry chip, and marker positions were analyzed based on the ‘Wongyo 3115’ genome. Genetic maps were constructed with 1,049 bin markers, spanning the 3,861 cM. Using firmness data of ‘BS F2’ obtained from 2 consecutive years, five QTLs were identified on chromosomes 3-3, 5-1, 6-1, and 6-4. Furthermore, we predicted the candidate genes associated with firmness in strawberries by utilizing transcriptome data and QTL information. Overall, we present the chromosome-level assembly and annotation of a homozygous octoploid strawberry inbred line and a linkage map constructed to identify QTLs associated with fruit firmness.

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Aligning optical maps to de Bruijn graphs

Bioinformatics ◽

10.1093/bioinformatics/btz069 ◽

2019 ◽

Vol 35 (18) ◽

pp. 3250-3256 ◽

Cited By ~ 1

Author(s):

Kingshuk Mukherjee ◽

Bahar Alipanahi ◽

Tamer Kahveci ◽

Leena Salmela ◽

Christina Boucher

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Sequence Data ◽

Supplementary Information ◽

De Bruijn Graph ◽

Structural Variations ◽

Regular Feature ◽

A Genome ◽

De Bruijn ◽

Optical Maps

Abstract Motivation Optical maps are high-resolution restriction maps (Rmaps) that give a unique numeric representation to a genome. Used in concert with sequence reads, they provide a useful tool for genome assembly and for discovering structural variations and rearrangements. Although they have been a regular feature of modern genome assembly projects, optical maps have been mainly used in post-processing step and not in the genome assembly process itself. Several methods have been proposed for pairwise alignment of single molecule optical maps—called Rmaps, or for aligning optical maps to assembled reads. However, the problem of aligning an Rmap to a graph representing the sequence data of the same genome has not been studied before. Such an alignment provides a mapping between two sets of data: optical maps and sequence data which will facilitate the usage of optical maps in the sequence assembly step itself. Results We define the problem of aligning an Rmap to a de Bruijn graph and present the first algorithm for solving this problem which is based on a seed-and-extend approach. We demonstrate that our method is capable of aligning 73% of Rmaps generated from the Escherichia coli genome to the de Bruijn graph constructed from short reads generated from the same genome. We validate the alignments and show that our method achieves an accuracy of 99.6%. We also show that our method scales to larger genomes. In particular, we show that 76% of Rmaps can be aligned to the de Bruijn graph in the case of human data. Availability and implementation The software for aligning optical maps to de Bruijn graph, omGraph is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/omGraph. Supplementary information Supplementary data are available at Bioinformatics online.

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