Visualization Tools for Genomic Conservation

Bandi, Venkat; Gutwin, Carl; Siri, Jorge Núñez; Neufeld, Eric; Sharpe, Andrew; Parkin, Isobel A. P.

doi:10.1007/978-1-0716-2067-0_16

Cited by 42 publications

(45 citation statements)

References 20 publications

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“…Finding extra copies of the same genes was enabled with a minimum sequence identity of 95% in exons/CDSs. Synteny analysis of orthologous pairs of transferred genes was performed using MCScanX [ 79 ] and visually inspected using SynVisio [ 80 ].…”

Section: Methodsmentioning

confidence: 99%

The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

Lim

Patrignani

et al. 2022

GigaScience

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Background Cassava (Manihot esculenta) is an important clonally propagated food crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has been limited, partially because cassava is a highly heterozygous crop with a repetitive and difficult-to-assemble genome. Findings Here we demonstrate that Pacific Biosciences high-fidelity (HiFi) sequencing reads, in combination with the assembler hifiasm, produced genome assemblies at near complete haplotype resolution with higher continuity and accuracy compared to conventional long sequencing reads. We present 2 chromosome-scale haploid genomes phased with Hi-C technology for the diploid African cassava variety TME204. With consensus accuracy >QV46, contig N50 >18 Mb, BUSCO completeness of 99%, and 35k phased gene loci, it is the most accurate, continuous, complete, and haplotype-resolved cassava genome assembly so far. Ab initio gene prediction with RNA-seq data and Iso-Seq transcripts identified abundant novel gene loci, with enriched functionality related to chromatin organization, meristem development, and cell responses. During tissue development, differentially expressed transcripts of different haplotype origins were enriched for different functionality. In each tissue, 20–30% of transcripts showed allele-specific expression (ASE) differences. ASE bias was often tissue specific and inconsistent across different tissues. Direction-shifting was observed in <2% of the ASE transcripts. Despite high gene synteny, the HiFi genome assembly revealed extensive chromosome rearrangements and abundant intra-genomic and inter-genomic divergent sequences, with large structural variations mostly related to LTR retrotransposons. We use the reference-quality assemblies to build a cassava pan-genome and demonstrate its importance in representing the genetic diversity of cassava for downstream reference-guided omics analysis and breeding. Conclusions The phased and annotated chromosome pairs allow a systematic view of the heterozygous diploid genome organization in cassava with improved accuracy, completeness, and haplotype resolution. They will be a valuable resource for cassava breeding and research. Our study may also provide insights into developing cost-effective and efficient strategies for resolving complex genomes with high resolution, accuracy, and continuity.

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Section: Methodsmentioning

confidence: 99%

The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

Lim

Patrignani

et al. 2022

GigaScience

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“…We used BUSCO v4 (Waterhouse et al, 2017) to evaluate protein sequences of annotated genes. Syntenic blocks were identified by MCScanX (Wang et al, 2012) and visualized by SynVisio (Bandi and Gutwin, 2020).…”

Section: Methodsmentioning

confidence: 99%

Genome sequence of 12 Vigna species as a knowledge base of stress tolerance and resistance

Naito

Wakatake

Shibata

et al. 2022

Preprint

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Harnessing plant genetic resources including wild plants enables exploitation of agronomically unfavorable lands to secure food in the future. The genus Vigna, family Fabaceae, consists of many species of such kind, as they are often adapted to harsh environments including marine beach, arid sandy soil, acidic soil, limestone karst and marshes. Here we report long-read assemblies of 12 Vigna species, achieving 95% or higher BUSCO scores. The comparative analyses discovered a new class of WUSCHEL-related homeobox (WOX) transcription factor superfamily that are incorporated into LTR retrotransposons and have dramatically amplified in some species of the genus Vigna. Except WOX transcription factors, however, gene contents are highly conserved among Vigna species with few copy number variations. On the other hand, transcriptome data provided some insights that transcriptional alterations played more important roles in evolution of stress tolerance in the genus Vigna. The whole genome sequences presented in this study will facilitate understanding genetic mechanisms of stress tolerance and application for developing new crops that are adapted to unfavorable environments.

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“…We visualized syntenic blocks on a genome-wide scale with SynVisio (Bandi & Gutwin, 2020), requiring a minimum MATCH_SIZE of 9, corresponding to at least ten anchor genes per block. We also ran MCScanX with default settings for downstream analysis, and visualized the blocks with Integrative Genomics Viewer (IGV) (Robinson et al , 2011).…”

Section: Methodsmentioning

confidence: 99%

A chromosome-level assembly of the “Cascade” hop (Humulus lupulus) genome uncovers signatures of molecular evolution and improves time of divergence estimates for the Cannabaceae family

Padgitt-Cobb

Matthews

Henning

et al. 2022

Preprint

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We present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly resulted in fragmented assemblies. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur. The chromosome-level assembly of Cascade was developed by scaffolding the previously-reported Cascade assembly generated with PacBio long-read sequencing, and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations, and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assess molecular evolution in gene sequences, gene family expansion and contraction, and time divergence using Bayesian inference. We identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families. The Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.

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Visualization Tools for Genomic Conservation

Cited by 42 publications

References 20 publications

The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

Genome sequence of 12 Vigna species as a knowledge base of stress tolerance and resistance

A chromosome-level assembly of the “Cascade” hop (Humulus lupulus) genome uncovers signatures of molecular evolution and improves time of divergence estimates for the Cannabaceae family

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