Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.

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Whole-Genome Assemblies for Three Yersinia pestis Strains Isolated in Erenhot, China

Microbiology Resource Announcements ◽

10.1128/mra.01084-20 ◽

2020 ◽

Vol 9 (45) ◽

Author(s):

Jing Wang ◽

Xifeng Yang ◽

Hongyuan Zheng ◽

Li Tian ◽

Qi Shi ◽

...

Keyword(s):

Genetic Diversity ◽

Yersinia Pestis ◽

Draft Genome ◽

Meriones Unguiculatus ◽

Whole Genome ◽

Genome Sequences ◽

Content Type ◽

Genome Assemblies

ABSTRACT To explore the genetic diversity of Yersinia pestis strains in Erenhot, China, and their relationship with Mongolian strains, we collected and sequenced three Y. pestis strains from Erenhot, China, in 2018. Here, we report the draft genome sequences of three Y. pestis bv. Medievalis strains belonging to the 2.MED phylogroup that were circulating in Meriones unguiculatus populations.

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Chromosome-Level Genome Assemblies: Expanded Capabilities for Conservation Biology Research

Proceedings ◽

10.3390/iecge-07149 ◽

2020 ◽

Vol 76 (1) ◽

pp. 10

Author(s):

Azamat Totikov ◽

Andrey Tomarovsky ◽

Lorena Derezanin ◽

Olga Dudchenko ◽

Erez Lieberman-Aiden ◽

...

Keyword(s):

Genetic Diversity ◽

High Throughput ◽

Conservation Biology ◽

Threatened Species ◽

Draft Genome ◽

Chromosome Conformation ◽

Genome Wide ◽

Genome Assemblies ◽

Biology Research ◽

Chromosome Level

Genome assemblies are becoming increasingly important for understanding genetic diversity in threatened species. However, due to limited budgets in the area of conservation biology, genome assemblies, when available, tend to be highly fragmented with tens of thousands of scaffolds. The recent advent of high throughput chromosome conformation capture (Hi-C) makes it possible to generate more contiguous assemblies containing scaffolds that are length of entire chromosomes. Such assemblies greatly facilitate analyses and visualization of genome-wide features. We compared genetic diversity in seven threatened species that had both draft genome assemblies and newer chromosome-level assemblies available. Chromosome-level assemblies allowed better estimation of genetic diversity, localization, and, especially, visualization of low heterozygosity regions in the genomes.

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Trypanosoma cruzi Genome Assemblies: Challenges and Milestones of Assembling a Highly Repetitive and Complex Genome

Methods in Molecular Biology - T. cruzi Infection ◽

10.1007/978-1-4939-9148-8_1 ◽

2019 ◽

pp. 1-22 ◽

Cited By ~ 2

Author(s):

João Luís Reis-Cunha ◽

Daniella C. Bartholomeu

Keyword(s):

Trypanosoma Cruzi ◽

Genome Assemblies ◽

Complex Genome

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Natural Genetic Diversity in Tomato Flavor Genes

Frontiers in Plant Science ◽

10.3389/fpls.2021.642828 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lara Pereira ◽

Manoj Sapkota ◽

Michael Alonge ◽

Yi Zheng ◽

Youjun Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Solanum Lycopersicum ◽

Fruit Quality ◽

Tomato Fruit ◽

Expression Patterns ◽

High Genetic Diversity ◽

Tomato Flavor ◽

Main Determinants ◽

Fruit Flavor ◽

Genome Assemblies

Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance of sugars, acids and volatile compounds. Several genes controlling the levels of these metabolites in tomato fruit have been cloned, including LIN5, ALMT9, AAT1, CXE1, and LoxC. The aim of this study was to identify any association of these genes with trait variation and to describe the genetic diversity at these loci in the red-fruited tomato clade comprised of the wild ancestor Solanum pimpinellifolium, the semi-domesticated species Solanum lycopersicum cerasiforme and early domesticated Solanum lycopersicum. High genetic diversity was observed at these five loci, including novel haplotypes that could be incorporated into breeding programs to improve fruit quality of modern tomatoes. Using newly available high-quality genome assemblies, we assayed each gene for potential functional causative polymorphisms and resolved a duplication at the LoxC locus found in several wild and semi-domesticated accessions which caused lower accumulation of lipid derived volatiles. In addition, we explored gene expression of the five genes in nine phylogenetically diverse tomato accessions. In general, the expression patterns of these genes increased during fruit ripening but diverged between accessions without clear relationship between expression and metabolite levels.

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MaGuS: a tool for map-guided scaffolding and quality assessment of genome assemblies

10.1101/032045 ◽

2015 ◽

Author(s):

Mohammed-Amin Madoui ◽

Carole Dossat ◽

Leo d'Agata ◽

Edwin van der Vossen ◽

Jan van Oeveren ◽

...

Keyword(s):

High Throughput ◽

Genome Assembly ◽

High Throughput Sequencing ◽

Draft Genome ◽

Genetic Maps ◽

Sequencing Data ◽

A Genome ◽

Genome Map ◽

Genome Assemblies ◽

Complex Genome

Background Scaffolding is a crucial step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in continuity but often lack consistency in repetitive regions, resulting in fragmented assemblies. Here, we describe a novel tool to link assemblies to a genome map to aid complex genome reconstruction by detecting assembly errors and allowing scaffold ordering and anchoring. Results We present MaGuS (map-guided scaffolding), a modular tool that uses a draft genome assembly, a genome map, and high-throughput paired-end sequencing data to estimate the quality and to enhance the continuity of an assembly. We generated several assemblies of the Arabidopsis genome using different scaffolding programs and applied MaGuS to select the best assembly using quality metrics. Then, we used MaGuS to perform map-guided scaffolding to increase continuity by creating new scaffold links in low-covered and highly repetitive regions where other commonly used scaffolding methods lack consistency. Conclusions MaGuS is a powerful reference-free evaluator of assembly quality and a map-guided scaffolder that is freely available at https://github.com/institut-de-genomique/MaGuS. Its use can be extended to other high-throughput sequencing data (e.g., long-read data) and also to other map data (e.g., genetic maps) to improve the quality and the continuity of large and complex genome assemblies.

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Use of RAPD Marker Analysis to Assess Changes in the Genetic Diversity of Potato Genebanks

HortScience ◽

10.21273/hortsci.31.4.595d ◽

1996 ◽

Vol 31 (4) ◽

pp. 595d-595

Author(s):

A. del Rio ◽

J.B. Bamberg ◽

Z. Huaman ◽

R. Hoekstra ◽

A. Salas ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Rapd Marker ◽

Solanum Species ◽

Breeding Systems ◽

Common Source ◽

Wild Potato Species ◽

Tetraploid Potato ◽

Potato Germplasm

Effects of genebank seed increases on the genetic integrity and whether germplasm in the genebank still represents the in situ populations from which it was collected are major concerns of the recently formed Association of Potato Intergenebank Collaborators (APIC), a consortium of world potato genebank leaders. This cooperative APIC research used RAPDs and morphological markers 1) to establish genetic relationships between seed increased populations within accessions and (2) to measure genetic differentiation between diploid and tetraploid potato germplasm maintained for many years and current in situ populations from the same collection sites in the wild. Solanum jamesii Torrey (2n = 2x = 24) and S. fendleri A. Gray (2n = 4x = 48), two wild potato species native to North America, were used as plant material. These species represented two major breeding systems found among Solanum species: outcrossing diploids and inbreeding disomic tetraploids, respectively. Comparisons made between populations one generation apart and between sister populations generated from a common source indicated that there has been minimal loss of genetic diversity in captive germplasm using the genebank techniques standard at NRSP-6 and other world potato genebanks. RAPD markers also revealed that significant genetic differences were found between genebank-conserved and re-collected in situ populations for all diploid potato comparisons and for about half of the comparisons within tetraploid potato populations.

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Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data

10.1101/459453 ◽

2018 ◽

Author(s):

Xiaomeng Tian ◽

Ran Li ◽

Weiwei Fu ◽

Yan Li ◽

Xihong Wang ◽

...

Keyword(s):

Genetic Diversity ◽

De Novo ◽

3D Structure ◽

Regulatory Elements ◽

Protein Coding ◽

Web Based ◽

Coding Regions ◽

Pan Genome ◽

Enhanced Resolution ◽

Genome Assemblies

AbstractPigs (Sus scrofa) exhibit diverse phenotypes in different breeds shaped by the combined effects of various local adaptation and artificial selection. To comprehensively characterize the genetic diversity of pigs, we construct a pig pan-genome by comparing genome assemblies of 11 representative pig breeds with the reference genome (Sscrofa11.1). Approximately 72.5 Mb non-redundant sequences were identified as pan-sequences which were absent from the Sscrofa11.1. On average, 41.7 kb of spurious heterozygous SNPs per individual are removed and 12.9 kb novel SNPs per individual are recovered using pan-genome as the reference for SNP calling, thereby providing enhanced resolution for genetic diversity in pigs. Homolog annotation and analysis using RNA-seq and Hi-C data indicate that these pan-sequences contain protein-coding regions and regulatory elements. These pan-sequences can further improve the interpretation of local 3D structure. The pan-genome as well as the accompanied web-based database will serve as a primary resource for exploration of genetic diversity and promote pig breeding and biomedical research.

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Genetic Characterisation and Diversity Assessment of Potato Genotypes Using SSR Markers

Journal of Agricultural Science ◽

10.5539/jas.v9n8p99 ◽

2017 ◽

Vol 9 (8) ◽

pp. 99 ◽

Cited By ~ 1

Author(s):

Prossy Namugga ◽

Julia Sibiya ◽

Rob Melis ◽

Alex Barekye

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Distance ◽

Ssr Markers ◽

Null Alleles ◽

Tetraploid Potato ◽

Genetic Characterisation ◽

Diversity Assessment ◽

Selection For ◽

Linear Correlations

Information on diversity of genetic materials is vital for choosing parents in a breeding program. The objective of the study was to determine the pattern and level of genetic diversity among the selected 20 tetraploid potato genotypes using 16 SSR markers to identify suitable parents for breeding purposes. The microsatellites showed considerable variation among genotypes and sixty four alleles were amplified by the 16 primer pairs. The number of polymorphic alleles per locus ranged from 2 to 8 with an average of 3.9. The highest number of null alleles was observed was six for genotype Nakpot1. The overall size of the amplified product varied from 48 bp (marker STI0023) to 309 bp (marker STM5121). PIC values ranged from 0.0948 to 0.7832, with an average of 0.4307 per locus. Heterozygosity values ranged from 0.0997 to 0.805 with an average of 0.466919. Significant positive linear correlations were observed between PIC values and number of alleles (r = 0.905); and heterozygosity and number of alleles (r = 0.8659) at p < 0.001. Cluster analysis separated the genotypes into three different groups. The genetic distance between clones ranged from 1 to 5.7. Cruza had the highest genetic distance while the shortest genetic distance was observed between 396026.103 and 396034.104. The microsatellites used in this study provided useful information regarding the variability of the tested genotypes and their selection for breeding purposes.

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