How the pan-genome is changing crop genomics and improvement

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Abstract

Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-020-02224-8.

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The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

Alberto Casagrande (2007)

The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.

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The Sorghum bicolor genome and the diversification of grasses.

Andrew Paterson, John Bowers, Rémy Bruggmann … (2009)

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

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RepeatModeler2 for automated genomic discovery of transposable element families

Jullien Flynn, Robert Hubley, Clément Goubert … (2020)

The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types and sequences of TEs are highly variable across species, automated TE discovery and annotation are challenging and time-consuming tasks. A critical first step is the de novo identification and accurate compilation of sequence models representing all of the unique TE families dispersed in the genome. Here we introduce RepeatModeler2, a pipeline that greatly facilitates this process. This program brings substantial improvements over the original version of RepeatModeler, one of the most widely used tools for TE discovery. In particular, this version incorporates a module for structural discovery of complete long terminal repeat (LTR) retroelements, which are widespread in eukaryotic genomes but recalcitrant to automated identification because of their size and sequence complexity. We benchmarked RepeatModeler2 on three model species with diverse TE landscapes and high-quality, manually curated TE libraries: Drosophila melanogaster (fruit fly), Danio rerio (zebrafish), and Oryza sativa (rice). In these three species, RepeatModeler2 identified approximately 3 times more consensus sequences matching with >95% sequence identity and sequence coverage to the manually curated sequences than the original RepeatModeler. As expected, the greatest improvement is for LTR retroelements. Thus, RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license ( https://github.com/Dfam-consortium/RepeatModeler , http://www.repeatmasker.org/RepeatModeler/ ).

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Author and article information

Contributors

Rafael Della Coletta: della028@umn.edu

Yinjie Qiu: qiuxx221@umn.edu

Shujun Ou: oushujun@iastate.edu

Matthew B. Hufford: mhufford@iastate.edu

Candice N. Hirsch:

ORCID: http://orcid.org/0000-0002-8833-3023

cnhirsch@umn.edu

Journal

Journal ID (nlm-ta): Genome Biol

Journal ID (iso-abbrev): Genome Biol

Title: Genome Biology

Publisher: BioMed Central (London )

ISSN (Print): 1474-7596

ISSN (Electronic): 1474-760X

Publication date (Electronic): 4 January 2021

Publication date PMC-release: 4 January 2021

Publication date Collection: 2021

Volume: 22

Electronic Location Identifier: 3

Affiliations

[1 ]GRID grid.17635.36, ISNI 0000000419368657, Department of Agronomy and Plant Genetics, , University of Minnesota, ; St. Paul, MN 55108 USA

[2 ]GRID grid.34421.30, ISNI 0000 0004 1936 7312, Department of Ecology, Evolution, and Organismal Biology, , Iowa State University, ; Ames, IA 50011 USA

Author information

Candice N. Hirsch http://orcid.org/0000-0002-8833-3023

Article

Publisher ID: 2224

DOI: 10.1186/s13059-020-02224-8

PMC ID: 7780660

PubMed ID: 33397451

SO-VID: f63c2728-631d-4abd-b873-0a2c7039b2a4

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 27 August 2020

Date accepted : 7 December 2020

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100008982, National Science Foundation;

Award ID: IOS-1546727

Award ID: IOS-1934384

Award ID: IOS-1744001

Award ID: IOS-1546719

Award Recipient : Matthew B. Hufford

Funded by: FundRef http://dx.doi.org/10.13039/100005825, National Institute of Food and Agriculture;

Award ID: 2018-67013-27571

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ScienceOpen disciplines: Genetics

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How the pan-genome is changing crop genomics and improvement

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Abstract

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Arabidopsis genomics

Most cited references 177

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

The Sorghum bicolor genome and the diversification of grasses.

RepeatModeler2 for automated genomic discovery of transposable element families

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