Improved maize reference genome with single-molecule technologies

By Yinping Jiao, P. Peluso, Jinghua Shi, Tiffany Y. Liang, Michelle C. Stitzer, Bo Wang, Michael Campbell, J. Stein, Xuehong Wei, Chen-Shan Chin and 17 more. Nature, 2017

1,069 citations recorded by the source corpus.

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/f31ecdc0001e130087184e9b13a3137220a95237

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Citations in the corpus

RepeatModeler2: automated genomic discovery of transposable element families (2019, background): “The zebrafish, D. rerio, is dominated by class II, DNA-TIR transposons, but also exhibits a very diverse assortment of LTR retroelements with many unique families (Howe et al. 2013).”
Piercing the dark matter: bioinformatics of long-range sequencing and mapping (2018, background): “Indeed, several ‘reference’ genomes established using older technologies, such as the genomes of maize 15 , fruit fly 16 , mosquito 12 and many others, have been reassembled with the new technologies to fix errors and improve their resolution.”
RaGOO: fast and accurate reference-guided scaffolding of draft genomes (2019, background): “One popular reference-free scaffolding approach is to anchor genome assembly contigs to some variety of genomic map [4], such as an optical, physical, or linkage map [5].”
Assessing genome assembly quality using the LTR Assembly Index (LAI) (2018, result): “reported similar findings in the new maize (Zea mays) reference genome (v4) sequenced by PacBio long-read techniques (13).”
Improving Flooding Tolerance of Crop Plants (2018, background): “Zea mays yes yes (Table 2) [45,46] available Triticum aestivum yes yes [47] not available Hordeum vulgare yes yes (Table 3) [48] not available Avena sativa unknown no not available not available Secale cereale unknown no [49] not available Lolium perenne yes yes [50] not available”
LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons1[OPEN] (2017, background): “…of LTR_retriever can be reproduced with other genomes, we chose four other genomes with variable amounts of LTR elements, including two maize genomes (cv B73 and cv Mo17; Xin et al., 2013, Jiao et al., 2017), Arabidopsis (Arabidopsis Genome Initiative, 2000), and sacred lotus (Ming et al., 2013).”
RepeatModeler2 for automated genomic discovery of transposable element families (2020, background): “The genome of rice, O. sativa , is known to contain almost equal proportions and numbers of DNA-TIR and LTR elements (38), and this profile is recovered by our RepeatModeler2 library (Fig.”
Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline (2019, methodology): “To demonstrate its utility in other species, we applied the pipeline to maize [4, 66] and Drosophila [20], both of which have high-quality”