Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

Read, Andrew C.; Moscou, Matthew J.; Zimin, Aleksey V.; Pertea, Geo; Meyer, Rachel S.; Purugganan, Michael D.; Leach, Jan E.; Triplett, Lindsay R.; Salzberg, Steven L.; Bogdanove, Adam J.

doi:10.1101/675678

Cited by 12 publications

(25 citation statements)

References 86 publications

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“…NLR-gene coordinates of all NLR gene sequences, and the relationships of the 712 based on an NB-ARC domain maximum likelihood tree are included in Supplementary Table S5, S6, and S7 as well as Supplementary Figure S1. This number is roughly twice the number found in (Zhou et al, 2004;Read et al, 2020) and is consistent with other conifers (Van Ghelder et al, 2019).…”

Section: Orthology Assignment and Gene Family Evolutionsupporting

confidence: 91%

The giant sequoia genome and proliferation of disease resistance genes

Zimin

Puiu

Workman

et al. 2020

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The giant sequoia ( Sequoiadendron giganteum ) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. As they grow primarily in isolated groves within a narrow range, conservation of existing trees has been a national goal for over 150 years.Genomic data are limited in giant sequoia, and the assembly and annotation of the first giant sequoia genome has been an important goal to allow marker development for restoration and management. Using Illumina and Oxford Nanopore sequencing combined with Dovetail chromosome conformation capture libraries, 8.125 Gbp of sequence was assembled into eleven chromosome-scale scaffolds. This giant sequoia assembly represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management. Beyond conservation and management applications, the giant sequoia assembly is a resource for answering questions about the life history of this enigmatic and robust species. Here we provide an example by taking an inventory of the large and complex family of NLR type disease resistance genes.assembly and annotation presented here is an unprecedented resource in conifer genomics, both for the quality of the assembly and because it represents an understudied branch of the gymnosperm tree of life. MATERIALS AND METHODS Sequencing and assembly Megagametophyte DNA extraction and sequencingCones were collected from a 1,360-year-old giant sequoia (SEGI21, Sillett et al., 2015) in Sequoia/Kings Canyon National Park in 2012. As in previous conifer genome sequencing projects (e.g. Zimin et al., 2014), the megagametophyte from a single fertilized seed was dissected out and its haploid DNA extracted with a Qiagen DNeasy Plant Kit (Hilden, Germany), followed by library preparation with an Illumina TruSeq Nano kit using the low throughput protocol. This megagametophyte library was then sequenced on 10 lanes of an Illumina HiSeq 4000 with 150 bp paired-end reads at the UC Davis Genome Center DNA Technologies Core facility. Foliage DNA extraction and Nanopore sequencingIn 2017 foliage was collected from the upper canopy of the same giant sequoia tree (SEGI21).From this foliage, high molecular weight DNA was extracted following the protocol described here (dx.doi.org/10.17504/protocols.io.4vbgw2n) . Briefly, purified genomic DNA was isolated through a nuclei extraction and lysis protocol. First, mature leaf tissue was homogenized in liquid nitrogen until well-ground, then added to a gentle lysis buffer (after Zhang et al.,

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Section: Orthology Assignment and Gene Family Evolutionsupporting

confidence: 91%

The giant sequoia genome and proliferation of disease resistance genes

Zimin

Puiu

Workman

et al. 2020

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“…Recently, by whole genome sequencing, we determined that the Xo1 locus in Carolina Gold comprises 14 NLR genes. We identified one of these, Xo1 11 , as a strong candidate based on its structural similarity to the previously cloned and only known NLR resistance gene for bacterial blight, Xa1 (Read et al, 2020). Xa1, originally identified in the rice variety Kogyoku, maps to the same location (Yoshimura et al, 1998) and behaves similarly to Xo1: it mediates recognition of TALEs with distinct DNA-binding specificities (and thus confers resistance also to bacterial leaf streak), and its activity is suppressed by truncTALEs (Ji et al, 2016).…”

Section: Readmentioning

confidence: 99%

“…Xa1, originally identified in the rice variety Kogyoku, maps to the same location (Yoshimura et al, 1998) and behaves similarly to Xo1: it mediates recognition of TALEs with distinct DNA-binding specificities (and thus confers resistance also to bacterial leaf streak), and its activity is suppressed by truncTALEs (Ji et al, 2016). Xo1 11 and Xa1 are members of a small subfamily of NLR genes that encode an unusual N-terminal domain comprising a zinc finger BED (zfBED) motif (Read et al, 2020).…”

Section: Readmentioning

confidence: 99%

“…To gain insight into the nature of Xo1-mediated resistance, we compared the global profile of differentially expressed genes during Xo1-mediated defense to those of two other NLR genes in rice and to the profile associated with an executor gene. We used our previously reported RNAseq data from Carolina Gold plants inoculated with CFBP7331(EV) or mock inoculum (Read et al, 2020), data for the NLR gene Pia for resistance to the rice blast pathogen Magnaporthe oryzae (Tanabe et al, 2014), data from rice resistant to bacterial leaf streak due to transgenic expression of the maize NLR gene Rxo1 (Xie et al, 2007;Zhou et al, 2010), and data for the transcriptomic response associated with induction of the executor resistance gene Xa23 by an Xoo strain with the corresponding TALE (Tariq et al, 2018). Though limited, these datasets include the only currently available expression data for NLR and executor gene-mediated resistance to Xanthomonas in rice.…”

Section: Of 20mentioning

confidence: 99%

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Cloning of the rice Xo1 resistance gene and interaction of the Xo1 protein with the defense-suppressing Xanthomonas effector Tal2h

Read

Hutin

Moscou

et al. 2020

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The Xo1 locus in the heirloom rice variety Carolina Gold Select confers resistance to bacterial leaf streak and bacterial blight, caused by Xanthomonas oryzae pvs. oryzicola and oryzae, respectively. Resistance is triggered by pathogen-delivered transcription activator-like effectors (TALEs) independent of their ability to activate transcription, and is suppressed by variants called truncTALEs common among Asian strains. By transformation of the susceptible variety Nipponbare, we show that one of 14 nucleotide-binding, leucine-rich repeat (NLR) protein genes at the locus, with a zfBED domain, is the Xo1 gene. Analyses of published transcriptomes revealed that the Xo1-mediated response is similar to those of NLR resistance genes Pia and Rxo1 and distinct from that associated with induction of the executor resistance gene Xa23, and that a truncTALE dampens or abolishes activation of defense-associated genes by Xo1. In Nicotiana benthamiana leaves, fluorescently-tagged Xo1 protein, like TALEs and truncTALEs, localized to the nucleus. And, endogenous Xo1 specifically co-immunoprecipitated from rice leaves with a pathogen-delivered, epitope-tagged truncTALE. These observations suggest that suppression of Xo1-function by truncTALEs occurs through direct or indirect physical interaction. They further suggest that effector co-immunoprecipitation may be effective for identifying or characterizing other resistance genes.

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“…Plant disease resistance genes (R-genes) play a key role in recognizing proteins expressed by specific avirulence (Avr) genes of pathogens 4 . The proteins encoded by the resistance genes share common domains such as coiled-coil (CC), nucleotide binding region (NB), Tollinterleukin region (TIR), leucine rich region (LRR) and kinase domain (K).Hundreds of NBS-LRR, RLK and RLP genes have been reported in plants [5][6][7][8] , though such information is lacking in blackgram. This could be attributed to the lack of genomic resources coupled with limited understanding of the molecular basis of gene expression and phenotypic variation.…”

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confidence: 99%

Draft genome sequence of the pulse crop blackgram [Vigna mungo (L.) Hepper] reveals potential R-genes

Souframanien¹,

Raizada²,

Dhanasekar³

et al. 2020

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Blackgram [Vigna mungo (L.) Hepper] (2n = 2x = 22), an important Asiatic legume crop, is a major source of dietary protein for the predominantly vegetarian population. Here we construct a draft genome sequence of blackgram, for the first time, by employing hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. The final de novo whole genome of blackgram is ~ 475 Mb (82 % of the genome) and has maximum scaffold length of 6.3 Mb with scaffold N50 of1.42 Mb. Genome analysis identified 18655 genes with mean coding sequence length of 970bp. Around 96.7 % of predicted genes were annotated. Nearly half of the assembled sequence is composed of repetitive elements with retrotransposons as major (47.3% of genome) transposable elements, whereas, DNA transposons made up only 2.29% of the genome. A total of 166014 SSRs, including 65180 compound SSRs, were identified and primer pairs for 34816 SSRs were designed. Out of the 18665 proteins, 678 proteins showed presence of R-gene related domains. KIN class was found in majority of the proteins (372) followed by RLK (79) and N (79). The genome sequence of blackgram will facilitate identification of agronomically important genes and accelerate the genetic improvement of blackgram.

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Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

Cited by 12 publications

References 86 publications

The giant sequoia genome and proliferation of disease resistance genes

The giant sequoia genome and proliferation of disease resistance genes

Cloning of the rice Xo1 resistance gene and interaction of the Xo1 protein with the defense-suppressing Xanthomonas effector Tal2h

Draft genome sequence of the pulse crop blackgram [Vigna mungo (L.) Hepper] reveals potential R-genes

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