A high-quality, phased genome assembly of broomcorn millet reveals the features of its subgenome evolution and 3D chromatin organization

Wang, Zhiheng; Huang, Shihui; Yang, Zhengyue; Lai, Jinsheng; Gao, Xiang; Shi, Junpeng

doi:10.1016/j.xplc.2023.100557

Cited by 7 publications

(4 citation statements)

References 13 publications

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“…Detailed annotation statistics are found in Table S3. Overall, these results show that the quality of our assembly lags behind that of recent chromosome-scale assemblies produced using combined longread sequencing and chromatin conformation capture technologies (e.g., Hi-C; Wang et al, 2023) in terms of accuracy and contiguity.…”

Section: Genome Assembly and Annotationmentioning

confidence: 84%

A pooled‐sample draft genome assembly provides insights into host plant‐specific transcriptional responses of a Solanaceae‐specializing pest, Tupiocoris notatus (Hemiptera: Miridae)

Goldberg,

Allan,

Copetti

et al. 2024

Ecology and Evolution

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The assembly of genomes from pooled samples of genetically heterogenous samples of conspecifics remains challenging. In this study, we show that high‐quality genome assemblies can be produced from samples of multiple wild‐caught individuals. We sequenced DNA extracted from a pooled sample of conspecific herbivorous insects (Hemiptera: Miridae: Tupiocoris notatus) acquired from a greenhouse infestation in Tucson, Arizona (in the range of 30–100 individuals; 0.5 mL tissue by volume) using PacBio highly accurate long reads (HiFi). The initial assembly contained multiple haplotigs (>85% BUSCOs duplicated), but duplicate contigs could be easily purged to reveal a highly complete assembly (95.6% BUSCO, 4.4% duplicated) that is highly contiguous by short‐read assembly standards (N50 = 675 kb; Largest contig = 4.3 Mb). We then used our assembly as the basis for a genome‐guided differential expression study of host plant‐specific transcriptional responses. We found thousands of genes (N = 4982) to be differentially expressed between our new data from individuals feeding on Datura wrightii (Solanaceae) and existing RNA‐seq data from Nicotiana attenuata (Solanaceae)‐fed individuals. We identified many of these genes as previously documented detoxification genes such as glutathione‐S‐transferases, cytochrome P450s, and UDP‐glucosyltransferases. Together our results show that long‐read sequencing of pooled samples can provide a cost‐effective genome assembly option for small insects and can provide insights into the genetic mechanisms underlying interactions between plants and herbivorous pests.

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Section: Genome Assembly and Annotationmentioning

confidence: 84%

A pooled‐sample draft genome assembly provides insights into host plant‐specific transcriptional responses of a Solanaceae‐specializing pest, Tupiocoris notatus (Hemiptera: Miridae)

Goldberg,

Allan,

Copetti

et al. 2024

Ecology and Evolution

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“…comm.) Leersia perrieri Cutgrass 12 12 0.267 [ 175 ] Oryza sativa f. spontanea Weedy rice 12 12 0.37 [ 176 ] Panicum miliaceum Wild proso millet 9 18 0.85 [ 177 ] Poa annua Annual bluegrass 7 14 1.78 [ 178 ] 1.89 [ 129 ] Poa infirma Early meadow-grass 7 7 1.17 [ 179 ] 1.13 [ 179 ] Poa supina Supine bluegrass 7 7 0.66 [ 179 ] 0.64 [ 179 ] Poa trivialis Roughstalk bluegrass 7 7 1.35 [ 180 ] Pueraria montana var. lobata Kudzu 11 11 0.98 [ 181 ] Setaria viridis Green foxtail 9 9 …”

Section: Development Of Weed Genomics Resources By the Iwgcmentioning

confidence: 99%

Current status of community resources and priorities for weed genomics research

Montgomery,

Morran,

MacGregor

et al. 2024

Genome Biol

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Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.

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“…Broomcorn millet has an allotetraploid genome consisting of 36 (2n = 4x = 36) chromosomes 6 . Although four chromosome-level of broomcorn millet, Jinshu7 7 , LM_v1 8 , LM_v2 9 , and Pm_0390 8 , have been made available, there are still missing segments within the genome due to the presence of highly repetitive sequences clustered across the genome, particularly in the telomere and centromere regions. In recent years, T2T and gap-free genomes have been successfully obtained in various important crops, including rice 10 , barley 11 , and maize 12 .…”

Section: Background and Summarymentioning

confidence: 99%

A complete reference genome of broomcorn millet

Wang,

Chen

et al. 2024

Sci Data

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Broomcorn millet (Panicum miliaceum L.), known for its traits of drought resistance, adaptability to poor soil, short growth period, and high photosynthetic efficiency as a C4 plant, represents one of the earliest domesticated crops globally. This study reports the telomere-to-telomere (T2T) gap-free reference genome for broomcorn millet (AJ8) using PacBio high-fidelity (HiFi) long reads, Oxford Nanopore long-read technologies and high-throughput chromosome conformation capture (Hi-C) sequencing data. The size of AJ8 genome was approximately 834.7 Mb, anchored onto 18 pseudo-chromosomes. Notably, 18 centromeres and 36 telomeres were obtained. The assembled genome showed high quality in terms of completeness (BUSCO score: 99.6%, QV: 61.7, LAI value: 20.4). In addition, 63,678 protein-coding genes and 433.8 Mb (~52.0%) repetitive sequences were identified. The complete reference genome for broomcorn millet provides a valuable resource for genetic studies and breeding of this important cereal crop.

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A high-quality, phased genome assembly of broomcorn millet reveals the features of its subgenome evolution and 3D chromatin organization

Cited by 7 publications

References 13 publications

A pooled‐sample draft genome assembly provides insights into host plant‐specific transcriptional responses of a Solanaceae‐specializing pest, Tupiocoris notatus (Hemiptera: Miridae)

A pooled‐sample draft genome assembly provides insights into host plant‐specific transcriptional responses of a Solanaceae‐specializing pest, Tupiocoris notatus (Hemiptera: Miridae)

Current status of community resources and priorities for weed genomics research

A complete reference genome of broomcorn millet

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