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Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals.

ABSTRACT: Non-random gene organization in eukaryotes plays a significant role in genome evolution. Here, we investigate the origin of a biosynthetic gene cluster for production of defence compounds in oat-the avenacin cluster. We elucidate the structure and organisation of this 12-gene cluster, characterise the last two missing pathway steps, and reconstitute the entire pathway in tobacco by transient expression. We show that the cluster has formed de novo since the divergence of oats in a subtelomeric region of the genome that lacks homology with other grasses, and that gene order is approximately colinear with the biosynthetic pathway. We speculate that the positioning of the late pathway genes furthest away from the telomere may mitigate against a 'self-poisoning' scenario in which toxic intermediates accumulate as a result of telomeric gene deletions. Our investigations reveal a striking example of adaptive evolution underpinned by remarkable genome plasticity.

SUBMITTER: Li Y

PROVIDER: S-EPMC8105312 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals.

Li Yan Y Leveau Aymeric A Zhao Qiang Q Feng Qi Q Lu Hengyun H Miao Jiashun J Xue Zheyong Z Martin Azahara C AC Wegel Eva E Wang Jing J Orme Anastasia A Rey Maria-Dolores MD Karafiátová Miroslava M Vrána Jan J Steuernagel Burkhard B Joynson Ryan R Owen Charlotte C Reed James J Louveau Thomas T Stephenson Michael J MJ Zhang Lei L Huang Xuehui X Huang Tao T Fan Danling D Zhou Congcong C Tian Qilin Q Li Wenjun W Lu Yiqi Y Chen Jiaying J Zhao Yan Y Lu Ying Y Zhu Chuanrang C Liu Zhenhua Z Polturak Guy G Casson Rebecca R Hill Lionel L Moore Graham G Melton Rachel R Hall Neil N Wulff Brande B H BBH Doležel Jaroslav J Langdon Tim T Han Bin B Osbourn Anne A

Nature communications 20210507 1

Non-random gene organization in eukaryotes plays a significant role in genome evolution. Here, we investigate the origin of a biosynthetic gene cluster for production of defence compounds in oat-the avenacin cluster. We elucidate the structure and organisation of this 12-gene cluster, characterise the last two missing pathway steps, and reconstitute the entire pathway in tobacco by transient expression. We show that the cluster has formed de novo since the divergence of oats in a subtelomeric re ...[more]

PMID: 33963185

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Project description:BackgroundPlanning and evaluating malaria control strategies relies on accurate definition of parasite prevalence in the population. A large proportion of asymptomatic parasite infections can only be identified by surveillance with molecular methods, yet these infections also contribute to onward transmission to mosquitoes. The sensitivity of molecular detection by PCR is limited by the abundance of the target sequence in a DNA sample; thus, detection becomes imperfect at low densities. We aimed to increase PCR diagnostic sensitivity by targeting multi-copy genomic sequences for reliable detection of low-density infections, and investigated the impact of these PCR assays on community prevalence data.Methods and findingsTwo quantitative PCR (qPCR) assays were developed for ultra-sensitive detection of Plasmodium falciparum, targeting the high-copy telomere-associated repetitive element 2 (TARE-2, ∼250 copies/genome) and the var gene acidic terminal sequence (varATS, 59 copies/genome). Our assays reached a limit of detection of 0.03 to 0.15 parasites/μl blood and were 10× more sensitive than standard 18S rRNA qPCR. In a population cross-sectional study in Tanzania, 295/498 samples tested positive using ultra-sensitive assays. Light microscopy missed 169 infections (57%). 18S rRNA qPCR failed to identify 48 infections (16%), of which 40% carried gametocytes detected by pfs25 quantitative reverse-transcription PCR. To judge the suitability of the TARE-2 and varATS assays for high-throughput screens, their performance was tested on sample pools. Both ultra-sensitive assays correctly detected all pools containing one low-density P. falciparum-positive sample, which went undetected by 18S rRNA qPCR, among nine negatives. TARE-2 and varATS qPCRs improve estimates of prevalence rates, yet other infections might still remain undetected when absent in the limited blood volume sampled.ConclusionsMeasured malaria prevalence in communities is largely determined by the sensitivity of the diagnostic tool used. Even when applying standard molecular diagnostics, prevalence in our study population was underestimated by 8% compared to the new assays. Our findings highlight the need for highly sensitive tools such as TARE-2 and varATS qPCR in community surveillance and for monitoring interventions to better describe malaria epidemiology and inform malaria elimination efforts.

Dataset Information

Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals.

Publications

Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals.

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