The NanDeSyn database for <i>Nannochloropsis</i> systems and synthetic biology

Gong, Yanhai; Kang, Nak Heon; Kim, Young U; Wang, Zengbin; Wei, Li; Yi, Xin; Shen, Chen; Wang, Qintao; You, Wuxin; Lim, Jong‐Min; Jeong, S H; Park, Youn‐Il; Oh, Hee‐Mock; Pan, Kehou; Poliner, Eric; Yang, Guanpin; Li‐Beisson, Yonghua; Li, Yantao; Hu, Qiang; Poetsch, Ansgar; Farré, Eva M.; Chang, Yong Keun; Jeong, Won-Joong; Jeong, Byeong‐ryool; Xu, Jian

doi:10.1111/tpj.15025

Cited by 43 publications

(48 citation statements)

References 113 publications

(144 reference statements)

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“…To determine the ‘non‐essential’ regions under a particular condition, we analyzed transcriptomic datasets of N. oceanica IMET1 that we previously published under nitrogen repletion (N+) and nitrogen depletion (N−) conditions (Jia et al ., 2015; Li et al ., 2014; also available in the NanDeSyn database at http://nandesyn.single-cell.cn/; Gong et al ., 2020). We identified 10 such regions, named LER (for low or no expression regions), based on the threshold of mapped mRNA‐Seq reads < 10 under N+ and N− conditions (average genome‐wide sequence coverage of 53.3), i.e.…”

Section: Resultsmentioning

confidence: 99%

“…Among these, LER1 is the largest, and is located at the distal end of the 5′‐end of Chr 30 (Figure 1a). LER1 harbors 22 annotated genes (NO30G00010 – NO30G00220; details in NanDeSyn; Gong et al ., 2020) spanning over 98 kb of Chr 30 (Table S1). Among these, four genes encode unknown functions, six encode membrane proteins, two encode PAS proteins, etc.…”

Section: Resultsmentioning

confidence: 99%

“…To select the LERs, we scanned the whole genome and N+/N− transcriptome of N. oceanica IMET1 from the NanDeSyn database (http://nandesyn.single-cell.cn; Gong et al ., 2020). Low expression genomic regions (local coverage < 10) were detected using transcriptome dataset SRP017310 (Li et al ., 2014).…”

Section: Methodsmentioning

confidence: 99%

“…also feature extensive omics resources for functional assessment of chromosomal regions genome‐wide. For example, in Nannochloropsis oceanica IMET1, which is an industrial strain for both TAG and EPA, rich resources are available for genomic (Gong et al ., 2020; Wang et al ., 2014a; Wei et al ., 2013), transcriptomic (Hu et al ., 2014; Jia et al ., 2015; Li et al ., 2014; Wei et al ., 2019a; You et al ., 2020), proteomic (Chen et al ., 2019; Dong et al ., 2013; Wei et al ., 2019a; You et al ., 2020), lipidomic (Jia et al ., 2015; Li et al ., 2014) as well as physiological data (Han et al ., 2017; He et al ., 2017; Lu et al ., 2014; Wang et al ., 2014b; Xiao et al ., 2015). Taking advantage of these resources, we employed this strain to establish a method to precisely and serially delete large genome fragments of ~100 kb from its 30.01 Mb nuclear genome.…”

Section: Introductionmentioning

confidence: 99%

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Genome engineering of Nannochloropsis with hundred‐kilobase fragment deletions by Cas9 cleavages

Wang

Gong

et al. 2021

The Plant Journal

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Industrial microalgae are promising photosynthetic cell factories, yet tools for large-scale targeted genome engineering are limited. Here for the model industrial oleaginous microalga Nannochloropsis oceanica, we established a method to precisely and serially delete large genome fragments of~100 kb from its 30.01 Mb nuclear genome. We started by identifying the 'non-essential' chromosomal regions (i.e. low expression region or LER) based on minimal gene expression under N-replete and N-depleted conditions. The largest such LER (LER1) is~98 kb in size, located near the telomere of the 502.09-kb-long Chromosome 30 (Chr 30). We deleted 81 kb and further distal and proximal deletions of up to 110 kb (21.9% of Chr 30) in LER1 by dual targeting the boundaries with the episome-based CRISPR/Cas9 system. The telomere-deletion mutants showed normal telomeres consisting of CCCTAA repeats, revealing telomere regeneration capability after losing the distal part of Chr 30. Interestingly, the deletions caused no significant alteration in growth, lipid production or photosynthesis (transcript-abundance change for < 3% genes under N depletion). We also achieved double-deletion of both LER1 and LER2 (from Chr 9) that total~214 kb at maximum, which can result in slightly higher growth rate and biomass productivity than the wild-type. Therefore, loss of the large, yet 'non-essential' regions does not necessarily sacrifice important traits. Such serial targeted deletions of large genomic regions had not been previously reported in microalgae, and will accelerate crafting minimal genomes as chassis for photosynthetic production.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genome engineering of Nannochloropsis with hundred‐kilobase fragment deletions by Cas9 cleavages

Wang

Gong

et al. 2021

The Plant Journal

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“…Because of this, as well as their fast growth rate, much research effort has been devoted to developing Nannochloropsis as an industrial biofuel alga. The genomes of several Nannochloropsis species and strains have been sequenced (Pan et al 2011;Radakovits et al 2012;Vieler et al 2012;Wang et al 2014;Corteggiani Carpinelli et al 2014;Schwartz et al 2018;Ohan et al 2019;Guo et al 2019;Brown et al 2019;Gong et al 2020), although only a few assemblies have reached high contig continuity and completeness (Fig. 1A).…”

Section: Introductionmentioning

confidence: 99%

Monodopsis and Vischeria genomes elucidate the biology of eustigmatophyte algae

Yang

Wenzel

Hauser

et al. 2021

Preprint

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Members of eustigmatophyte algae, especially Nannochloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. While extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis (60 Mb) and Vischeria (106 Mb), which are the sister groups to Nannochloropsis. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis, LINE repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and non-mevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis that has only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.

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Epigenetic Regulation in Response to CO2 Fluctuation in Marine Microalga Nannochloropsis oceanica

Liu,

Wei

2023

Microb Ecol

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The NanDeSyn database for Nannochloropsis systems and synthetic biology

Cited by 43 publications

References 113 publications

Genome engineering of Nannochloropsis with hundred‐kilobase fragment deletions by Cas9 cleavages

Genome engineering of Nannochloropsis with hundred‐kilobase fragment deletions by Cas9 cleavages

Monodopsis and Vischeria genomes elucidate the biology of eustigmatophyte algae

Epigenetic Regulation in Response to CO2 Fluctuation in Marine Microalga Nannochloropsis oceanica

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