The genome and transcriptome of Trichormus sp. NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau

Qiao, Qin; Huang, Ying; Qi, Ji-I.; Qu, Mingzhi; Jiang, Chen; Lin, Peng-Cheng; Li, Renhui; Song, Lirong; Yonezawa, Takahiro; Hasegawa, Masami; Crabbe, M. James C.; Chen, Fan; Zhang, Ticao; Zhong, Yang

doi:10.1038/srep29404

Cited by 30 publications

(35 citation statements)

References 59 publications

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Section: Introductionmentioning

confidence: 99%

“…The Tibetan Plateau is characterized by an extreme environment with rapid fluctuations in temperature, low oxygen concentration, and strong ultraviolet radiation (Qiao et al, ). Species endemic to the region have undergone significant evolutionary genetic changes to take on ecologically adaptive characteristics (Qiao et al, ). In the last decade, most studies on adaptive evolution at the genome level from this region have focused on terrestrial animals, such as the yak (Qiu et al, ), the Tibetan antelope (Ge et al, ), ground tits (Qu, Zhao, & Han, ), the Tibetan boar (Li, Fan, et al, ) and the Tibetan chicken (Wang, Cao, & Zhang, ).…”

Section: Introductionmentioning

confidence: 99%

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Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Yang

et al. 2019

Molecular Ecology Resources

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Triplophysa is an endemic fish genus of the Tibetan Plateau in China. Triplophysa tibetana, which lives at a recorded altitude of ~4,000 m and plays an important role in the highland aquatic ecosystem, serves as an excellent model for investigating high‐altitude environmental adaptation. However, evolutionary and conservation studies of T. tibetana have been limited by scarce genomic resources for the genus Triplophysa. In the present study, we applied PacBio sequencing and the Hi‐C technique to assemble the T. tibetana genome. A 652‐Mb genome with 1,325 contigs with an N50 length of 3.1 Mb was obtained. The 1,137 contigs were further assembled into 25 chromosomes, representing 98.7% and 80.47% of all contigs at the base and sequence number level, respectively. Approximately 260 Mb of sequence, accounting for ~39.8% of the genome, was identified as repetitive elements. DNA transposons (16.3%), long interspersed nuclear elements (12.4%) and long terminal repeats (11.0%) were the most repetitive types. In total, 24,372 protein‐coding genes were predicted in the genome, and ~95% of the genes were functionally annotated via a search in public databases. Using whole genome sequence information, we found that T. tibetana diverged from its common ancestor with Danio rerio ~121.4 million years ago. The high‐quality genome assembled in this work not only provides a valuable genomic resource for future population and conservation studies of T. tibetana, but it also lays a solid foundation for further investigation into the mechanisms of environmental adaptation of endemic fishes in the Tibetan Plateau.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Yang

et al. 2019

Molecular Ecology Resources

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“…Another highly similar cluster (although lacking two tailoring genes) was mined from the genome draft of Trichormus sp. NMC-1, which has recently appeared in the NCBI database [34]. The production of NoA in this strain was not studied.…”

Section: Discussionmentioning

confidence: 99%

The cyanobacterial metabolite nocuolin a is a natural oxadiazine that triggers apoptosis in human cancer cells

Voráčová¹,

Hájek²,

Mareš³

et al. 2017

PLoS ONE

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Oxadiazines are heterocyclic compounds containing N-N-O or N-N-C-O system within a six membered ring. These structures have been up to now exclusively prepared via organic synthesis. Here, we report the discovery of a natural oxadiazine nocuolin A (NoA) that has a unique structure based on 1,2,3-oxadiazine. We have identified this compound in three independent cyanobacterial strains of genera Nostoc, Nodularia, and Anabaena and recognized the putative gene clusters for NoA biosynthesis in their genomes. Its structure was characterized using a combination of NMR, HRMS and FTIR methods. The compound was first isolated as a positive hit during screening for apoptotic inducers in crude cyanobacterial extracts. We demonstrated that NoA-induced cell death has attributes of caspase-dependent apoptosis. Moreover, NoA exhibits a potent anti-proliferative activity (0.7–4.5 μM) against several human cancer lines, with p53-mutated cell lines being even more sensitive. Since cancers bearing p53 mutations are resistant to several conventional anti-cancer drugs, NoA may offer a new scaffold for the development of drugs that have the potential to target tumor cells independent of their p53 status. As no analogous type of compound was previously described in the nature, NoA establishes a novel class of bioactive secondary metabolites.

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“…Signal transduction-related genes were also found to have undergone both significant positive selection and expansion events on the adaptive evolution of Crucihimalaya himalaica [34] and cyanobacterium Trichormus sp. NMC-1 [46] on the QTP. In the present study, unigenes related to the signal transduction pathways were significantly upregulated in the tissues of flowering arrow bamboo plants.…”

Section: Carbohydrate Metabolism and Signal Transport May Be Major Famentioning

confidence: 99%

De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae)

Zhang

Yang

et al. 2020

Preprint

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Background: Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2,000 ~ 3,800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment. Results: Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-flowering and flowering tissues revealed that expressions of FmFT and FmHd3a, two putative F. macclureana orthologs, were differently regulated in NF- vs F- leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9,296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions: F. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.

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The genome and transcriptome of Trichormus sp. NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau

Cited by 30 publications

References 59 publications

Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

Chromosome‐level genome assembly of Triplophysa tibetana, a fish adapted to the harsh high‐altitude environment of the Tibetan Plateau

The cyanobacterial metabolite nocuolin a is a natural oxadiazine that triggers apoptosis in human cancer cells

De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae)

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