The complete chloroplast genome of Bretschneidera sinensis (Bretschneideraceae)

Huang, Songyi; Zhou, Qiujie; Shen, Haicen; Chen, Zheng; Zhu, Qiaoming; Wu, Wei

doi:10.1007/s12686-017-0921-z

Cited by 1 publication

(2 citation statements)

References 13 publications

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“…sinensis was supposed to belong (Introduction), but more species in the former were selected considering the phylogeny shown in Huang et al . 17 For the Iso-seq reads, we first processed them in IsoSeq v3 ( https://github.com/ben-lerch/IsoSeq-3.0 , last accessed 12 October, 2019) to obtain the full-length transcripts. After LoReAn prediction, we used the results as input for the funannotate pipeline v1.8.2 ( https://github.com/nextgenusfs/funannotate , last accessed 19 October 2020) to acquire final integrated and consensus gene sets using the command of ‘funannotate predict’.…”

Section: Methodsmentioning

confidence: 99%

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The genome of the Paleogene relic treeBretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs

et al. 2022

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Among relic species, genomic information may provide the key to inferring their long-term survival. Therefore, in this study, we investigated the genome of the Paleogene relic tree species, Bretschneidera sinensis, which is a rare endemic species within southeastern Asia. Specifically, we assembled a high-quality genome for B. sinensis using PacBio high-fidelity and high-throughput chromosome conformation capture reads and annotated it with long and short RNA sequencing reads. Using the genome, we then detected a trade-off between active and passive disease defences among the gene families. Gene families involved in salicylic acid and MAPK signalling pathways expanded as active defence mechanisms against disease, but families involved in terpene synthase activity as passive defences contracted. When inferring the long evolutionary history of B. sinensis, we detected population declines corresponding to historical climate change around the Eocene–Oligocene transition and to climatic fluctuations in the Quaternary. Additionally, based on this genome, we identified 388 single nucleotide polymorphisms (SNPs) that were likely under selection, and showed diverse functions in growth and stress responses. Among them, we further found 41 climate-associated SNPs. The genome of B. sinensis and the SNP dataset will be important resources for understanding extinction/diversification processes using comparative genomics in different lineages.

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Section: Methodsmentioning

confidence: 99%

“…16 The phylogeny using the complete chloroplast genome sequence of B. sinensis and other species of malvids further indicated that B. sinensis is genetically closest to Carica papaya . 17 …”

Section: Introductionmentioning

confidence: 99%