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Genome survey and complete chloroplast genome structure of a bamboo species (Bambusa grandis) provide a useful basis in genomic research

文献类型： 外文期刊

作者： Liu, Yu 1 ; Xu, Huanwen 2 ; Liu, Xing 1 ; Li, Xiaowen 1 ; Chen, Guanju 1 ; Wei, Xin 1 ; Wang, Yueying 1 ; Jin, Chuan 1 ; Wang, Jinwang 1 ; Xia, Haitao 1 ;

作者机构： 1.Zhejiang Acad Agr Sci, Zhejiang Inst Subtrop Crops, Wenzhou Key Lab Resource Plant Innovat & Utilizat, Wenzhou 325005, Zhejiang, Peoples R China

2.Wenzhou Acad Agr Sci, Wenzhou Vocat Coll Sci & Technol, Southern Zhejiang Key Lab Crop Breeding, Wenzhou 325006, Zhejiang, Peoples R China

关键词： Bambusa; Bambusa grandis; chloroplast genome; phylogeny

期刊名称：SCIENCEASIA （ 影响因子：0.6； 五年影响因子：0.7 ）

ISSN： 1513-1874

年卷期： 2024 年 50 卷 4 期

页码：

收录情况： SCI

摘要： Bambusa grandis is a bamboo species with high ecological and economic value. In this study, we sequenced the B. grandis chloroplast (cp) genome and reconstructed the phylogeny of the genus Bambusa. The B. grandis cp genome was 139,443 bp in length, which included 136 unique genes and had a GC content of 38.91%. The usage rates of three codons (ATG, TTA, and AGA) were particularly high, indicating codon-biased usage. Multi-genome comparative analyses indicated that the cp genome was highly conserved across species; the contraction and expansion of the IR region appeared to be the primary driver of IR/SC boundary variation across Bambusa species. Four regions with high-level polymorphism were discovered with the potential to be used as molecular markers. Phylogenetic analysis indicated that B. grandis is most closely related to B. basihirsuta, B. cornigera, and B. intermedia. In addition, we also carried out genome survey sequencing of B. grandis and identified genome-wide microsatellite motifs. The results revealed an estimated genome size for B. grandis of 1.18 Gb with 5.63% heterozygosity and a repeat ratio of 55.80%. A total of 326,184 SSRs were identified from the genome survey assembly, most of which were mononucleotide motifs with a frequency of 43.84%. The findings will be beneficial to future research on the systematics, genetic diversity, and evolutionary history of the genus Bambusa as well as the conservation and sustainable utilization of B. grandis genetic resources.

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