Volume 49 Number 3

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

Yu Liu^a, Huanwen Xu^b, Xing Liu^a, Xiaowen Li^a, Guanju Chen^a, Xin Wei^a, Yueying Wang^a, Chuan Jin^a, Jinwang Wang^a,*, Haitao Xia^a,*

 
ABSTRACT:     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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* Corresponding author, E-mail: kingwwang@163.com, xiaht@zaas.ac.cn

Received 25 Aug 2023, Accepted 8 Aug 2024