Announcing the Genome Atlas of Bamboo and Rattan (GABR) project: promoting research in evolution and in economically and ecologically beneficial plants

Zhao, Hansheng; Zhao, Shancen; Rattan,; Fei, Benhua; Liu, Huan; Yang, Huanming; Dai, Hui; Wang, Dan; Jin, Wei; Tang, Feng; Gao, Qiang; Xun, Hang; Wang, Yuwei; Qi, Lin; Yue, Xianghua; Lin, Shuyan; Gu, Lianfeng; Li, Lubin; Zhu, Tiansheng; Wei, Qiang; Su, Zhen; Wan, Tarmeze Bin Wanoup Ariffin; Ofori, Daniel; Muthike, George M.; Mengesha, Yigardu Mulatu; Silva, Roberto Magno de Castro E; Beraldo, Antônio Ludovico; Gao, Zhimin; Liu, Xin; Jiang, Zehui

doi:10.1093/gigascience/gix046

Cited by 32 publications

(22 citation statements)

References 3 publications

(3 reference statements)

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“…Bamboo (Bambusoideae) is a fast-growing plant with substantial potential for generating income, restoring degraded landscapes, and combating climate change in numerous Asian and African countries. Approximately 2.5 billion people economically depend on bamboo, reaching an annual international trade of more than $2.5 billion US dollars [ 1 ]. Bamboo is a perennial grass in temperate and tropical forests worldwide, with a cellulose and hemicellulose content comparable to that of woody trees [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)

et al. 2018

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BackgroundBamboo is one of the most important nontimber forestry products worldwide. However, a chromosome-level reference genome is lacking, and an evolutionary view of alternative splicing (AS) in bamboo remains unclear despite emerging omics data and improved technologies.ResultsHere, we provide a chromosome-level de novo genome assembly of moso bamboo (Phyllostachys edulis) using additional abundance sequencing data and a Hi-C scaffolding strategy. The significantly improved genome is a scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version. A total of 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,711 unique AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and Pacific Biosciences sequencing platforms. Through comparisons with orthologous genes in related plant species, we observed that the AS genes are concentrated among more conserved genes that tend to accumulate higher transcript levels and share less tissue specificity. Furthermore, gene family expansion, abundant AS, and positive selection were identified in crucial genes involved in the lignin biosynthetic pathway of moso bamboo.ConclusionsThese fundamental studies provide useful information for future in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo.

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Section: Introductionmentioning

confidence: 99%

Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)

et al. 2018

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“…Bamboo is a member of the Gramineae family, is widely distributed worldwide and is a rapid-growing plant species. Bamboo forests can provide young bamboo shoots for food, fibrous raw material, building materials, raw materials for furniture and crafts and so on within a short time [ 42 ]. In addition to its economic benefits, bamboo also has important ecological functions, such as the ability to restore degraded landscapes and combat global climate change [ 42 , 43 ].…”

Section: Introductionmentioning

confidence: 99%

“…Bamboo forests can provide young bamboo shoots for food, fibrous raw material, building materials, raw materials for furniture and crafts and so on within a short time [ 42 ]. In addition to its economic benefits, bamboo also has important ecological functions, such as the ability to restore degraded landscapes and combat global climate change [ 42 , 43 ]. The moso bamboo ( Phyllostachys edulis ) planting area is approximately 3.27 million ha and constitutes most of the bamboo forest region in China [ 43 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots

Wang

Yan

et al. 2021

BMC Genomics

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Background Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant development and environmental adaptation. However, there are few reports about APs in fast-growing moso bamboo. Result In this study, we identified a total of 129 AP proteins (PhAPs) encoded by the moso bamboo genome. Phylogenetic and gene structure analyses showed that these 129 PhAPs could be divided into three categories (categories A, B and C). The PhAP gene family in moso bamboo may have undergone gene expansion, especially the members of categories A and B, although homologs of some members in category C have been lost. The chromosomal location of PhAPs suggested that segmental and tandem duplication events were critical for PhAP gene expansion. Promoter analysis revealed that PhAPs in moso bamboo may be involved in plant development and responses to environmental stress. Furthermore, PhAPs showed tissue-specific expression patterns and may play important roles in rapid growth, including programmed cell death, cell division and elongation, by integrating environmental signals such as light and gibberellin signals. Conclusion Comprehensive analysis of the AP gene family in moso bamboo suggests that PhAPs have experienced gene expansion that is distinct from that in rice and may play an important role in moso bamboo organ development and rapid growth. Our results provide a direction and lay a foundation for further analysis of plant AP genes to clarify their function during rapid growth.

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“…Bamboos, owing to the faster growth, can easily be harvested within 4–5 years, unlike that of most softwoods, which take 15–20 years. Thus, annual international trade of bamboo stands more than $2.5 billion (https://www.inbar.int) (Wang, Sun, Ding, et al, 2019; Zhao et al., 2017). So, we, in this review, attempt to take a comprehensive view of how biotechnology, particularly in areas of molecular genetics, genomics, and quantitative genetics, can play a decisive role in the development of bamboo for industries.…”

Section: Introductionmentioning

confidence: 99%

Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry

Ramakrishnan

Yrjälä

Vinod

et al. 2020

Food and Energy Security

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Announcing the Genome Atlas of Bamboo and Rattan (GABR) project: promoting research in evolution and in economically and ecologically beneficial plants

Cited by 32 publications

References 3 publications

Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)

Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)

Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots

Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry

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