Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos

Guo, Zhenhua; Ma, Ping; Yang, Guoqian; Hu, Jin‐Yong; Liu, Yunlong; Xia, Enhua; Zhong, Mingyu; Zhao, Lei; Sun, Guiling; Xu, Yuxing; Zhao, Yanjie; Zhang, Yichi; Zhang, Yu‐Xiao; Zhang, Xuemei; Zhou, Mengyuan; Guo, Ying; Guo, Cen; Liu, Jing‐Xia; Ye, Xia‐Ying; Chen, Yunmei; Yang, Yang; Han, Bin; Lin, Chun-Shin; Lu, Ying; D, Li

doi:10.1016/j.molp.2019.05.009

Cited by 123 publications

(140 citation statements)

References 78 publications

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“…We used the plastome-based phylogenetic trees of Gallaher et al (2019), dropping the tips of taxa not represented by phytolith data. There are two major alternate phylogenetic hypotheses for the relationships among Bambusoideae tribes (Triplett et al, 2014;Guo et al, 2019). The first, supported by plastome phylogenies, reconstructs the woody bamboos (Bambuseae + Arundinarieae) as paraphyletic with the herbaceous tribe Olyreae as sister to Bambuseae.…”

Section: Researchmentioning

confidence: 99%

3D shape analysis of grass silica short cell phytoliths: a new method for fossil classification and analysis of shape evolution

et al. 2020

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Summary Fossil grass silica short cell phytoliths (GSSCP) have been used to reconstruct the biogeography of Poaceae, untangle crop domestication history and detect past vegetation shifts. These inferences depend on accurately identifying the clade to which the fossils belong. Patterns of GSSCP shape and size variation across the family have not been established and current classification methods are subjective or based on a 2D view that ignores important 3D shape variation. Focusing on Poaceae subfamilies Anomochlooideae, Pharoideae, Pueliodieae, Bambusoideae and Oryzoideae, we observed in situ GSSCP to establish their orientation and imaged isolated GSSCP using confocal microscopy to produce 3D models. 3D geometric morphometrics was used to analyze GSSCP shape and size. Classification models were applied to GSSCP from Eocene sediments from Nebraska, USA, and Anatolia, Turkey. There were significant shape differences between nearly all recognized GSSCP morphotypes and between clades with shared morphotypes. Most of the Eocene GSSCP were classified as woody bamboos with some distinctive Nebraska GSSCP classified as herbaceous bamboos. 3D morphometrics hold great promise for GSSCP classification. It accounts for the complete GSSCP shape, automates size measurements and accommodates the complete range of morphotypes within a single analytical framework.

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Section: Researchmentioning

confidence: 99%

3D shape analysis of grass silica short cell phytoliths: a new method for fossil classification and analysis of shape evolution

et al. 2020

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“…Around 2.5 billion people are directly producing and consuming bamboo, and its international trade reached 68.8 billion US dollars in 2018 (Data from International Bamboo and Rattan Organization). One major bamboo species in Asia is Ma bamboo ( Dendrocalamus latiflorus Munro ), which is a hexaploid species with three subgenomes (2 n = 72, AABBCC; Guo et al , ). Despite its agronomic importance, it is nearly impossible to modify bamboo traits by traditional breeding as it takes over 70 years to flower.…”

mentioning

confidence: 99%

Robust CRISPR/Cas9 mediated genome editing and its application in manipulating plant height in the first generation of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro)

Chen

Kohnen

et al. 2020

Plant Biotechnology Journal

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“…Peng et al (Peng et al, 2013) reported the first draft genome of tetraploid moso bamboo ( Phyllostachys edulis ). Recently, Guo et al (Guo et al, 2019) have released four draft genomes of bamboo lineages, including O. latifolia, R. guianensis, Guadua angustifolia , and Bonia amplexicaulis . The lack of a high-quality genome sequence for a diploid bamboo has been an impediment to our understanding of bamboo biology and evolution.…”

Section: Introductionmentioning

confidence: 99%

The draft genome sequence of herbaceous diploid bamboo Raddia distichophylla

Shi

et al. 2020

Preprint

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17 Bamboos are important non-timber forest plants widely distributed in the tropical and 18 subtropical regions of Asia, Africa, America, and Pacific islands. They comprise the 19 Bambusoideae in the grass family (Poaceae), including approximately 1,700 described 20 species in 127 genera. In spite of the widespread uses of bamboo for food, construction 21 and bioenergy, the gene repertoire of bamboo still remains largely unexplored. Raddia 22 distichophylla (Schrad. ex Nees) Chase, belonging to the tribe Olyreae (Bambusoideae, 23 Poaceae), is diploid herbaceous bamboo with only slightly lignified stems. In this study, 24 we report a draft genome assembly of the approximately ~589 Mb whole-genome 25 sequence of R. distichophylla with a contig N50 length of 86.36 Kb. Repeated sequences 26 account for ~49.08% of the genome, of which LTR retrotransposons occupy ~35.99% of 27 whole genome. A total of 30,763 protein-coding genes were annotated in the R. 28 distichophylla genome with an average transcript size of 2,887 bp. Access to this 29 herbaceous bamboo genome sequence will provide novel insights into biochemistry, 30 molecular-assisted breeding programs and germplasm conservation for bamboo species 31 world-wide. 32 33 KEYWORDS 34 Bamboos, Raddia distichophylla, whole-genome sequence 35 36 37 65 Clark et al., 2015). Herbaceous bamboos are characterized by usually weakly developed 66 rhizomes and less lignification in the culms. Culm leaves and foliage leaves with the 67

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Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos

Cited by 123 publications

References 78 publications

3D shape analysis of grass silica short cell phytoliths: a new method for fossil classification and analysis of shape evolution

3D shape analysis of grass silica short cell phytoliths: a new method for fossil classification and analysis of shape evolution

Robust CRISPR/Cas9 mediated genome editing and its application in manipulating plant height in the first generation of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro)

The draft genome sequence of herbaceous diploid bamboo Raddia distichophylla

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