A practical guide to amplicon and metagenomic analysis of microbiome data

YX Liu, Y Qin, T Chen, M Lu, X Qian, X Guo… - Protein & cell, 2021 - academic.oup.com
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the
field of microbiome research, and massive microbiome datasets are now being generated …

NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice

J Zhang, YX Liu, N Zhang, B Hu, T Jin, H Xu… - Nature …, 2019 - nature.com
Nitrogen-use efficiency of indica varieties of rice is superior to that of japonica varieties. We
apply 16S ribosomal RNA gene profiling to characterize root microbiota of 68 indica and 27 …

LNCipedia 5: towards a reference set of human long non-coding RNAs

PJ Volders, J Anckaert, K Verheggen… - Nucleic acids …, 2019 - academic.oup.com
While long non-coding RNA (lncRNA) research in the past has primarily focused on the
discovery of novel genes, today it has shifted towards functional annotation of this large …

CNSA: a data repository for archiving omics data

X Guo, F Chen, F Gao, L Li, K Liu, L You, C Hua… - Database, 2020 - academic.oup.com
With the application and development of high-throughput sequencing technology in life and
health sciences, massive multi-omics data brings the problem of efficient management and …

Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa

X Cai, L Chang, T Zhang, H Chen, L Zhang, R Lin… - Genome biology, 2021 - Springer
Background Despite the prevalence and recurrence of polyploidization in the speciation of
flowering plants, its impacts on crop intraspecific genome diversification are largely …

Population sequencing enhances understanding of tea plant evolution

X Wang, H Feng, Y Chang, C Ma, L Wang… - Nature …, 2020 - nature.com
Tea is an economically important plant characterized by a large genome, high
heterozygosity, and high species diversity. In this study, we assemble a 3.26-Gb high-quality …

Brassica carinata genome characterization clarifies U's triangle model of evolution and polyploidy in Brassica

X Song, Y Wei, D Xiao, K Gong, P Sun, Y Ren… - Plant …, 2021 - academic.oup.com
Ethiopian mustard (Brassica carinata) in the Brassicaceae family possesses many excellent
agronomic traits. Here, the high-quality genome sequence of B. carinata is reported …

Deciphering the mechanism of fungal pathogen‐induced disease‐suppressive soil

T Wen, Z Ding, LS Thomashow, L Hale, S Yang… - New …, 2023 - Wiley Online Library
One model of a disease‐suppressive soil predicts that the confrontation of plant with a
phytopathogen can lead to the recruitment and accumulation of beneficial microorganisms …

Mapping regulatory variants controlling gene expression in drought response and tolerance in maize

S Liu, C Li, H Wang, S Wang, S Yang, X Liu, J Yan, B Li… - Genome biology, 2020 - Springer
Background Gene expression is a key determinant of cellular response. Natural variation in
gene expression bridges genetic variation to phenotypic alteration. Identification of the …

Smart breeding driven by advances in sequencing technology

C Zhang, S Jiang, Y Tian, X Dong, J Xiao… - Modern …, 2023 - Wiley Online Library
Crop breeding has undergone numerous advancements throughout history with the next
revolution being uncertain. This review provides an overview of breeding techniques from …