Genome-wide analysis of the GRAS gene family exhibited expansion model and functional differentiation in sea buckthorn (Hippophae rhamnoides L.)

Yu Liyang,Zhang Guoyun,Lyu Zhongrui,He Caiyun,Zhang Jianguo 한국식물생명공학회 2021 Plant biotechnology reports Vol.15 No.4

Key message Genome-wide identification of the sea buckthorn GRAS genes and their transcription profiles in dif- ferent organizations. Abstract GRAS proteins comprise a large family of transcription factors that experienced extensive replication, and play important roles in many aspects of growth regulatory and environmental signals. Sea buckthorn is a unique and valuable plant which has tremendous value for medical researching, ecological protection, and providing daily necessities. We iden- tified, characterized, and distinguished duplication models of GRAS transcription factors in sea buckthorn. A systematic whole-genome analysis was performed to identify and characterize the GRAS gene family of sea buckthorn, especially the comparative genome method was used to demonstrate its different duplication models. We identified 62 sea buckthorn GRAS (HrGRAS) genes and renamed based on their respective chromosome distribution. Fifty-nine HrGRASs were classified into nine subgroups and three HrGRASs did not belong to any of the subfamilies according to their phylogenetic features. HrGRAS genes tend to have a representative GRAS domain, few introns, and unevenly distributed on chromosomes. Seg- mental duplication was the main driver of the GRAS gene family expansion, followed by whole-genome duplication (WGD) and tandem duplication, according to the results of comparative genome analysis. GRAS genes involved in duplication expe- rienced strong purifying selection pressure according to the Ka/Ks ratios. The expression profile derived from transcriptome data shows the expression patterns of HrGRAS gene in different tissues and the characterization of differentially expressed genes. This systematic analysis provided a foundation to understand the expansion and potential functions of GRAS genes with an aim of sea buckthorn crop improvement.

Insights into the evolutionary origin and expansion of the BBX gene family

Yu Liyang,Lyu Zhongrui,Liu Hong,Zhang Guoyun,He Caiyun,Zhang Jianguo 한국식물생명공학회 2022 Plant biotechnology reports Vol.16 No.2

The B-box proteins are a class of zinc finger transcription factors and play important roles in regulating plant growth, devel- opment, and stress response. However, their origin and expansion model in plants have been very vague. In this study, 208 B-box genes were identified in 18 plant species, and phylogenetic analyses divided them into five structure groups. Subse- quently, the sequence analysis including theoretical isoelectric point, instability index, and aliphatic index showed the wide variation of B-box gene in different species. Our multispecies genome-wide analysis reveals that the structure groups III and IV in the plant BBX gene family have the earliest origin (Rhodophyta) and are extensively expanded in land plants, while the other three structure groups (I, II, and V) seem to originate at least in the last common ancestor of land plants. Further- more, whole genome duplication (WGD) was the main driver (28 gene pairs, 65.12%) of the B-box gene family expansion, followed by segmental duplication, which tend to have more introns and are subject to more intense purification selections. We also analyzed the sequence differences between B-box domains to propose a new evolutionary model of B-box domain. These analyses provide new insights for understanding the origin and evolution of the B-box gene family.

The complete mitochondrial genome of parasitoid wasp Pseudoligosita yasumatsui (Hymenoptera: Trichogrammatidae) and its phylogenetic implications

Wang Liyang,Wu Hongxuan,He Wei,Zhou Qiang 한국응용곤충학회 2023 Journal of Asia-Pacific Entomology Vol.26 No.4

Pseudoligosita yasumatsui (Viggiani and Rao, 1978) (Hymenoptera: Trichogrammatidae) is an egg parasitoid wasp that preys on rice planthoppers, one of the most significant pests in Asian rice-growing regions. An enriched mitochondrial genome database of rice planthopper egg parasitoids is the basis for phylogenetic analysis. Therefore, the complete mitochondrial genome of P. yasumatsui was sequenced using NGS sequencing. The total length of the mitochondrial genome of P. yasumatsui is 16,036 bp, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region (CR). The mitochondrial genome showed a negative AT skew (-0.09) and a positive GC skew (0.19). Thirteen PCGs all started with ATN codons and ended with TAA. All 22 tRNAs have a typical cloverleaf structure. A comparison with the presumed arthropod ancestral mitochondrial genome using CREx web serve observed a large number of tRNAs as well as PCGs inversions, rearrangements, and inversion reversals of large gene segments (trnE-rrnL). Based on the Bayesian inference (BI) and maximum likelihood (ML) phylogenetic tree of P. yasumatsui and other 14 mito chondrial genomes from the Chalcidoidea superfamily, the phylogenetic relationship of P. yasumatsui within the Trichogrammatidae family was found to be ((Pseudoligosita + Megaphragma) + Trichogamma), and the phylo genetic relationship of five families was (Mymaridae + (Trichogrammatidae + (Aphelinidae + (Eulophidae + Pteromalidae)))). The close relationship between Pseudoligosita and Megaphragma as sister groups was suggested, and the data provide support for the monophyly of Oligositini.

Backstepping method based controller design for third-order truck platoon robust to dynamic uncertainty and external disturbance

Jianbo Feng,Liyang He,Yanxue Wang,Jianwei Yang,Hongbin Ren 대한기계학회 2023 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.37 No.3

The vehicle platoon is subject to dynamic uncertainty and external disturbance, such as air drag and parameter variation in practice, so lack of consideration for those factors can deteriorate control performance. This paper proposes a nonlinear control algorithm based on a novel adaptive backstepping method to cope with the uncertainty and disturbance. The virtual controller in the backstepping method utilizes only the local information of the individual vehicle, rather than the global state information, in the control algorithm design. A third-order vehicle dynamics model was built to incorporate the nonlinearity and the factor of actuation delay. The fuzzy logic system (FLS) is applied to estimate the nonlinearity in vehicle dynamics to facilitate the adaptive control. Five scenarios with different settings were constructed to verify the control performance in the simulation, which indicates the effectiveness and robustness of the controller to dynamic uncertainty and external disturbance.

DC‑side admittance model of converters with constant power control considering DC‑side voltage fluctuation

Xin Tang,Zhen Li,Yang He,Liyang Wang,Yufei Yue,Wen Wang 전력전자학회 2023 JOURNAL OF POWER ELECTRONICS Vol.23 No.2

In the stability analysis of DC (direct-current) power grids, AC (alternating current)/DC converters are usually treated as linear proportional amplifiers or inertial links. However, this approximation will have a considerable effect on the DC-side impedance model of a constant active power control converter and then affect the accuracy of the stability analysis of DC grids. In this paper, in view of the DC-side of the voltage fluctuations, the DC-side admittance model is established after the nonlinear relationship between the port voltage and the modulation signal function is determined. A comparison is made between the traditional modeling method and the proposed modeling method in the analysis of the phase–frequency characteristics and amplitude–frequency characteristics of the admittance. Results show that the proposed small-signal model can better fit the measured admittance in the low-frequency bands. The proposed admittance model in this paper is further applied to assess the small-signal stability of a DC grid. Finally, PSCAD/EMTDC simulation and lab-scaled prototype experiment are used to verify the correctness and effectiveness of the established admittance model. Results show that the small-signal model deduced in this paper can better fit and measure the admittance in the low-frequency band, and can more accurately judge the stability of the DC system.