Chengyi Tang

Proserpinaca palustris, a representative heterophyllous plant, represents an emerging model for studying morphological plasticity and adaptive evolution in amphibious environments. However, the absence of a high-quality reference genome has hindered molecular investigations into its heterophylly regulation mechanisms. Here, we present the first chromosome-level genome assembly of P. palustris. The final assembly spans 385.32 Mb, anchored onto seven pseudochromosomes (1n = 7), and encodes 22,756 predicted protein-coding genes. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment demonstrated high completeness, with scores of 95.61% for the genome assembly and 96.43% for the gene set. Comparative genomic analyses revealed that P. palustris underwent only the ancient γ whole-genome triplication (γ-WGT) event, with no subsequent whole-genome duplication (WGD). Nevertheless, the genome has experienced extensive re-diploidization, likely facilitated by structural rearrangements. Transcriptomic profiling identified three KNOTTED1-like homeobox (KNOX) genes (i.e., PPA02C1640, PPA03C1159, and PPA01C1293) that were significantly differentially expressed between submerged and terrestrial leaves in P. palustris, suggesting their potential role in regulating heterophylly. This study provides the first high-quality genomic resource for the genus Proserpinaca (Haloragaceae) and identifies key KNOX genes implicated in heterophylly regulation in P. palustris.

The Chinese lizardtail herb, Saururus chinensis, holds a prominent position in traditional Chinese medicine. In this study, we present a comprehensive genomic dataset for S. chinensis. Furthermore, comparative genomic analysis indicates that the extant genome of S. chinensis retains extensive traces of a paleo‐tetraploidization event. These traces are observable at both the macroscopic level of chromosomes and the microscopic level within specific gene families, such as the PEL (pseudo‐etiolation in light) gene family. Additionally, our findings further suggest that this paleo‐tetraploidization event drives an expansion of the PEL gene family in the S. chinensis genome, potentially facilitating its neo‐ and sub‐functionalization, and thereby contributing to the evolutionary adaptability of this species.

Several months earlier, other researchers had achieved the inaugural publication of the Chinese Lizardtail Herb ( Saururus chinensis ) genome dataset. However, the quality of that genome dataset is not deeply satisfactory, especially in terms of genome continuity (Contig N50 length ≈ 1.429 Mb) and gene-set completeness (BUSCO evaluation ≈ 91.32%). In this study, we present an improved chromosome-level genome of S. chinensis , characterized by heightened genome continuity (Contig N50 length ≈ 4.180 Mb) and a more complete gene-set (BUSCO evaluation ≈ 95.91%). Our investigation reveal that the extant S . chinensis genome preserves abundant vestiges of a paleo-tetraploidization event that are discernible both at the macroscopic chromosome level and within microscopic gene families, such as the PEL (pseudo-etiolation in light) family. Moreover, we elucidate that this paleo-tetraploidization event is associated with an expansion of the PEL family, potentially initiating a process conducive to its neofunctionalization and/or subfunctionalization.

Increasing genome data are coming out. Genome size estimation plays an essential role in guiding genome assembly. Several months ago, other researchers were the first to publish a draft genome of the red gromwell (i.e. Lithospermum erythrorhizon). However, we considered that the genome size they estimated and assembled was incorrect. This study meticulously estimated the L. erythrorhizon genome size to should be ∼708.74 Mb and further provided a reliable genome version (size ≈ 693.34 Mb; contig_N50 length ≈ 238.08 Kb) to support our objection. Furthermore, according to our genome, we identified a gene family of the alkannin/shikonin O-acyltransferases (i.e. AAT/SAT) that catalysed enantiomer-specific acylations in the alkannin/shikonin biosynthesis (a characteristic metabolic pathway in L. erythrorhizon’s roots) and further explored its evolutionary process. The results indicated that the existing AAT/SAT were not generated from only one round of gene duplication but three rounds; after different rounds of gene duplication, the existing AAT/SAT and their recent ancestors were under positive selection at different amino acid sites. These suggested that a combined power from gene duplication plus positive selection plausibly propelled AAT/SAT’s functional differentiation in evolution.

Boraginales (the forget‐me‐not order) is a core group within the lamiids clade. However, until now, no genome from Boraginales has been reported, and published transcriptomes are also rare. Here, we report the first Boraginales species de novo genome (i.e. Echium plantagineum genome) and seven other Boraginales species transcriptomes to probe three issues: (i) Boraginales' phylogenetic position within the lamiids clade; (ii) potential whole genome duplications (WGDs) in Boraginales; and (iii) candidate key enzyme genes in the alkannin/shikonin core pathway. The results showed that: (i) Boraginales was most probably closer to the Solanales/Gentianales clade than the Lamiales clade, at least based on the single‐copy orthologous genes from genome/transcriptome data; (ii) after the gamma (γ) event, Boraginaceae (classified into the Boraginales I clade) probably underwent at least two rounds of WGD, whereas Heliotropiaceae and Ehretiaceae (classified into the Boraginales II clade) probably underwent only one round of WGD; and (iii) several candidate key enzyme genes in the alkannin/shikonin core pathway were inferred, e.g. genes corresponding to geranyl cyclase, naphthol hydroxylase and O‐acyl transferase.

MicroRNAs (miRNAs) play an important role in plant growth, development, and response to environment. For identifying and comparing miRNAs and their targets in seed development between two maize inbred lines (i.e. PH6WC and PH4CV), two sRNAs and two degradome libraries were constructed. Through high-throughput sequencing and miRNA identification, 55 conserved and 24 novel unique miRNA sequences were identified in two sRNA libraries; moreover, through degradome sequencing and analysis, 137 target transcripts corresponding to 38 unique miRNA sequences were identified in two degradome libraries. Subsequently, 16 significantly differentially expressed miRNA sequences were verified by qRT-PCR, in which 9 verified sequences obviously target 30 transcripts mainly involved with regulation in flowering and development in embryo. Therefore, the results suggested that some miRNAs (e.g. miR156, miR171, miR396 and miR444) related reproductive development might differentially express in seed development between the PH6WC and PH4CV maize inbred lines in this present study.

MicroRNAs (miRNAs) are a class of noncoding small RNAs (sRNAs) that play many roles in plant growth, development, and the stress response. Recently, the Brassica napus (B. napus) genome was reported, which allows the genome-wide identification of miRNAs and their targets in B. napus cv. Westar and its transgenic cultivar. Thus, two sRNAs libraries and two degradome libraries of the transgenic B. napus (TG) and its acceptor (B. napus cv. Westar, WA) were constructed. Following high-throughput sequencing and miRNA identification, 139 unique conserved and 305 unique novel miRNA sequences were identified in the two sRNA libraries, and through degradome analysis, 540 targets corresponding to 167 unique miRNA sequences were identified in the two degradome libraries. 11 differentially expressed unique miRNA sequences were verified by quantitative real-time PCR (qRT-PCR), and the results nearly agreed with the high-throughput sequencing data. The present study increases the number of miRNAs identified in B. napus and suggests that there are possible differences in the miRNA expression between transgenic B. napus and its acceptor.