The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences

Abstract

Protein-coding gene annotation. To search for homologous genes, the protein sequences from all ferns and lycophytes transcriptomes in the OneKP project 1 were retrieved and aligned to the A. capillus-veneris genome, using GeneWise 2 . For transcriptome-based prediction, nineteen transcriptomes covering the entire life cycle of A. capillus-veneris were generated in this study (Supplementary Table 8). RNA was extracted using the Qiagen RNeasy protocol and sequenced on an Illumina HiSeq 4000 with a 300 bp insert size. For transcriptome-based prediction, the HISAT2 3 and StringTie 4 programs were used for transcript assembly 5 . The program PASA (http://pasapipeline.github.io) was used to align spliced transcripts and annotate candidate genes. Ab initio prediction was performed with AUGUSTUS 6 , GlimmerHMM 7 , and SNAP 8 . Finally, nonredundant gene models were obtained with EVidenceModeler (version 1.1.0) 9 to integrate the gene models developed by different datasets.To validate the assembly quality, RNA-seq reads from nineteen tissues (Supplementary Table 8), together with publicly available EST sequences from the NCBI database (downloaded from http://togodb.dbcls.jp/library), were mapped to the A. capillus-veneris genome using HISAT2 3 and BLAT 10 with default parameters, respectively. The BLAT results were filtered with an identity and coverage cutoff of 0.9.Identification of noncoding RNAs. We used tRNAscan-SE (version 2.0rc2) 11 , with default parameters, to search for tRNAs in the A. capillus-veneris genome. A total of 1,624 tRNAs were found. Moreover, the Rfam14.0 database 12 , including 3,445 noncoding RNA families, was used to annotate additional noncoding RNAs (ncRNAs), including miRNAs, snRNAs, and tRNAs, using INFERNAL (version 1.1.2) 13 program.We predicted rRNA (5S, 5.8S, 28S, 18S) by using HMM searching based rRNA predicator Barrnap (version 0.9, https://github.com/tseemann/barrnap#barrnap), with default parameters. We finally identified 145 5S, 75 5.8S, 155 28S, and 165 18S sequences and their locations within the genome assembly of A. capillus-veneris.

Origins of the seed: The “golden-trio hypothesis”

“…" Wang and Bai (2019) have proposed a possible scenario regarding the transition from homospory to heterospory. Similar adaptive advantages of this transition might underlie the retention of the megasporangia in Fang et al, 2022), such LEC1-centered regulatory networks found in Adiantum capillus-veneris might have been available for integration with other evolutionary innovations, resulting in the origin of seeds, which would represent the kind of "tinkering" event suggested by Jacob (1977). Twenty years have passed since the original idea to explore the role of LEC1 in seed origin.…”

“…A recently published work provides strong support for that hypothesis; based on the genome sequence and transcriptome analysis of Adiantum capillus-veneris , Fang et al (2022) determined that AcdLEC1 (previously designated as AcLEC1 ) is not only expressed during homosporangium development, but also resides at a hub of a regulatory network that is conserved in the Arabidopsis seed program. The work further elucidated the function of AcdLEC1 in pteridophytes, which consistent to the previous finding that the AcdLEC1 expressed in sporophytes under stress conditions ( Xie et al, 2008 ).…”

“…Similar adaptive advantages of this transition might underlie the retention of the megasporangia in sporophyte development, which ultimately led to the emergence of the spermatophytes. Based on the conservation of LEC1-centered regulatory networks between Adiantum capillus-veneris homosporangium development and the Arabidopsis seed program ( Fang et al, 2022 ), such LEC1-centered regulatory networks found in Adiantum capillus-veneris might have been available for integration with other evolutionary innovations, resulting in the origin of seeds, which would represent the kind of “tinkering” event suggested by Jacob (1977) .…”

The barley DIR gene family: An expanded gene family that is involved in stress responses

“…An extended gene family in Mango is the chalcone synthase ( CHS ) family, and certain genes within this family are likely to be involved in the biosynthesis of urushiols and related phenols ( Wang et al, 2020 ). The leaf and stem vascular regulator BRI1-BRL gene family was found to be expanded in Adiantum capillus-veneris L. and functionally conserved for vascular development regulation in euphyllophytes, suggesting that complicated vascular system formation led to the origin of true leaves or euphylls ( Fang et al, 2022 ).…”

Rickettsial DNA invasions and a scrambled rRNA cluster with a trans-splicing group I intron: The highly unorthodox mitogenome of the fern Haplopteris ensiformis

“…10,000 species, the H. ensiformis mitogenome again adds to the list of astonishing molecular peculiarities that are hallmarks of vascular plant mtDNAs 44,45 . Given its extraordinary complexity, it comes as no surprise that no other leptosporangiate mitogenome has previously been assembled despite multiple NGS efforts including the water fern genera Azolla and Salvinia 46,47 or the "flying spider-monkey" tree fern Alsophila spinulosa 48 or, most recently, the model ferns Adiantum capillus-veneris 49 and Ceratopteris richardii 50 . Likewise no mitogenome was reported in a genome assembly effort for the lycophyte Isoetes taiwanensis 51 , possibly owing to even higher complexity than the ones reported previously for Isoetes engelmannii and Selaginella moellendorffii 7,8 .…”