A chromosome‐level genome assembly ofPyropia haitanensis(Bangiales, Rhodophyta)

Abstract

Pyropia haitanensis (Bangiales, Rhodophyta), a major economically important marine crop, is also considered as an ideal research model of Rhodophyta to address several major biological questions such as sexual reproduction and adaptation to intertidal abiotic stresses. However, comparative genomic analysis to decipher the underlying molecular mechanisms is hindered by the lack of high‐quality genome information. Therefore, we integrated sequencing data from Illumina short‐read sequencing, PacBio single‐molecule sequencing and BioNano optical genome mapping. The assembled genome was approximately 53.3 Mb with an average GC% of 67.9%. The contig N50 and scaffold N50 were 510.3 kb and 5.8 Mb, respectively. Additionally, 10 superscaffolds representing 80.9% of the total assembly (42.7 Mb) were anchored and orientated to the 5 linkage groups based on markers and genetic distance; this outcome is consistent with the karyotype of five chromosomes (n = 5) based on cytological observation in P. haitanensis. Approximately 9.6% and 14.6% of the genomic region were interspersed repeat and tandem repeat elements, respectively. Based on full‐length transcriptome data generated by PacBio, 10,903 protein‐coding genes were identified. The construction of a genome‐wide phylogenetic tree demonstrated that the divergence time of P. haitanensis and Porphyra umbilicalis was ~204.4 Ma. Interspecies comparison revealed that 493 gene families were expanded and that 449 were contracted in the P. haitanensis genome compared with those in the Po. umbilicalis genome. The genome identified is of great value for further research on the genome evolution of red algae and genetic adaptation to intertidal stresses.

Pyropia yezoensis genome reveals diverse mechanisms of carbon acquisition in the intertidal environment

“…An interesting feature of the P. yezoensis genome is the high overall GC content of 65%, which reaches 71% in coding regions. This attribute is shared with other Bangiophyceae including P. haitanensis 10 (67.9%), Bangia fuscopurpurea 32 (64%), and P. umbilicalis 9 (66%), whereas the GC content ranges from 37 to 57% in other red algae (e.g., C. crispus 33 , P. purpureum 34 , Galdieria sulphuraria 29 , and C. merolae 35 ; Supplementary Fig. 19a ).…”

“…The genome-wide impact of this alternation of heteromorphic generations is poorly understood. The genomes of P. umbilicalis and P. haitanensis have recently been published 9 , 10 . Here we present the genome of P. yezoensis and analyze Bangiales genome and transcriptomic data to gain insights into the evolutionary mechanisms that allow these species to thrive in their stressful habitats vis-à-vis their dimorphic life cycle.…”

Comparative Quantitative Proteomics Reveals the Desiccation Stress Responses of the Intertidal Seaweed NEOPORPHYRA haitanensis

“…We used a laboratory-cultured pure line of Neoporphyra haitanensis (PH-40) to perform the proteomic study. Its ancestral gametophytes were collected in 2010 in the upper intertidal zone in Fuding, Fujian Province, China, and then used to prepare the genetically homozygous PH-40 strain through a method described previously (Cao et al 2020). The gametophytes of strain PH-40 were cultured in Provasoli's enrichment solution (PES) medium under 50-60 lmol photons Á m -2 Á s -1 at 20 AE 1°C with a 12:12 h light:dark photoperiod.…”

“…THE PROTEOMIC RESPONSES TO DESICCATION IN PYROPIA MS data processing. Pyropia proteins were identified by matching to the annotated protein sequences from the genome database (Cao et al 2020) using the Andromeda algorithm embedded in MaxQuant software version 1.5.5.1 (Cox et al 2011). In silico digestion of the N. haitanensis proteome was done with an in-house-developed PERL script ( Fig.…”

A Pyropia haitanensis putative ABA-GPCR homologous protein as an early evolution transmembrane receptor protein?

“…The protein from unicellular red alga G. sulphuraria appears to be the earliest origin of G-A family, thereafter they form two clades: one is for red algae, including multicellular red algae and unicellular P. purpureum. Their branching situations are consistent with the evolutionary relationship of their genomes [17][18][19]. Another gradual evolutionary branch has formed two large clusters, one large group includes mainly homologous proteins of fungi, amoeba and metazoans, which share an ancestral homologous sequence with that of cryptoalgae Guillardia theta and that of a collar agellate Monosiga brevicollis.…”