Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava)

Abstract

Tunicates occupy the evolutionary position at the boundary of invertebrates and vertebrates. It exhibits adaptation to broad environmental conditions and is distributed globally. Despite hundreds of years of embryogenesis studies, the genetic basis of the invasive habits of ascidians remains largely unknown. The leathery sea squirt, Styela clava, is an important invasive species. We used the chromosomal‐level genome and transcriptome of S. clava to explore its genomic‐ and molecular‐network‐based mechanisms of adaptation to environments. Compared with Ciona intestinalis type A (C. robusta), the size of the S. clava genome was expanded by 2‐fold, although the gene number was comparable. An increase in transposon number and variation in dominant types were identified as potential expansion mechanisms. In the S. clava genome, the number of genes encoding the heat‐shock protein 70 family and members of the complement system was expanded significantly, and cold‐shock protein genes were transferred horizontally into the S. clava genome from bacteria. The expanded gene families potentially play roles in the adaptation of S. clava to its environments. The loss of key genes in the galactan synthesis pathway might explain the distinct tunic structure and hardness compared with the ascidian Ciona species. We demonstrated further that the integrated thyroid hormone pathway participated in the regulation of larval metamorphosis that provides S. clava with two opportunities for adapting to their environment. Thus, our report of the chromosomal‐level leathery sea squirt genome provides a comprehensive genomic basis for the understanding of environmental adaptation in tunicates.

Genome-Wide Identification, Comparison, and Expression Analysis of Transcription Factors in Ascidian Styela clava

“…A total of 17,428 protein-coding genes were identified, 15,734 of which were annotated in the S. clava genome [ 28 ]. Based on our previous study, we further identified 553 TF genes, which were distributed in 60 TF families in the S. clava genome, according to the domain annotation of proteins and the types of DBD.…”

“…To explore the expression profiles of TFs during the development of S. clava , we acquired the fragments Per Kilobase of gene per million mapped reads (FPKM) value of each TF in 2-cell–8-cell embryos (2–8 cells), gastrula embryos (gast), neurula embryos (neu), tailbud-stage embryos (tb), hatched swimming larvae (hsl), tail-regressed larvae (trl), and metamorphic juveniles (mj) by RNA-sequencing [ 28 ]. These data were further validated through quantitative real-time PCR.…”

“…The results showed that they belonged to PG4 ( e -value = 2 × 10 −57 ) and PG5 ( e -value = 5 × 10 −52 ), respectively. All Hox genes identified in the S. clava genome were distributed on one single chromosome according to the Hi-C result [ 28 ]. Hox genes were also distributed on one single chromosome in Halocynthia roretzi with similar arrangement, and on two chromosomes in the C. robusta genome ( Figure 4 A).…”

“…Styela clava is a globally distributed ascidian species that shows a strong environmental adaptation [ 28 , 29 , 30 ]. In this study, we performed genome-wide identification and analysis for TFs in S. clava .…”

Seasonal dynamics and starvation impact on the gut microbiome of urochordate ascidian Halocynthia roretzi

“…Natural selection in genomes of several marine animals, such as oyster and scallop, could play a role of molecular adaptation to marine environment [5,6]. Recently, the genome of leathery sea squirt (Styela clava) has also been sequenced and analyzed for the understanding of their environmental adaptation [7]. However, the genetic basis driving ascidians to contribute and adapt marine ecosystem remains to be elusive.…”