Abstract
The liverwort Marchantia polymorpha is a member of the most basal lineage of land plants (embryophytes) and likely retains many ancestral morphological, physiological and molecular characteristics. Despite its phylogenetic importance and the availability of previous EST studies, M. polymorpha’s lack of economic importance limits accessible genomic resources for this species. We employed Illumina RNA-Seq technology to sequence the gametophyte transcriptome of M. polymorpha. cDNA libraries from 6 different male and female developmental tissues were sequenced to delineate a global view of the M. polymorpha transcriptome. Approximately 80 million short reads were obtained and assembled into a non-redundant set of 46,533 transcripts (> = 200 bp) from 46,070 loci. The average length and the N50 length of the transcripts were 757 bp and 471 bp, respectively. Sequence comparison of assembled transcripts with non-redundant proteins from embryophytes resulted in the annotation of 43% of the transcripts. The transcripts were also compared with M. polymorpha expressed sequence tags (ESTs), and approximately 69.5% of the transcripts appeared to be novel. Twenty-one percent of the transcripts were assigned GO terms to improve annotation. In addition, 6,112 simple sequence repeats (SSRs) were identified as potential molecular markers, which may be useful in studies of genetic diversity. A comparative genomics approach revealed that a substantial proportion of the genes (35.5%) expressed in M. polymorpha were conserved across phylogenetically related species, such as Selaginella and Physcomitrella, and identified 580 genes that are potentially unique to liverworts. Our study presents an extensive amount of novel sequence information for M. polymorpha. This information will serve as a valuable genomics resource for further molecular, developmental and comparative evolutionary studies, as well as for the isolation and characterization of functional genes that are involved in sex differentiation and sexual reproduction in this liverwort.
Highlights
IntroductionBryophytes (e.g., liverworts, mosses, and hornworts) represent an early diverging lineage of embryophytes
Bryophytes represent an early diverging lineage of embryophytes
To globally define the gametophyte transcriptome of M. polymorpha, RNA samples were collected from six different developmental stages of male and female tissues: vegetative thallus male (VM); vegetative thallus female (VF); immature reproductive male (IMM); immature reproductive female (IMF); mature reproductive male (MM); and mature reproductive female (MF) (Figure S1)
Summary
Bryophytes (e.g., liverworts, mosses, and hornworts) represent an early diverging lineage of embryophytes. Liverworts are an ideal group for exploring the following: a) the evolution of dorsiventral development vs radial development in plants, b) the functions of the genetic network in haploid and diploid generations of land plants and c) the requirement for different developmental programs for body plans in different generations [2]. The exploration of these questions requires the development of genomic resources that facilitate comparative and evolutionary studies. M. polymorpha is an emerging model plant that is appropriate for molecular, comparative and developmental genetics studies
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