The Caenorhabditis globin gene family reveals extensive nematode-specific radiation and diversification

<p>Abstract</p> <p>Background</p> <p>Globin isoforms with variant properties and functions have been found in the pseudocoel, body wall and cuticle of various nematode species and even in the eyespots of the insect-parasite <it>Mermis nigrescens</it>. In fact, much higher levels of complexity exist, as shown by recent whole genome analysis studies. <it>In silico </it>analysis of the genome of <it>Caenorhabditis elegans </it>revealed an unexpectedly high number of globin genes featuring a remarkable diversity in gene structure, amino acid sequence and expression profiles.</p> <p>Results</p> <p>In the present study we have analyzed whole genomic data from <it>C. briggsae</it>, <it>C. remanei</it>, <it>Pristionchus pacificus </it>and <it>Brugia malayi </it>and EST data from several other nematode species to study the evolutionary history of the nematode globin gene family. We find a high level of conservation of the <it>C. elegans </it>globin complement, with even distantly related nematodes harboring orthologs to many <it>Caenorhabditis </it>globins. Bayesian phylogenetic analysis resolves all nematode globins into two distinct globin classes. Analysis of the globin intron-exon structures suggests extensive loss of ancestral introns and gain of new positions in deep nematode ancestors, and mainly loss in the <it>Caenorhabditis </it>lineage. We also show that the <it>Caenorhabditis </it>globin genes are expressed in distinct, mostly non-overlapping, sets of cells and that they are all under strong purifying selection.</p> <p>Conclusion</p> <p>Our results enable reconstruction of the evolutionary history of the globin gene family in the nematode phylum. A duplication of an ancestral globin gene occurred before the divergence of the Platyhelminthes and the Nematoda and one of the duplicated genes radiated further in the nematode phylum before the split of the Spirurina and Rhabditina and was followed by further radiation in the lineage leading to <it>Caenorhabditis</it>. The resulting globin genes were subject to processes of subfunctionalization and diversification leading to cell-specific expression patterns. Strong purifying selection subsequently dampened further evolution and facilitated fixation of the duplicated genes in the genome.</p

Chromosome‐level reference genome of the soursop (Annona muricata) : a new resource for Magnoliid research and tropical pomology

The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers, we report a chromosome-level genome assembly of the soursop (Annona muricata). We assembled the genome using 444.32 Gb of DNA sequences (676x sequencing depth) from PacBio and Illumina short-reads, in combination with 10x Genomics and Bionano data (v1). A total of 949 scaffolds were assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo-chromosomes using Hi-C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb). Heterozygosity was very low (0.06%), while repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size showed a slow continuous contraction, probably related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry

Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology

The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers, we report a chromosome‐level genome assembly of the soursop (Annona muricata). We assembled the genome using 444.32 Gb of DNA sequences (676× sequencing depth) from PacBio and Illumina short‐reads, in combination with 10× Genomics and Bionano data (v1). A total of 949 scaffolds were assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo‐chromosomes using Hi‐C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb). Heterozygosity was very low (0.06%), while repeat sequences accounted for 54.87% of the genome, and 23,375 protein‐coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA‐seq and homology‐based approaches. Reconstruction of the historical population size showed a slow continuous contraction, probably related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages. Both genome‐assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry

Plastid and Seed Morphology Data Support a Revised Infrageneric Classification and an African Origin of the Pantropical Genus Xylopia (Annonaceae)

International audienceThe floristic treatment of Engler and Diels, published in 1901, provides the only infrageneric classification of the pantropical genusXylopia (Annonaceae). Here we test and extend that classification using molecular and seed morphology characters. Phylogenetic relationships werereconstructed using data from four plastid regions obtained from 44 of the approximately 165 species in the genus, recovering four well-supportedmajor clades. Seed characters were examined for these taxa, and six aril morphologies, three previously undocumented, were distinguished; we alsodocument the presence of a sarcotesta on the seeds of many species. Molecular and seed data support recognition of five sections within the genus;one, Xylopia sect. Rugosperma, is proposed here as new. Our phylogenetic results suggest an African origin for the genus and reveal complexbiogeographic patterns, likely facilitated by long-distance dispersa

Early evolutionary history of the flowering plant family Annonaceae : steady diversification and boreotropical geodispersal

Aim : Rain forest-restricted plant families show disjunct distributions between the three major tropical regions: South America, Africa and Asia. Explaining these disjunctions has become an important challenge in biogeography. The pantropical plant family Annonaceae is used to test hypotheses that might explain diversification and distribution patterns in tropical biota: the museum hypothesis (low extinction leading to steady accumulation of species); and dispersal between Africa and Asia via Indian rafting versus boreotropical geodispersal. Location : Tropics and boreotropics. Methods : Molecular age estimates were calculated using a Bayesian approach based on 83% generic sampling representing all major lineages within the family, seven chloroplast markers and two fossil calibrations. An analysis of diversification was carried out, which included lineage-through-time (LTT) plots and the calculation of diversification rates for genera and major clades. Ancestral areas were reconstructed using a maximum likelihood approach that implements the dispersal-extinction-cladogenesis model. Results : The LTT plots indicated a constant overall rate of diversification with low extinction rates for the family during the first 80 Ma of its existence. The highest diversification rates were inferred for several young genera such as Desmopsis, Uvariopsis and Unonopsis. A boreotropical migration route was supported over Indian rafting as the best fitting hypothesis to explain present-day distribution patterns within the family. Main conclusions : Early diversification within Annonaceae fits the hypothesis of a museum model of tropical diversification, with an overall steady increase in lineages possibly due to low extinction rates. The present-day distribution of species within the two largest clades of Annonaceae is the result of two contrasting biogeographic histories. The 'long-branch clade' has been diversifying since the beginning of the Cenozoic and underwent numerous geodispersals via the boreotropics and several more recent long-distance dispersal events. In contrast, the 'short-branch clade' dispersed once into Asia via the boreotropics during the Early Miocene and further dispersal was limited

Maximum likelihood analysis of psbA-trnH spacer

Maximum likelihood analysis of psbA-trnH spacer, showing bootstrap suppor

Early evolutionary history of the flowering plant family Annonaceae : steady diversification and boreotropical geodispersal

Abstract Aim Rain forest-restricted plant families show disjunct distributions between the three major tropical regions: South America, Africa and Asia. Explaining these disjunctions has become an important challenge in biogeography. The pantropical plant family Annonaceae is used to test hypotheses that might explain diversification and distribution patterns in tropical biota: the museum hypothesis (low extinction leading to steady accumulation of species); and dispersal between Africa and Asia via Indian rafting versus boreotropical geodispersal. Location Tropics and boreotropics. Methods Molecular age estimates were calculated using a Bayesian approach based on 83% generic sampling representing all major lineages within the family, seven chloroplast markers and two fossil calibrations. An analysis of diversification was carried out, which included lineage-through-time (LTT) plots and the calculation of diversification rates for genera and major clades. Ancestral areas were reconstructed using a maximum likelihood approach that implements the dispersal–extinction–cladogenesis model. Results The LTT plots indicated a constant overall rate of diversification with low extinction rates for the family during the first 80 Ma of its existence. The highest diversification rates were inferred for several young genera such as Desmopsis, Uvariopsis and Unonopsis. A boreotropical migration route was supported over Indian rafting as the best fitting hypothesis to explain present-day distribution patterns within the family. Main conclusions Early diversification within Annonaceae fits the hypothesis of a museum model of tropical diversification, with an overall steady increase in lineages possibly due to low extinction rates. The present-day distribution of species within the two largest clades of Annonaceae is the result of two contrasting biogeographic histories. The ‘long-branch clade’ has been diversifying since the beginning of the Cenozoic and underwent numerous geodispersals via the boreotropics and several more recent long-distance dispersal events. In contrast, the ‘short-branch clade’ dispersed once into Asia via the boreotropics during the Early Miocene and further dispersal was limited

Maximum parsimony reconstruction of sarcotesta

Maximum parsimony reconstruction of sarcotesta (presence vs. absence), implemented in Mesquit