Convergent Evolution Within CEA Gene Families in Mammals: Hints for Species-Specific Selection Pressures

AbstractGinger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.

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Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils

10.1101/459362 ◽

2018 ◽

Cited By ~ 1

Author(s):

Veronica Preite ◽

Christian Sailer ◽

Lara Syllwasschy ◽

Sian Bray ◽

Ute Krämer ◽

...

Keyword(s):

Convergent Evolution ◽

Arabidopsis Halleri ◽

Individual Genome ◽

Genetic Changes ◽

Association Analyses ◽

Systematic Testing ◽

Related Plant ◽

Arabidopsis Arenosa ◽

Species Specific ◽

Degree Of Convergence

AbstractIt is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa, which co-occur at two calamine metalliferous sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from 8 populations on metalliferous and non-metalliferous soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical SNPs in several A. halleri genes at two independently colonized metalliferous sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine metalliferous soils involves convergent evolution, which will likely be more pervasive across sites purposely chosen for maximal similarity in soil composition.

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The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis

Nature Communications ◽

10.1038/s41467-019-12607-6 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 10

Author(s):

Lisong Hu ◽

Zhongping Xu ◽

Maojun Wang ◽

Rui Fan ◽

Daojun Yuan ◽

...

Keyword(s):

Reference Genome ◽

Gene Families ◽

Black Pepper ◽

Piper Nigrum ◽

Comparative Genomic ◽

Specific Gene ◽

Phylogenomic Analysis ◽

Genomic Analyses ◽

Species Specific ◽

Insight Into

Abstract Black pepper (Piper nigrum), dubbed the ‘King of Spices’ and ‘Black Gold’, is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the glycosyltransferase, cytochrome P450, shikimate hydroxycinnamoyl transferase, lysine decarboxylase, and acyltransferase gene families. Comparative transcriptomic analyses disclose berry-specific upregulated expression in representative genes in each of these gene families. These data provide an evolutionary perspective and shed light on the metabolic processes relevant to the molecular basis of species-specific piperine biosynthesis.

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Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1715531115 ◽

2018 ◽

Vol 115 (5) ◽

pp. 968-973 ◽

Cited By ~ 20

Author(s):

Bronwyn A. Lucas ◽

Eitan Lavi ◽

Lily Shiue ◽

Hana Cho ◽

Sol Katzman ◽

...

Keyword(s):

Convergent Evolution ◽

Regulatory Networks ◽

Parallel Evolution ◽

Orthologous Gene ◽

Control Networks ◽

Short Interspersed Elements ◽

Gene Pairs ◽

Sine Insertion ◽

Rapid Divergence ◽

Species Specific

Primate-specific Alu short interspersed elements (SINEs) as well as rodent-specific B and ID (B/ID) SINEs can promote Staufen-mediated decay (SMD) when present in mRNA 3′-untranslated regions (3′-UTRs). The transposable nature of SINEs, their presence in long noncoding RNAs, their interactions with Staufen, and their rapid divergence in different evolutionary lineages suggest they could have generated substantial modification of posttranscriptional gene-control networks during mammalian evolution. Some of the variation in SMD regulation produced by SINE insertion might have had a similar regulatory effect in separate mammalian lineages, leading to parallel evolution of the Staufen network by independent expansion of lineage-specific SINEs. To explore this possibility, we searched for orthologous gene pairs, each carrying a species-specific 3′-UTR SINE and each regulated by SMD, by measuring changes in mRNA abundance after individual depletion of two SMD factors, Staufen1 (STAU1) and UPF1, in both human and mouse myoblasts. We identified and confirmed orthologous gene pairs with 3′-UTR SINEs that independently function in SMD control of myoblast metabolism. Expanding to other species, we demonstrated that SINE-directed SMD likely emerged in both primate and rodent lineages >20–25 million years ago. Our work reveals a mechanism for the convergent evolution of posttranscriptional gene regulatory networks in mammals by species-specific SINE transposition and SMD.

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Lineage-Specific Genes and Family Expansions in Dictyostelid Genomes Display Expression Bias and Evolutionary Diversification during Development

Genes ◽

10.3390/genes12101628 ◽

2021 ◽

Vol 12 (10) ◽

pp. 1628

Author(s):

Saara K. Luna ◽

Frédéric J. J. Chain

Keyword(s):

Gene Families ◽

Developmental Time ◽

Multicellular Development ◽

Adaptive Diversification ◽

Evolutionary Diversification ◽

New Genes ◽

Expression Bias ◽

Species Specific ◽

Molecular Signals ◽

Lineage Specific Genes

Gene duplications generate new genes that can contribute to expression changes and the evolution of new functions. Genomes often consist of gene families that undergo expansions, some of which occur in specific lineages that reflect recent adaptive diversification. In this study, lineage-specific genes and gene family expansions were studied across five dictyostelid species to determine when and how they are expressed during multicellular development. Lineage-specific genes were found to be enriched among genes with biased expression (predominant expression in one developmental stage) in each species and at most developmental time points, suggesting independent functional innovations of new genes throughout the phylogeny. Biased duplicate genes had greater expression divergence than their orthologs and paralogs, consistent with subfunctionalization or neofunctionalization. Lineage-specific expansions in particular had biased genes with both molecular signals of positive selection and high expression, suggesting adaptive genetic and transcriptional diversification following duplication. Our results present insights into the potential contributions of lineage-specific genes and families in generating species-specific phenotypes during multicellular development in dictyostelids.

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Deciphering conserved identical sequences of mature miRNAs among six members of great apes

Zoosystematics and Evolution ◽

10.3897/zse.94.28099 ◽

2018 ◽

Vol 94 (2) ◽

pp. 401-408

Author(s):

Aftab Ali Shah ◽

Mushtaq Ahmad ◽

Taqweem Ul-Haq

Keyword(s):

Gene Families ◽

Mature Mirnas ◽

Neighbor Joining ◽

Species Comparison ◽

Rna Molecules ◽

Sequence Identity ◽

Species Specific ◽

Post Transcriptional Regulation ◽

Cross Species Comparison

MicroRNAs (miRNAs) are a group of small RNA molecules which act as negative regulators of gene expression by controlling post-transcriptional regulation through binding to their corresponding mRNAs. Due to their small size, their nucleotide compositions are expected to be similar, but until now, the extent of similarity has not been reported in humans and their six phylogenetically closely related members of hominids. The present study allows direct comparison among six members of hominid species (Homosapiens, Gorillagorilla, Panpaniscus, Pongopygmaeus, Pantroglodytes and Symphalangussyndactylus) in terms of their miRNA repertoire, their evolutionary distance to human, as well as, the categorization of identical species-specific miRNAs. For this purpose, a total of 2694, 370, 157, 673, 590 and 10 mature miRNA sequences of Homosapiens, Gorillagorilla, Panpaniscus, Pongopygmaeus, Pantroglodytes and Symphalangussyndactylus respectively were retrieved from miRbase 22. A total of 12, 4, 4 and 3 conserved clusters with identical miRNA sequences that belong to the same gene families were found in Homosapiens, Gorillagorilla, Pongopygmaeus, Pantroglodytes respectively by neighbor-joining method using MEGA7 software. Interestingly, cross-species comparison has also shown a set of conserved identical miRNA sequences. Homologs of human mature miRNAs with 100% sequence identity are expected to have similar functions in the studied primates. Further in-vitro study is required to investigate common targets for identical miRNAs in the studied primates.

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On Amphibolocypris arida sp.nov. (Crustacea, Ostracoda), from rock pools in Botswana (southern Africa)

Zootaxa ◽

10.11646/zootaxa.2408.1.3 ◽

2010 ◽

Vol 2408 (1) ◽

pp. 47 ◽

Cited By ~ 2

Author(s):

MERLIJN JOCQUE ◽

LUC BRENDONCK ◽

BRUCE J RIDDOCH ◽

KOEN MARTENS

Keyword(s):

New Species ◽

Southern Africa ◽

Convergent Evolution ◽

Ancient Lakes ◽

Large Species ◽

Rock Pools ◽

Present Contribution ◽

Species Specific ◽

A New Species ◽

Zoogeographical Region

The ostracod fauna of southern Africa remains ill-known, in spite of the fact that the temporary pools of this zoogeographical region hold degrees of endemicity comparable only to those of the ancient lakes of East Africa. The present contribution describes a new species of the cypridid genus Amphibolocypris, A. arida sp.nov., and announces the existence of at least two further new species from the same area. The genus, up to now presumed monospecific, might constitute an extensive radiation across southern Africa. Unusually large species-specific differences in hemipenis outline morphology appear to indicate that speciation occurred through sexual, rather than through natural selection. The occurrence of the claw-like subapical seta on the walking limb in at least four genera could be a case of convergent evolution, at least in one, maybe even in two cases between species of different genera and even subfamilies.

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The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene

Genome Biology and Evolution ◽

10.1093/gbe/evaa008 ◽

2020 ◽

Vol 12 (2) ◽

pp. 3832-3849 ◽

Cited By ~ 1

Author(s):

Pernille Nilsson ◽

Monica H Solbakken ◽

Boris V Schmid ◽

Russell J S Orr ◽

Ruichen Lv ◽

...

Keyword(s):

Gene Families ◽

Meriones Unguiculatus ◽

Comparative Genomic ◽

Great Gerbil ◽

Main Host ◽

Rhombomys Opimus ◽

Vector Borne ◽

Species Specific ◽

Close Relatives ◽

Genome Assemblies

Abstract The great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious pathogens including the well-known plague bacterium (Yersinia pestis). Here, we present a continuous annotated genome assembly of the great gerbil, covering over 96% of the estimated 2.47-Gb genome. Taking advantage of the recent genome assemblies of the sand rat (Psammomys obesus) and the Mongolian gerbil (Meriones unguiculatus), comparative immunogenomic analyses reveal shared gene losses within TLR gene families (i.e., TLR8, TLR10, and the entire TLR11-subfamily) for Gerbillinae, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes as well as Leishmania and Leptospira epitopes, putatively leading to increased capability to withstand infections by these pathogens. Our study demonstrates the power of whole-genome sequencing combined with comparative genomic analyses to gain deeper insight into the immunogenomic landscape of the great gerbil and its close relatives.

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A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance

Horticulture Research ◽

10.1038/s41438-020-00422-w ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Li Huang ◽

Yazhen Ma ◽

Jiebei Jiang ◽

Ting Li ◽

Wenjie Yang ◽

...

Keyword(s):

Stress Tolerance ◽

Repetitive Sequences ◽

High Stress ◽

Genomic Analysis ◽

Gene Families ◽

Ornamental Plant ◽

Comparative Genomic ◽

Chromosome Conformation ◽

Lobularia Maritima ◽

Species Specific

AbstractLobularia maritima (L.) Desv. is an ornamental plant cultivated across the world. It belongs to the family Brassicaceae and can tolerate dry, poor and contaminated habitats. Here, we present a chromosome-scale, high-quality genome assembly of L. maritima based on integrated approaches combining Illumina short reads and Hi–C chromosome conformation data. The genome was assembled into 12 pseudochromosomes with a 197.70 Mb length, and it includes 25,813 protein-coding genes. Approximately 41.94% of the genome consists of repetitive sequences, with abundant long terminal repeat transposable elements. Comparative genomic analysis confirmed that L. maritima underwent a species-specific whole-genome duplication (WGD) event ~22.99 million years ago. We identified ~1900 species-specific genes, 25 expanded gene families, and 50 positively selected genes in L. maritima. Functional annotations of these genes indicated that they are mainly related to stress tolerance. These results provide new insights into the stress tolerance of L. maritima, and this genomic resource will be valuable for further genetic improvement of this important ornamental plant.

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Hearing with the mouthparts: behavioural responses and the structural basis of ultrasound perception in acherontiine hawkmoths

Journal of Experimental Biology ◽

10.1242/jeb.202.8.909 ◽

1999 ◽

Vol 202 (8) ◽

pp. 909-918 ◽

Cited By ~ 1

Author(s):

M.C. Gopfert ◽

L.T. Wasserthal

Keyword(s):

Convergent Evolution ◽

Sensory Organ ◽

Structural Basis ◽

Flight Pattern ◽

Behavioural Responses ◽

Tethered Flight ◽

Hearing Organ ◽

Structural Differences ◽

Auditory Functions ◽

Species Specific

In contrast to previous assumptions, mouthparts form hearing organs not only in choerocampine hawkmoths but also in some distantly related acherontiine hawkmoth species. Four of the six acherontiine species studied revealed responses to ultrasonic sounds when stimulated during tethered flight. The responses included changes in flight speed and non-directional turns. Individuals from two species also responded by emitting sound. The minimum thresholds of the flight pattern changes were approximately 70 dB in all species studied, with species-specific best frequencies between 30 and 70 kHz. Some acherontiine species also move their tongue in a stereotyped way when stimulated acoustically. The activity of the muscles involved in this tongue reflex was characterized in the present study and used in combination with ablation experiments to localize the hearing organ. These experiments revealed auditory functions of the labial palps and the labral pilifers similar to those found in Choerocampina. The palp contributes a 20–25 dB rise in sensitivity, whereas the pilifer appears to contain the sensory organ. Structural differences suggest a convergent evolution of hearing in hawkmoths: in the place of the swollen palps of Choerocampina, acherontiine species capable of hearing possess a scale-plate of the palps that interacts with an articulating pilifer, while this modification is absent in closely related non-hearing species.

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