Research Article: Phylomitogenomics reconfirm the phylogenetic position of the genus Metaplax inferred from the two grapsid crabs (Decapoda: Brachyura: Grapsoidea)

Date Published: January 25, 2019

Publisher: Public Library of Science

Author(s): Jianqin Chen, Yuhui Xing, Wenjia Yao, Xue Xu, Chenling Zhang, Zhenhua Zhang, Qing Liu, Ling Ming Tsang.

http://doi.org/10.1371/journal.pone.0210763

Abstract

Two new complete mitogenomes of the grapsids, Metaplax longipes Stimpson, 1858 and Nanosesarma minutum (De Man, 1887) were sequenced using next-generation sequencing (NGS). By analyzing a combination of 75 Brachyura taxa, our phylomitogenomic inferences suggested that Metaplax crab seperated earlier from the sesarmid crabs and closely related to the varunids with respect to Nanosesarma crab. It reconfirmed that the Metaplax should be removed from the Sesarmidae and assinged to the Varunidae. Additional mitogenomic comparisons including gene rearrangement and genomic organization were conducted among the 33 taxa of Grapsoidea and Ocypodoidea, and a shared rearrangement pattern between Metaplax longipes and the varunids were recovered, which also strongly supported the inference for the phylogenetic position of the Metaplax.

Partial Text

The genus Metaplax H. Milne Edwards, 1852, which currently contains 12 species [1], along with three other genera, Cyclograpsus, Chasmagnathus and Helice, found in the China Seas, were historically assigned to the Sesarminae [2–3], based on the presence of a hairy crest on the third maxilliped and distinct characters in the pterygostomian and ventrolateral regions of the carapace [3–6]. However, the cladistic analysis proposed by Sternberg and Cumberlidge [7] found that Metaplax and the five genera Chasmagnathus De Haan, 1833, Helice De Haan, 1833; Cyclograpsus H. Milne Edwards, 1837; Paragrapsus H. Milne Edwards, 1853; and Helograpsus Campbell & Griffin, 1966 fail to conform to the other sesarmine genera. The early molecular phylogenetic analysis based on partial sequences of 12S rRNA and/or 16S rRNA revealed that these six genera were more closely related to other varunid crabs and suggested that Metaplax and the five related genera were excluded from the Sesarminae and were included in the Varuninae [8–11]. The validity of the character of a hairy crest on the 3rd maxilliped for intergeneric taxonomy, therefore, needs to be reevaluated, as proposed by Schubart et al [8, 9]. The morphological characters, such as the adult morphological characters, i.e., the location of the male genital openings [12], typically a stridulatory suborbital crest that is relatively straight and extends some distance across the lateral branchial region [13] and several larval characters, i.e., the 2, 2 seta l pattern on the endopod of the maxilla and the type of antenna and telson [14], provide strong support that these genera are included to the Varunidae. Therefore, these six genera, including Metaplax, combined with Helicana K. Sakai & Yatsuzuka, 1980, in the updated system of the Brachyurans of the world, were assigned to the Cyclograpsinae and Grapsidae by Davie in 2002 [13] and, more recently, to the Cyclograpsinae, Varunidae, and Grapsoidea by Ng et al. in 2008 [1]. However, the updated position of the genus Metaplax that proposed by Ng et al. was not commonly accepted, as in recent years the genus still has been included within the Grapsidae rather than in the Varunidae in some researchs [15, 16]. The phylogenetic position of the Metaplax needs to be further confirmed.

Comparisons of mitogenomes, usually using both gene orders and DNA sequences (PCGs and the two rRNAs), provide strong support for brachyuran phylogenies [17, 18, 21–23, 39]. The length of the mitogenome is a basic character for each animal organism, with the entire set of 37 genes (except for several groups), which are closely packed and probably reflect a strong purifying selection over the evolutionary history, being highly conserved [17, 40, 41]. However, it was found here that there was an increase in the genome size of the mitogenome of the Metaplax crab. In addition, this length is similar to that found in the varunid crabs known to date. Further comparisons of gene orders and intergenic spacers revealed a consistent gene rearrangement pattern shared by the Metaplax and varunid crabs (Figs 3 and 4) with concordant multiple minor noncoding regions scattered in the mitogenomes. The genome organization with multiple intergenic spacers was first discovered in a varunid crab, Eriocheir, and was recognized as retention resulting from gene duplication and incomplete deletion, which further resulted in the gene rearrangement and increased genome size [17].

In this study, we first determined the complete mitogenomes of the grapsid crabs M. longipes and N. minutum. Further, phylomitogenomic inferences suggested that N. minutum formed a clade with other sesarmids, while the M. longipes seperated earlier from the sesarmid clade. It reconfirmed that the Metaplax should be removed from the Sesarmidae and assinged to the Varunidae that proposed by Ng et al. or even older literature [1, 8–11]. New evidence that a consistent rearrangement pattern between M. longipes and the varunids was recovered, which also strongly supported the inference for the phylogenetic position of the Metaplax.

 

Source:

http://doi.org/10.1371/journal.pone.0210763

 

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