Characterization of the complete mitochondrial genome of Alectryonella plicatula (Bivalvia: Ostreidae)

Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia)

Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.

Adaptive mitochondrial genome functioning in ecologically different farm-impacted natural seedbeds of the endemic blue mussel Mytilus chilensis

We assessed the adaptive contribution of the mitochondrial genes involved with the respiratory chain and oxidative phosphorylation of the blue mussel Mytilus chilensis, a native and heavily exploited species in the inner sea of Chiloé Island, southern Chile. The assembled mitochondrial transcriptome of individuals from two ecologically different farm-impacted natural seedbeds, Cochamó (41°S) and Yaldad (42°S), represented about 4.5% of the whole de novo transcriptome of the species and showed location and tissue (gills, mantle) specific expression differences in 13 protein-coding mitochondrial genes. The RNA-Seq analysis detected differences in the number of up-regulated mitogenes between individuals from Cochamó (7) and Yaldad (11), some being tissue-specific (ND4L and COX2). However, the analysis did not detect transcripts-per-million (TPM = 0) of ND2 and ND5 in gills and ATP6 in mantle samples from Cochamó. Likewise, for ND6 and ATP8 in any sample. Several monomorphic location-specific mitochondrial genetic variants were detected in samples from Cochamó (78) and Yaldad (207), representing standing genetic variability to optimize mitochondrial functioning under local habitats. Overall, these mitochondrial transcriptomic differences reflect the impact of environmental conditions on the mitochondrial genome functioning and offer new markers to assess the effects on mussel fitness of habitat translocations, a routine industry practice. Likewise, these mitochondrial markers should help monitor and maintain adaptive population differences in this keystone and heavily exploited native species.

Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia

In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.

Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change on Toddalia asiatica (L.) Lam. (Rutaceae) from Africa and Asia

In the present study, two samples of Toddalia asiatica species, both collected from Kenya, were sequenced and comparison of their genome structures carried out with T. asiatica species from China, available in the NCBI database. The genome size of both species from Africa was 158, 508 base pairs, which was slightly larger, compared to the reference genome of T. asiatica from Asia (158, 434 bp). The number of genes was 113 for both species from Africa, consisting of 79 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Toddalia asiatica from Asia had 115 genes with 81 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Both species compared displayed high similarity in gene arrangement. The gene number, orientation, and order were highly conserved. The IR/SC boundary structures were the same in all chloroplast genomes. A comparison of pairwise sequences indicated that the three regions (trnH-psbA, rpoB, and ycf1) were more divergent and can be useful in developing effective genetic markers. Phylogenetic analyses of the complete cp genomes and 79 protein-coding genes indicated that the Toddalia species collected from Africa were sister to T. asiatica collected from Asia. Both species formed a sister clade to the Southwest Pacific and East Asian species of Zanthoxylum. These results supported the previous studies of merging the genus Toddalia with Zanthoxylum and taxonomic change of Toddalia asiatica to Zanthoxylum asiaticum, which should also apply for the African species of Toddalia. Biogeographic results demonstrated that the two samples of Toddalia species from Africa diverged from T. asiatica from Asia (3.422 Mya, 95% HPD). These results supported an Asian origin of Toddalia species and later dispersal to Africa and Madagascar. The maxent model analysis showed that Asia would have an expansion of favorable areas for Toddalia species in the future. In Africa, there will be contraction and expansion of the favorable areas for the species. The availability of these cp genomes will provide valuable genetic resources for further population genetics and biogeographic studies of these species. However, more T. asiatica species collected from a wide geographical range are required.

Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico

The eastern oyster, Crassostrea virginica, is divided into four populations along the western North Atlantic, however, the only published mitochondrial genome sequence was assembled using one individual in Delaware. This study aimed to (1) assemble C. virginica mitochondrial genomes from Texas with pooled restriction-site-associated DNA sequencing (ezRAD), (2) evaluate the validity of the mitochondrial genome assemblies including comparison with Sanger sequencing data, and (3) evaluate genetic differentiation both between the Delaware and Texas genomes, as well as among three bays in Texas. The pooled-genome-assembled-genomes (PAGs) from Texas exhibited several characteristics indicating that they were valid, including elevated nucleotide diversity in non-coding and the third position of codons, placement as the sister haplotype of the genome from Delaware in a phylogenetic reconstruction of Crassostrea mitochondrial genomes, and a lack of genetic structure in the ND4 gene among the three Texas bays as was found with Sanger amplicons in samples from the same bays several years prior. In the comparison between the Delaware and Texas genome, 27 of 38 coding regions exhibited variability between the two populations, which were differentiated by 273 mutations, versus 1-13 mutations among the Texas samples. Using the full PAGs, there was no additional evidence for population structure among the three Texas bays. While population genetics is rapidly moving towards larger high-density datasets, studies of mitochondrial DNA (and genomes) can be particularly useful for comparing historic data prior to the modern era of genomics. As such, being able to reliably compile mitochondrial genomes from genomic data can improve the ability to compare results across studies.